Hostname: page-component-586b7cd67f-dlnhk Total loading time: 0 Render date: 2024-11-22T06:54:57.208Z Has data issue: false hasContentIssue false
  • English
  • Français

DNA structural forms

Published online by Cambridge University Press:  17 March 2009

Brigitte Hartmann  and
Richard Lavery
Brigitte Hartmann
Affiliation:
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris 75005, France
Richard Lavery
Affiliation:
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris 75005, France
Get access Rights & Permissions [Opens in a new window]

Extract

In the years that have passed since the publication of Wolfram Saenger's classic book on nucleic acid structure (Saenger, 1984), a considerable amount of new data has been accumulated on the range of conformations which can be adopted by DNA. Many unusual species have joined the DNA zoo, including new varieties of two, three and four stranded helices. Much has been learnt about intrinsic DNA curvature, dynamics and conformational transitions and many types of damaged or deformed DNA have been investigated. In this article, we will try to summarise this progress, pointing out the scope of the various experimental techniques used to study DNA structure, and, where possible, trying to discern the rules which govern the behaviour of this subtle macromolecule. The article is divided into six major sections which begin with a general discussion of DNA structure and then present successively, B-DNA, DNA deformations, A-DNA, Z-DNA and DNARNA hybrids. An extensive set of references is included and should serve the reader who wishes to delve into greater detai.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 29 , Issue 4 , December 1996 , pp. 309 - 368
Copyright
Copyright © Cambridge University Press 1996

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Altona, C. & Sundaralingam, M. (1972). Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94, 8205.CrossRefGoogle ScholarPubMed
Abagyan, R. A., Mironov, V. N., Chernov, B. K., Chuprina, V. P. & Ulyanov, A. V. (1989). Electrophoretic behavior of d(GGAAAAAAGG)n d(CCAAAAAACC)n and implications for a DNA bending model. Nucleic Acids Res. 18, 989–992.CrossRefGoogle Scholar
Aboul-Ela, F., Murchie, A. I. H., Homans, S. W. & Lilley, D. M. J. (1993). Nuclear Magnetic Resonance study of a deoxyoligonucleotide duplex containing a three base bulge. J. Mol. Biol. 229, 173–188.CrossRefGoogle ScholarPubMed
Alam, T. M. & Drobny, G. P. (1991). Solid state NMR studies of DNA structure and dynamics. Chem. Rev. 91, 1545–1590.CrossRefGoogle Scholar
Alam, T. A., Orban, J. & Drobny, G. P. (1990). A solid state deuterium NMR investigation of conformation and order in magnetically oriented d(CGCGAATTCGCG). Biochemistr. 29, 9610–9617.CrossRefGoogle ScholarPubMed
Albert, A.-C., Roman, A.-M., Bouche, G., Leng, M. & Rahmouni, A. R. (1994). Gradual and oriented B-Z transition in 5′ untranscribed region of mouse ribosomal DNA. J. Biol. Chem. 269, 19238–19244.CrossRefGoogle ScholarPubMed
Arnott, S. (1970). The geometry of nucleic acids. Prog. Biophys. Mol. Biol. 21, 265–319.CrossRefGoogle ScholarPubMed
Arnott, S. & Hukins, D. W. L. (1973). Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibres of biopolymers. J. Mol. Biol. 81, 93–105.CrossRefGoogle ScholarPubMed
Arnott, S., Chandrasekaran, R., Birdsall, D. L., Leslie, A. G. W. & Ratliff, R. L. (1980). Left handed DNA helices. Natur. 283, 743–757.CrossRefGoogle ScholarPubMed
Arnott, S., Chandrasekaran, R., Milane, R. P. & Park, H.-S. (1986). DNA-RNA hybrid secondary structures. J. Mol. Biol. 188, 631–640.CrossRefGoogle ScholarPubMed
Babcock, M. S., Pednault, E. P. D. & Olson, W. K. (1994). The effect of mathematics and coordinate system on compatibility and dependencies of nucleic acid structure parameters. J. Mol. Biol. 237, 125–156.CrossRefGoogle Scholar
Ban, C., Ramakrishnan, B. & Sundaralingam, M. (1994). A single 2′-hydroxyl group converts B-DNA to A-DNA. J. Mol. Biol. 236, 275–285.CrossRefGoogle ScholarPubMed
Bancroft, M., Williams, L. D., Rich, A. & Egli, M. (1994). The low temperature crystal structure of the pure spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove. Biochemistr. 33, 1073–1086.CrossRefGoogle ScholarPubMed
Basham, B., Schroth, G. P. & Ho, P. S. (1995). An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA. Proc. Natl. Acad. Sci. USA 92, 6464–6468CrossRefGoogle ScholarPubMed
Becker, M. M. & Wang, Z. (1989). B-A Transitions within a 5S ribosomal RNA gene are highly sequence-specific. J. Biol. Chem. 264, 4163–4167.CrossRefGoogle ScholarPubMed
Behe, M. & Felsenfeld, G. (1981). Effects of methylation on a synthetic polynucleotide: the B-Z transition in poly(dGm5dC). Proc. Natl. Acad. Sci. US. 78, 1619–1623.CrossRefGoogle Scholar
Benevides, J. M., Wang, A. H.-J., Van Der Marel, G. A., Van Boom, J. H. & Thomas, G. J. JR., (1989). Effect of the G.T mismatch on backbone and sugar conformations of Z-DNA and B-DNA: analysis by Raman spectroscopy of crystal and solution structures of d(CGCGTG) and d(CGCGCG). Biochemistr. 28, 304–310.CrossRefGoogle Scholar
Berman, H. M. (1991). Hydration of DNA. Current Opinion in Structural Biolog. 1, 423–427.CrossRefGoogle Scholar
Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database. Biophys. J. 63, 751–759.CrossRefGoogle ScholarPubMed
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B.; Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.CrossRefGoogle Scholar
Beutel, B. A. & Gold, L. (1992). In vitro evolution of intrinsically bent DNA. J. Mol. Biol. 228, 803–812.CrossRefGoogle ScholarPubMed
Beveridge, D. L. & Ravishankar, G. (1994). Modelling DNA conformational mechanisms. Curr. Op. Struct. Biol. 4, 246–297.CrossRefGoogle Scholar
Bingman, C. A., Zon, G. & Sundaralingam, M. (1992 a). Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). J. Mol. Biol. 227, 738–756.CrossRefGoogle ScholarPubMed
Bingman, C., Jain, S., Zon, G. & Sundaralingam, M. (1992 b). Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG). Nucleic Acids Res. 20, 6637–6647.CrossRefGoogle ScholarPubMed
Bolshoy, A., McNamara, P., Harrington, R. E. & Trifonov, E. N. (1991). Curved DNA without A-A tracts: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Set. US. 88, 2312–2316.CrossRefGoogle Scholar
Bonden, K. L. B., Jenkins, T. C., Skelly, J. V., Brown, T. & Lane, A. N. (1992). Conformational properties of the G-G mismatch in d(CGCGAATTGGCG)2 determined by NMR. Biochemistr. 31, 5411–5422.Google Scholar
Borer, P. N., LaPlante, S. R., Kumar, A., Zanatta, N., Martin, A., Hakkinen, A. & Levy, G. C. (1994). 13C-NMR relaxation in three DNA oligonucleotide duplexes: model-free analysis of internal and overall motion. Biochemistr. 33, 2441–2450.CrossRefGoogle ScholarPubMed
Boulard, Y., Cognet, J. A. H., Gabarro-Arpa, J., Le Bret, M., Sowers, L. C. & Fazakerley, G. V. (1992). The pH dependent configurations of the C.A mispair in DNA. Nucleic Acids Res. 20, 1933–1941.CrossRefGoogle Scholar
Boulard, Y., Cognet, J. A. H., Gabarro-Arpa, J., Le Bret, M., Carbonnaux, C. & Fazakerley, G. V. (1995). Solution structure of an oncogenic DNA duplex, the Kras gene and the sequence containing a central C.A or G.A mismatch as a function of pH: NMR and MD studies. J. Mol. Biol. 246, 194–208.CrossRefGoogle Scholar
Briki, F., Ramstein, J.Lavery, R. & D.Genest, D. (1991). Evidence for the stochastic nature of the base-pair opening in B-DNA. J. Am. Chem. Soc. 113, 2490.CrossRefGoogle Scholar
Brown, T., Hunter, W. N., Kneale, G. & Kennard, O. (1986 a). Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations. Proc. Natl. Acad. Sci. US. 83, 2402–2406.CrossRefGoogle Scholar
Brown, T., Kneale, G., Hunter, W. N. & Kennard, O. (1986 b). Structural characterisation of the bromouracil-guanine base-pair mismatch in a Z-DNA fragment. Nucleic Acids Res. 14, 1801–1809.CrossRefGoogle Scholar
Brown, T., Leonard, G. A., Booth, E. D. & Chambers, J. (1989). Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs. Mol. Biol. 207, 455–457.CrossRefGoogle ScholarPubMed
Brown, T., Leonard, G. A., Booth, E. D. & Kneale, G. (1990). Influence of pH on the conformation and stability of mismatch base-pairs in DNA. J. Mol. Biol. 212, 437–440.CrossRefGoogle ScholarPubMed
Bruckner, I., Dlakic, M., Savic, A., Susie, S., Pongor, S. & Suck, D. (1993). Evidence for opposite groove-directed curvature of GGGCCC and AAAA sequence elements. Nucleic Acids Res. 21, 1025–1029.CrossRefGoogle Scholar
Bruckner, I., Susie, S., Dlakic, M., Savic, A. & Pongor, S. (1994). Physiological Concentration of Magnesium Ions Induces a Strong Macroscopic Curvature in GGGCCC-containing DNA. J. Mol. Biol. 236, 26–32.CrossRefGoogle Scholar
Bruckner, I., Sanchez, R., Suck, D. & Pongor, S. (1995). Sequence dependent bending propensity of DNA as revealed by Dnase I: parameter for trinucleotides. EMBO J. 14, 1812–1818.CrossRefGoogle Scholar
Burkhoff, A. M. & Tullius, T. D. (1987). The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cel. 48, 935–943.CrossRefGoogle ScholarPubMed
Burkhoff, A. M. & Tullius, T. D. (1988). Structural details of an adenine tract that does not cause DNA to bend. Natur. 331, 455–457.CrossRefGoogle Scholar
Calladine, C. R. (1982). Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161, 343–352.CrossRefGoogle ScholarPubMed
Calladine, C. R. & Drew, H. R. (1984). A base-centered explanation of the B-to-A transition in DNA. y. Mol. Biol. 178, 773–782.CrossRefGoogle Scholar
Calladine, C. R., Collis, C. M., Drew, H. R. & Morr, M. R. (1991). A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J. Mol. Biol. 221, 981–1005.CrossRefGoogle ScholarPubMed
Carbonnaux, C., Fazakerley, G. V. & Sowers, L. C. (1990). NMR structural study of deaminated base pairs in DNA. Nucleic Acids Res. 18, 4075–4081.CrossRefGoogle ScholarPubMed
Carbonnaux, C., Van Der Marel, G. A., Van Boom, J. H., Guschlbauer, W. & Fazakerley, G. V. (1991). Solution structure of an oncogenic DNA duplex containing a G-A mismatch. Biochemistr. 30, 5449–5458.CrossRefGoogle ScholarPubMed
Celda, B., Widmer, H., Leupin, W., Chazin, W. J., Denny, W. A. & Wuthrich, K. (1989). Conformational studies of d(AAAAATTTTT)2 using constraints from nuclear Overhauser effects and from quantitative analysis of the cross-peak fine structures in two-dimensional 1H NMR spectra. Biochemistr. 28, 1462–1471.CrossRefGoogle Scholar
Chen, S., Leupin, W. & Chazin, W. J. (1992). Conformational studies of the duplex d(CCAAAAATTTCC)-d(GGAAATTTTTGG) containing an (dA)5 tract using two-dimensional 1H-NMR spectroscopy. Int. J. Biol. Macromol. 14, 57–64.CrossRefGoogle Scholar
Cheng, J.-W., Chou, S.-H., Salazar, M. & Reid, B. R. (1992 a). Solution structure of d(GCGTATACGC) 2. J. Mol. Biol. 228, 118–137.CrossRefGoogle ScholarPubMed
Cheng, J.-W., Chou, S.-H. & Reid, B. R. (1992 b). Base pairing geometry in GA mismatches depends entirely on the neighboring sequence. J. Mol. Biol. 228, 1037–1041.CrossRefGoogle Scholar
Chevrier, B., Dock, A. C., Hartmann, B., Leng, M., Moras, D., Thuong, M. T. & Westhof, E. (1986). Solvatation of the left-handed hexamer d(5BrC-G-5BrC-G-5BrC-G) in crystals grown at two temperatures. J. Mol. Biol. 188, 707–719.CrossRefGoogle ScholarPubMed
Chou, S.-H., Flynn, P. & Reid, B. R. (1989). High-resolution NMR study of a synthetic DNA-RNA hybrid dodecamer containing the consensus Pribnow promoter sequence: d(CGTTATAATGCG).r(CGCAUUAUAACG). Biochemistr. 28, 2435–2443.CrossRefGoogle ScholarPubMed
Chou, S.-H., Flynn, P., Wang, A. & Reid, B. R. (1991). High resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous bese stacking at junctions. Biochemistr. 30, 5248–5257.CrossRefGoogle Scholar
Chou, S.-H., Cheng, J.-W. & Reid, B. R. (1992 a). Solution structure of (d(ATGAGCGGAATA))2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups. J. Mol. Biol. 228, 138–155.CrossRefGoogle Scholar
Chou, S.-H., Cheng, J.-W., Fedoroff, O. Y., Chuprina, V. P. & Reid, B. R. (1992 b). Adjacent G.A mismatch base pairs contain BII phosphodiesters in solution. J. Am. Chem. Soc. 114, 3114–3115.CrossRefGoogle Scholar
Chuprina, V. P. (1985). Regularities in formation of the spine of hydratation in the DNA minor groove an its influence on the DNA structure. FEBS Lett. 186, 98–102.CrossRefGoogle ScholarPubMed
Chuprina, V. P., Lipanov, A. A., Fedoroff, O. Y., Kim, S-G., Kintanar, A. & Reid, B. R. (1991). Sequence effects on local DNA topology. Proc. Natl. Acad. Sci. US. 88, 9087–9091.CrossRefGoogle ScholarPubMed
Clark, G. R., Brown, D. G., Sanderson, M. R., Chwalinski, T., Neidle, S., Veal, J. M., Jones, R. L., Wilson, W. D., Zon, G., Garman, E. & Stuart, D. I. (1990). Crystal and solution structures of the oligonucleotide d(ATGCGCAT)2: a combined X-ray and NMR study. Nucleic Acids Res. 18, 5521–5528.CrossRefGoogle ScholarPubMed
Cognet, J. A. H., Gabarro-Arpa, J., Cuniasse, PH., Fazakerley, G. V. & Le Bret, M. (1990). Molecular mechanisms and dynamics of an abasic frameshift in DNA and comparison to NMR data. J. Biomol. Struct. Dynam. 7, 1095–1103.CrossRefGoogle Scholar
Cognet, J. A. H., Gabarro-Arpa, J., Le Bret, M., Van Der Marel, G.A.Van Boom, J. H. & Fazakerley, G. V. (1991). Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics. Nucleic Acids Res. 24, 6771–6779.CrossRefGoogle Scholar
Coll, M., Frederick, C. A., Wang, A. H. J. & Rich, A. (1987). A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl. Acad. Sci. US. 84, 8385–8389.CrossRefGoogle Scholar
Cremer, D. & Pople, J. A. (1975). A general definition of ring puckering coordinates. J. Am. Chem. Soc. 97, 1358–1368.CrossRefGoogle Scholar
Crick, F. H. C. (1966). Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548–555.CrossRefGoogle ScholarPubMed
Crothers, D. M. & Drak, J. (1992). Global features of DNA structure by comparative gel electrophoresis. Methods in Enzymolog. 212, 46–71.CrossRefGoogle ScholarPubMed
Crothers, D. M., Haran, T. E. & Nadeau, J. G. (1990). Intrinsically bent DNA. J. Biol. Chem. 265, 7093–7096.CrossRefGoogle ScholarPubMed
Crothers, D. M., Drak, J., Kahn, J. D. & Levene, S. D. (1992). DNA bending, flexibility, and helical repeat by cyclisation kinetics. Methods in Enzymolog. 212, 3–29.CrossRefGoogle Scholar
Cuniasse, PH., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A. H., Le Bret, M., Guschlbauer, W. & Fazakerley, G. V. (1989). Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanism calculations. Biochemistr. 28, 2018–2026.CrossRefGoogle Scholar
Cuniasse, PH., Fazakerley, G. V., Guschlbauer, W., Kaplan, B. E. & Sowers, L. C. (1990). The abasic site as a challenge to DNA polymerase. J. Mol. Biol. 213, 303–314.CrossRefGoogle ScholarPubMed
Dai, Z., Dauchez, M., Thomas, G. & Peticolas, W. L. (1992). Base sequence criteria and cartesian coordinates for stable B/Z and B/Z/B junctions in relaxed DNA. J. Biomol. Struct. Dynam. 9, 1155–1183.CrossRefGoogle Scholar
Danna, K. J. & Nathans, D. (1971). Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus Influenzae. Proc. Natl. Acad. Sci. US. 68, 2913–2917.CrossRefGoogle ScholarPubMed
De Santis, P., Palleschi, A., Savino, M. & Scipion, A. (1990). Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistr. 29, 9269–9273.CrossRefGoogle ScholarPubMed
Dickerson, R. E. (1983). Base sequence and helix structure variation in B and A-DNA. J. Mol. Biol. 166, 419–441.CrossRefGoogle Scholar
Dickerson, R. E. (1992). DNA structure from A to Z. Methods in Enzymolog. 211, 67–167.CrossRefGoogle ScholarPubMed
Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., Lavery, R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C. S., Von Kitzing, E., Wang, A. H. J. & Zhurkin, V. D. (1989). Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205, 787–791.Google ScholarPubMed
Diekmann, S. (1987 a). DNA curvature. Nucleic Acids and Molecular Biolog. 1, 138–156.CrossRefGoogle Scholar
Diekmann, S. (1987 b). DNA methylation can enhance or induce DNA curvature. EMBO J. 6, 4213–4217.CrossRefGoogle ScholarPubMed
Diekmann, S. (1992). Analysing DNA curvature in polyacrilamide gels. Methods in Enzymolog. 212, 30–46.CrossRefGoogle Scholar
Diekmann, S., Von Kitzing, E., McLaughlin, L. W., Ott, J. & Eckstein, F. (1987). The influence of exocyclic substituents of purine bases on DNA curvature. Proc. Natl. Acad. Sci. US. 84, 8257–8261.CrossRefGoogle ScholarPubMed
Diekmann, S., Mazzarelli, J. M., McLaughlin, L. W., Von Kitzing, E. & Travers, A. A. (1992). DNA curvature does not require bifurcated hydrogen bonds or pyrimidine methyl groups, J. Mol. Biol. 225, 729–738.CrossRefGoogle ScholarPubMed
Digabriele, A. D., Sanderson, M. R. & Steitz, T. A. (1989). Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl. Acad. Sci. US. 86, 1816–1820.CrossRefGoogle ScholarPubMed
Digabriele, A. D. & Steitz, T. A. (1993). A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. J. Mol. Biol. 231, 1024–1039.CrossRefGoogle Scholar
Doktycz, M. J., Benight, A. S. & Sheardy, R. D. (1990). Energetics of B-Z junction formation in a sixteen base-pair duplex DNA. J. Mol. Biol. 212, 3–6.CrossRefGoogle Scholar
Doucet, J., Benoit, J.-P., Cruse, W. B. T., Prange, T. & O.Kennard, O. (1989). Coexistence of A- and B-form DNA in a single crystal lattice. Natur. 337, 190–192.CrossRefGoogle Scholar
Drew, H., Takano, T., Tanaka, S., Itakura, K. & Dickerson, R. E. (1980). High-salt d(CGCG), a left-handed Z'-DNA double helix. Natur. 286, 567–573.CrossRefGoogle Scholar
Drew, H. R. & Travers, A. A. (1985). DNA Bending and its relation to nucleosome positioning. J. Mol. Biol. 186, 773–790.CrossRefGoogle ScholarPubMed
Ebel, S., Brown, T. & Lane, A. N. (1994). Thermodynamic stability and solution conformation of tandem G.A mismatches in RNA and RNA.DNA hybrid duplexes. Eur. J. Biochem. 220, 703–715.CrossRefGoogle ScholarPubMed
Edwards, K. J., Brown, D. G., Spink, N., Skelly, J. V. & Neidle, S. (1992). Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG). J. Mol. Biol. 226, 1161–1173.CrossRefGoogle ScholarPubMed
Egli, M., Usman, N., Zhang, S. & Rich, A. (1992). Crystal structure of an Okasaki fragment. Proc. Natl. Acad. Sci. US. 89, 534–538.CrossRefGoogle Scholar
Egli, M., Usman, N. & Rich, A. (1993). Conformation influence of the ribose 2′-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Biochemistr. 32, 3221–3237.CrossRefGoogle ScholarPubMed
Eimer, W., Williamson, J. R., Boxer, S. G. & Pecora, R. (1990). Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements. Biochemistr. 29, 799–811.CrossRefGoogle ScholarPubMed
Eisenstein, M. & Sharked, Z. (1995). Hydratation patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248, 662–678.CrossRefGoogle ScholarPubMed
El Antri, S., Bittoun, P., Mauffret, O., Monnot, M., Convert, O., Lescot, E. & Fermandjian, S. (1993). Structural deviation at CpG provides a plausible explanation for the high frequency of mutation at this site. Phosphorus NMR and CD studies. Biochemistr. 32, 7079–7083.CrossRefGoogle Scholar
Elgavish, T. & Harvey, S. C. (1996). J. Mol. Biol. submitted.Google Scholar
Ellison, M. J., Kelleher, R. J. III, Wang, A. H.-J., Habener, J. F. & Rich, A. (1985). Sequence dependent energetics of the B-Z transition in supercoiled DNA containing nonalternating purine-pyrimidine sequences. Proc. Natl. Acad. Sci. US. 82, 8320–8324.CrossRefGoogle ScholarPubMed
Fabian, H., Hölzer, W., Heinemann, U., Sklenar, H. & Welfle, H. (1993). Conformation of d(GGGATCCC)2 in crystals and solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling. Nucleic Acids Res. 21, 569–576.CrossRefGoogle ScholarPubMed
Falsafi, S. & Reich, N. O. (1993). Molecular dynamics simulations of B-DNA: an analysis of the role of initial molecular conformation, randomly assigned velocity distribution, long integration times, and nonconstrained termini. Biopolymer. 33, 459–473.CrossRefGoogle ScholarPubMed
Fedoroff, O. Y., Salazar, M. & Reid, B. R. (1993). Structure of a DNA:RNA hybrid duplex. J. Mol. Biol. 233, 509–523.CrossRefGoogle Scholar
Franklin, R. E. & Gosling, R. G. (1953). Molecular configuration in sodium thymonucleate. Natur. 171, 740–741.CrossRefGoogle ScholarPubMed
Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. (1982). Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J. Biol. Chem. 257, 14686–14707.CrossRefGoogle Scholar
Fritsch, V. & Wolf, R. M. (1994). Molecular dynamics simulations of a r(GA12G).d(CT12C) hybrid duplex. J. Biomol. Struct. Dynam. 11, 1161–1174.CrossRefGoogle Scholar
Fritsch, V., Ravishankar, G., Beveridge, D. L. & Westhof, E. (1993). Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations. Biopolymer. 33, 1537–1552.CrossRefGoogle ScholarPubMed
Fujii, S., Wang, A. H.-J., Van Der Marel, G., Van Boom, J. H. & Rich, A. (1982). Molecular sturcture of (m5dC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA. Nucleic Acids Res. 23, 7879–7891.CrossRefGoogle Scholar
Gaudin, F., Paquet, F., Chanteloup, L., Beau, J. M., Nguyen, T. T. & Lancelot, G. (1995). Selectively 13C-enriched DNA: dynamics of the CI′ -HI′ vector in d(CGCAAATTTGCG)2. J. Biomol. NMR. 5, 49–58.CrossRefGoogle Scholar
Garriga, P., Garcia-Quintana, D., Sagi, J. & Manyosa, J. (1993). As A-Form of Poly(amino2dA-dT).Poly(amino2dA-dT) induced by polyamine. Biochemistr. 32, 1067–1071.CrossRefGoogle Scholar
Genest, D., Mazeau, K. & Ptak, M. (1987). Two dimmensional 1H NMR study of d(br5C-G)3 in the Z-form. Self association and flexibility of the left handed double helix. J. Biomol. Struct. Dynam. 5, 67–78.CrossRefGoogle Scholar
Gervais, V., Cognet, J. A. H., Le Bret, M., Sowers, L. C. & Fazakerley, V. (1995). Solution structure of two mismatches A.A and T.T in the K-ras gene context by NMR and molecular dynamics. Eur. J. Biochem. 228, 279–290.CrossRefGoogle Scholar
Gessner, R. V., Quigley, G. J. & Egli, M. (1994). Comparative studies of high resolution Z-DNA crystal structures: common hydratation patterns of alternating dC-dG. J. Mol. Biol. 236, 1154–1168.CrossRefGoogle ScholarPubMed
Ginell, S. L., Vojtechovsky, J., Gaffney, B., Jones, R. & Berman, H. M. (1994). Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-Methylguanine. Biochemistr. 33, 3487–3493.CrossRefGoogle ScholarPubMed
Gochin, M. & James, T. L. (1990). Solution structure studies of d(AC)4.d(GT)4 via restrained molecular dynamics. Biochemistr. 29, 11172–11180.CrossRefGoogle ScholarPubMed
Goljer, I., Withka, J. M., Kao, J. Y. & Bolton, P. J. (1992). Effects of the presence of an aldehyde abasic site on the thermal stability and rates of helix opening and closing of duplex DNA. Biochemistr. 31, 11614–11619.CrossRefGoogle ScholarPubMed
Goljer, I., Kumar, S., & Bolton, P. J. (1995). Refined solution structure of a DNA containing an aldehydic abasic site. J. Biol. Chem. 270, 22980–22987.CrossRefGoogle ScholarPubMed
Goodman, S. D. & Nash, H. A. (1989). Functional replacement of a protein-induced bend in a DNA recombination site. Natur. 341, 251–254.CrossRefGoogle Scholar
Goodsell, D. S., Kopka, M. L., Cascio, D. & Dickerson, R. E. (1993). Crystal structure of CATGGCCATG and its implications for A-tract bending models. Proc. Natl. Acad. Sci. US. 90, 2930–2934.CrossRefGoogle ScholarPubMed
Goodsell, D. S. & Dickerson, R. E. (1994). Bending and curvature calculations in BDNA. Nucleic Acids Res. 22, 5497–5503.CrossRefGoogle ScholarPubMed
Goodsell, D. S., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1994). The Crystal structure of CCATTAATGG implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79–96.CrossRefGoogle ScholarPubMed
Gorenstein, D. G. (1992). 31P NMR of DNA. Methods in Enzymolog. 211, 254–284.CrossRefGoogle ScholarPubMed
Gray, D. M. & Ratliff, R. L. (1975). Circular dichroism spectra of poly(d(AC):d(GT)), poly(r(AC):r(GU)) and hybrids poly(d(AC):r(GU)) and poly(r(AC):d(GT)) in the presence of methanol. Biopolymer. 14, 487–498.CrossRefGoogle Scholar
Greene, K. L., Jones, R. L., Li, Y., Robinson, H., Wang, A. H.-J., Zon, G. & Wilson, W. D. (1994). Solution structure of a GA mismatch DNA sequence, d(CCATGAATGG)2, determined by 2D NMR and structural refinement methods. Biochemistr. 33, 1053–1062.CrossRefGoogle Scholar
Griffith, J., Bleyman, M., Rauch, C. A., Kitchin, P. A. & Englund, P. T. (1986). Vizualisation of the bent helix in kinetoplast DNA by electron microscopy. Cel. 46, 717–724.CrossRefGoogle Scholar
Grzeskowiak, K., Yanagi, K., Privé, G. G. & Dickerson, R. E. (1991). The structure of B helical CGATCGATCG and comparison with CCAACGTTGG. J. Biol. Chem. 266, 8861–8883.CrossRefGoogle ScholarPubMed
Grzeskowiak, K., Goodsell, D. S., Kaczor-Grzeskowiak, M., Cascio, D. & Dickerson, R. E. (1993). Crystallographic analysis of CCAAGCTTGG and its implications for bending in B-DNA. Biochemistr. 32, 8923–8931.CrossRefGoogle ScholarPubMed
Guéron, M. & Demaret, J.-P. (1992). A simple explanation of the electrostatics of the B-to-Z transition of DNA. Proc. Natl. Acad. Set. USA 89, 5740–5743.CrossRefGoogle ScholarPubMed
Guéron, M. & Leroy, J.-L. (1992). Base opening in double stranded nucleic acids. Nucleic Acids and Molecular Biology 6, eds. Eckstein, F. & Lilley, D. M. J., Berlin: Springer, 1–22.Google Scholar
Guest, C. R., Hochstrasser, R. A., Sowers, L. C. & Millar, D. P. (1991). Dynamics of mismatches base pairs in DNA. Biochemistr. 30, 3271–3279.CrossRefGoogle ScholarPubMed
Gupta, G., Bansal, M. & Sasisekharan, V. (1980). Conformational flexibility of DNA: polymorphism and handeness. Proc. Natl. Acad. Sci. USA. 77, 6486–6490.CrossRefGoogle Scholar
Hagerman, P. J. (1984). Evidence for the existence of stable curvature of DNA in solution. Proc. Natl. Acad. Sci. US. 81, 4632–4636.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1985). Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistr. 24, 7033–7037.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1986). Sequence directed curvature of DNA. Natur. 321, 449–450.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1990). Sequencez-directed curvature of DNA. Anna. Rev. Biochem. 59, 755–781.CrossRefGoogle ScholarPubMed
Hahn, M. & Heinemann, U. (1993). DNA helix structure and refinement algorithm: Comparison of models for (CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR. Acta Cryst. D49, 468–477.Google Scholar
Haran, T. E. & Crothers, D. M. (1989). Cooperativity in A-tract structure and bending properties of composite TNAN blocks. Biochemistr. 28, 2763–2767.CrossRefGoogle ScholarPubMed
Harrington, R. E. (1992). DNA curving and bending in protein-DNA recognition. Mol. Microbiol. 6, 2549–2555.CrossRefGoogle ScholarPubMed
Hartmann, B., Malfoy, B. & Lavery, R. (1989). Theoretical prediction of base sequence effects in Z-DNA. J. Mol. Biol. 207, 433–444.CrossRefGoogle ScholarPubMed
Hartmann, B., Piazzola, D. & Lavery, R. (1993). BI-BII transitions in B-DNA. Nucleic Acids Res. 21, 561–568.CrossRefGoogle ScholarPubMed
Harvey, S. C. & Prabhakaran, M. (1986). Ribose puckering: structure, dynamics, energetics and the pseudorotation cycle. J. Am. Chem. Soc. 108, 6128–6136.CrossRefGoogle Scholar
Harvey, S. C. (1983). DNA structural dynamics: longitudinal breathing as a possible mechanism for the B-Z transition. Nucleic Acids Res. 11, 4867–4873.CrossRefGoogle Scholar
Haworth, I. S., Rodger, A. & Richards, W. G. (1992). A possible mechanism for the B to Z transition. J. Biomol. Struct. & Dyn. 10, 195–211.CrossRefGoogle ScholarPubMed
Heinemann, U. (1991). A note on crystal packing and global helix structure in short A-DNA duplexes. J. Biomol. Struct. Dynam. 8, 801–811.CrossRefGoogle ScholarPubMed
Heinemann, U. & Hahn, M. (1992). CCAGCm5CTGG: helical fine structure, hydratation and comparison with CCAGGCCTGG. J. Biol. Chem. 267, 7332–7341.CrossRefGoogle ScholarPubMed
Heinemann, U., Alings, C. & Bansal, M. (1992). Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA. EMBO J. 11, 1931–1939.CrossRefGoogle Scholar
Heinemann, U., Alings, C. & Hahn, M. (1994). Crystallographic studies of DNA helix structure. Biophys. Chem. 50, 157–167.CrossRefGoogle ScholarPubMed
Hélène, C. & Toulme, J.-J. (1990). Specific regulation of gene expression by antisense, sense and antigene nucleic acids. Biochim. Biophys. Act. 1049, 99–125.CrossRefGoogle ScholarPubMed
Herrera, J. E., & Chaires, J. B. (1989). A premelting conformational transition in poly(dA)–poly(dT) coupled to daunomycin binding. Biochemistr. 28, 1993–2000.CrossRefGoogle ScholarPubMed
Ho, P. S., Ellison, M. J., Quigley, G. J. & Rich, A. (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occuring sequences. EMBO J. 5, 2737–2744.CrossRefGoogle ScholarPubMed
Holbrook, S. R., Wang, A. H.-J., Rich, A. & Kim, S.-H. (1986). Local mobility of nucleic acids as determined from crystallographic data: Z-form DNA. J. Mol. Biol. 187, 429–440.CrossRefGoogle ScholarPubMed
Hua, N., Van Der Marel, G. A., Van Boom, J. H. & Feigon, J. (1989). Non contiguous regions of Z-DNA in a DNA dodecamer. Nucleic Acids Res. 17, 7923–7944.CrossRefGoogle Scholar
Huang, W. C., Orban, J., Kintanar, A., Reid, B. R. & Drobny, G. P. (1990). A solid state deuterium NMR study of furanose ring dynamics in d(CGCGAATTCGCG). J. Am. Chem. Soc. 112, 9059–9068.CrossRefGoogle Scholar
Hunter, W. N., Kneale, G., Brown, T., Rabinovich, D. & Kennard, O. (1986a). Refined crystal structure of an octanucleotide duplex with G.T mismatched basepairs. J. Mol. Biol. 190, 605–618.CrossRefGoogle ScholarPubMed
Hunter, W. N., Brown, T. & Kennard, O. (1986 b). Structural features and hydration of d(CGCGAATTAGCG): a double helix containing two G.A mispairs. J. Biomol. Struct. Dynam. 4, 173–191.CrossRefGoogle Scholar
Hunter, W. N., Brown, T. & Kennard, O. (1987 a). Structural features and hydration of a dodecamer duplex containing two C–A mispairs. Nucleic Acids Res. 15, 6589–6606.CrossRefGoogle ScholarPubMed
Hunter, W. N., Brown, T., Kneale, G., Anand, N. N., Rabinovich, D. & Kennard, O. (1987 b). The structure of guanosine–thymidine mismatches in B-DNA at 2.5–A° resolution. J. Biol. Chem. 262, 9962–9970.CrossRefGoogle ScholarPubMed
Hunter, W. N., Langlois D'Estaintot, B. & Kennard, O. (1989). Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions. Biochemistr. 28, 2444–2451.CrossRefGoogle Scholar
Ikuta, S. & Wang, Y. S. (1990). Differential conformational mobilities in different time scales in B and Z-DNA oligomers in solution. J. Am. Chem. Soc. 112, 5901–5906.CrossRefGoogle Scholar
Jain, S. & Sundaralingam, M. (1989). Effect of crystal packing environment on conformation of the DNA duplex. J. Biol. Chem. 264, 12780–12784.CrossRefGoogle ScholarPubMed
Jain, S., Zon, G. & Sundaralingam, M. (1987). The potentially Z-DNA-forming sequence d(GTGTACAC) crystallizes as A-DNA. J. Mol. Biol. 197, 141–145.CrossRefGoogle ScholarPubMed
Jain, S., Zon, G. & Sundaralingam, M. (1991). Hexagonal crystal structure of the ADNA octamer d(GTGTACAC) and its comparison with the tetragonal structure: correlated variations in helical parameters. Biochemistry 30, 3567–3576.CrossRefGoogle ScholarPubMed
Jaishree, T. N. & Wang, A. H. J. (1993). NMR studies of pH-dependent conformational polymorphism of alternating (C-T)n. Nucleic Acids Res. 16, 3839–3844.CrossRefGoogle Scholar
Jaishree, T. N. & Wang, A. H. J. (1994). Conformations of the alternating (C-T)n sequence under neutral and low pH. FEBS Letters. 337, 139–144.CrossRefGoogle ScholarPubMed
Jaishree, T. N., van der Marel, G. A., van Boom, J. H. & Wang, A. H.-J. (1993). Structural influence of RNA incorporation in DNA: quantitative NMR refinement of d(CG)r(CG)d(CG) and d(CG)rC)d(ATGCG). Biochemistry 32, 4903–4911.CrossRefGoogle Scholar
James, T. L. (1994). Computational strategies pertinent to NMR solution structure determination. Current Opinion in Structural Biology 4, 275–284.CrossRefGoogle Scholar
Jernigan, R. L., Sarai, A., Ting, K. L. & Nussinov, R. (1986). Hydrophobic interactions in the major groove can influence DNA local structure. J. Biomol. Struct. Dynam. 4, 41–56.CrossRefGoogle ScholarPubMed
Johnston, B. H., Quigley, G. J., Ellison, M. J. & Rich, A. (1991). The Z-Z junction: the boundary between two out-of-phase Z-DNA regions. Biochemistry 30, 5257–5263.CrossRefGoogle ScholarPubMed
Johnston, B. H. (1992). Generation and detection of Z-DNA. Methods in Enzymology 211, 127–159.CrossRefGoogle ScholarPubMed
Joshua-Tor, L., Rabinovich, D., Hope, H., Frolow, F., Appella, E. & Sussman, J. L. (1988). The three-dimensional structure of a DNA duplex containing looped-out bases Nature 334, 82–84.Google Scholar
Joshua-Tor, L., Frolow, F., Appella, E., Hope, H., Rabinovich, D. & Sussman, J. L. (1992). Three-dimensional structures of bulge-containing DNA fragments. J. Mol. Biol. 225, 397–431.CrossRefGoogle ScholarPubMed
Kagawa, T. F., Stoddard, D., Zhou, G. & Ho, P. S. (1989). Quantitative analysis of DNA secondary structure from solvent accessible surfaces: the B to Z transition as a model. Biochemistry 28, 6642–6651.CrossRefGoogle Scholar
Kahn, J. D., Yun, E. & Crothers, D. M. (1994). Detection of localized DNA flexibility. Nature 368, 163–166.CrossRefGoogle ScholarPubMed
Kalnik, M. W., Kouchakdjian, M., Li, B. F. L., Swann, P. F. & Patel, D. J. (1988). Base pair mismatches and carcinogen-modified bases in DNA:.an NMR study of A.C and A.O4meT pairing in dodecanucleotide duplexes. Biochemistry 27, 100–108.CrossRefGoogle Scholar
Kalnik, M. W., Chang, C.-N., Johnson, F., Grollman, A. P. & Patel, D. J., (1989a). NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite acyclic lesions. Biochemistry 28, 3373–3383.CrossRefGoogle ScholarPubMed
Kalnik, M. W., Norman, D. G., Swann, P. F. & Patel, D. J. (1989b). Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution. J. Biol. Chem. 264, 3702–3712.CrossRefGoogle ScholarPubMed
Kalnik, M. W., Norman, D. G., Li, B. F., Swann, P. F. & Patel, D. J. (1990). Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. J. Biol. Chem. 265, 636–647.CrossRefGoogle ScholarPubMed
Kaluarachchi, K., Meadows, R. P. & Gorenstein, D. G. (1991). How accurately can oligonucleotide structure be determined from the hybrid relaxation rate matrix/NOESY distance restrained molecular dynamics approach Biochemistry 30, 8785–8797.CrossRefGoogle ScholarPubMed
Karslake, C., Botuyan, M. V. & Gorenstein, D. G. (1992). 31P NMR spectra of oligodeoxyribonucleotide duplex lac operator-repressor headpiece complexes: importance of phosphate ester backbone flexibility in protein-DNA recognition. Biochemistry 31, 1849–1858.CrossRefGoogle ScholarPubMed
Katahira, M., Sugeta, H., Kyogoku, Y., Fujii, S., Fujisawa, R. & Tomita, K. (1988). One and two dimensional NMR studies on the conformation of DNA containing the oligo(dA).oligo(dT) tract. Nucleic Acids Res. 16, 8619–8632.CrossRefGoogle ScholarPubMed
Katahira, M., Sugeta, H. & Kyogoku, Y. (1990). A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations. Nucleic Acids Res. 18, 613–618.CrossRefGoogle ScholarPubMed
Kennard, O. (1985). Structural Studies of DNA Fragments: The G.T wobble base-pair in A, B and Z-DNA; The G.A base pair in B-DNA. J. Biomol. Struct. Dynam. 3, 205–226.CrossRefGoogle Scholar
Kennard, O., Cruse, W. B. T. & Nachman, J. (1986). Ordered-water structure in an ADNA octamer at 1.7 Å resolution. J. Biomol. Struct. Dynam. 3, 623–647.CrossRefGoogle Scholar
Kim, S.-G. & Reid, B. R. (1992). Solution structure of the TnAn duplex GCCGTTAACGGC containing the Hpal restriction site. Biochemistry 31, 12103–12116.CrossRefGoogle Scholar
Kim, U.-S., Fujimoto, B. S., Furlong, C. E., Sundstrom, J. A., Humbert, R., Teller, D. C. & Schurr, J. M. (1993). Dynamics and structures of DNA: long range effects of a 16 base-pair (CG)8 sequence on secondary structure. Biopolymers 33, 1725–1745.CrossRefGoogle ScholarPubMed
Klement, R., Soumpasis, D. M., von Kitzing, E. & Jovin, T. M. (1990). Inclusion of ionic interactions in force field calculations of charged biomolecules – DNA structural transitions. Biopolymers 29, 1089–1103.CrossRefGoogle ScholarPubMed
Klump, H. H., Schmid, E. & Wosgien, M. (1993). Energetics of Z-DNA formation in poly d(A-T), poly d(G-C) and poly d(A-C).poly d(G-T). Nucleic Acids Res. 21, 2343–2348.CrossRefGoogle ScholarPubMed
Kochoyan, M., Leroy, J.-L. & Guéron, M. (1987). Proton exchange and base-pair lifetimes in a deoxy-duplex containing a purine-pyrimidine step and in the duplex of inverse sequence. J. Mol. Biol. 196, 599–609.CrossRefGoogle Scholar
Kochoyan, M., Leroy, J.-L. & Guéron, M. (1990). Processes of base-pair opening and proton exchange in Z-DNA. Biochemistry 29, 4799–4805.CrossRefGoogle ScholarPubMed
Koo, H. S. & Crothers, D. M. (1987). Chemical determinants of DNA bending at adenine-thymine tracts. Biochemistry 26, 3745–3748.CrossRefGoogle ScholarPubMed
Koo, H.-S. & Crothers, D. M. (1988). Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl. Acad. Sci. USA 85, 1763–1767.CrossRefGoogle Scholar
Koo, H. S., Wu, H. M. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature 320, 501–506.CrossRefGoogle ScholarPubMed
Koo, H.-S., Drak, J., Rice, J. A. & Crothers, D. M. (1990). Determination of the extent of DNA bending by an Adenine-Thymine tract. Biochemistry 29, 4227–4234.CrossRefGoogle ScholarPubMed
Kopka, M. L., Fratini, A. V., Drew, H. R. & Dickerson, R. E. (1983). Ordered water structure around a B-DNA dodecamer. J. Mol. Biol. 163, 129–146.CrossRefGoogle ScholarPubMed
Kouchakdjian, M., Li, B. F. L., Swann, P. F. & Patel, D. J. (1988). A Nuclear Magnetic Resonance study of T. T pairing at neutral pH and C.C pairing at acidic pH in dodecanucleotide duplexes. J. Mol. Biol. 202, 139–155.CrossRefGoogle Scholar
Kubinec, M. G. & Wemmer, D. E. (1992). NMR evidence for DNA bound water in solution. J. Am. Chem. Soc. 114, 8739–8740.CrossRefGoogle Scholar
Kypr, J., Sagi, J., Szakonyi, E., Ebinger, K., Penazova, H., Chladkova, J. & Vorlickova, M. (1994). Thymine methyl groups stabilize the putative A-Form of the synthetic DNA Poly(amino2dA-dT). Biochemistry 33, 3801–3806.CrossRefGoogle ScholarPubMed
Lane, A. N. (1990). Solution structure of d(CGTACG)2 determined from NMR experiments. Biochim. Biophys. Acta 1049, 205–212.CrossRefGoogle ScholarPubMed
Lane, A. N., Jenkins, T. C., Brown, D. J. S. & Brown, T. (1991). NMR determination of the solution conformation and dynamics of the A.G mismatch in the d(CGCAAATTGGCG)2 dodecamer. Biochem. J. 279, 269–281.CrossRefGoogle Scholar
Lane, A., Martin, S. R., Ebel, S. & Brown, T. (1992). Solution conformation of a deoxynucleotide containing tandem G.A mismatched base pairs and 3′-overhanging ends in d(GTGAACTT)2. Biochemistry 31, 12087–12095.CrossRefGoogle ScholarPubMed
Lane, A. N., Ebel, S. & Brown, T. (1993). NMR assignements and solution structure of the DNA.RNA hybrid duplex d(GTGAACTT).r(AAGUUCAC). Eur.J. Biochem. 215, 297–306.CrossRefGoogle Scholar
Lane, A., Ebel, S. & Brown, T. (1994). Properties of multiple G.A mismatches in stable oligonucleotide duplexes. Eur.J. Biochem. 220, 717–727.CrossRefGoogle ScholarPubMed
Lane, A. N. & Peck, B. (1995). Conformational flexibility in DNA duplexes containing G.G mismatches. Eur. J. Biochem. 230, 1073–1087.Google ScholarPubMed
Lavery, R. (1988). Junctions and bends in nucleic acids: a new theoretical modelling approach. In Structure and expression. Vol.2, DNA bending and curvature eds. Olson, W. K., Sarma, R. H., Sarma, M. H. & Sundaralingam, M., New York: Adenine Press. p. 191–211.Google Scholar
Lavery, R. & Hartmann, B. (1994). Modelling DNA conformational mechanisms. Biophys. Chem. 50, 33–45.CrossRefGoogle Scholar
Lavery, R. & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleicacids. J. Biomol. Struct. Dynam. 6, 655.CrossRefGoogle Scholar
Lavery, R. & Sklenar, H. (1989). Defining the structure of irregular nuclmeic acids: conventions and principles. J. Biomol. Struct. Dynam. 6, 655.CrossRefGoogle ScholarPubMed
Lavery, R., Zakrzewska, K., Sun, J.-S. & Harvey, S. C. (1992). A comprehensive classification of nucleic acid structural families based on strand direction and base pairing. Nucleic Acids Res. 20, 5011–5016.CrossRefGoogle ScholarPubMed
Lavigne, M., Kolb, A., Yeramian, E. & Buc, H. (1994). CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 13, 4983–4990.CrossRefGoogle ScholarPubMed
LeBlanc, D. A. & Morden, K. M. (1991). Thermodynamic characterizationn of deoxyribooligonucleotide duplexes containing bulges. Biochemistry 30, 4042–4047.CrossRefGoogle Scholar
Leng, M. (1985). Left-handed Z-DNA. Biochim. Biophys Acta 825, 339–344.CrossRefGoogle ScholarPubMed
Leonard, G. A., Thomson, J., Watson, W. P. & Brown, T. (1990). High resolution structure of a mutagenic lesion in DNA. Proc. Natl. Acad. Sci. USA 87, 9573–9576.CrossRefGoogle ScholarPubMed
Leonard, G. A., Booth, E. D., Hunter, W. N. & Brown, T. (1992). The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer. Nucleic Acids Res. 20, 4753–4759.CrossRefGoogle Scholar
Leroy, J.-L., Kochoyan, M., Huynh-Dinh, T., & Guéron, M., (1988a). Characterization of base-pair opening in deoxynucleotide duplexes using catalysed exchange of the imino proton. J. Mol. Biol. 200, 223–238.CrossRefGoogle ScholarPubMed
Leroy, J.-L., Charetier, E., Kochoyan, M., & Guéron, M., (1988b). Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry 27, 8894–8898.CrossRefGoogle ScholarPubMed
Levene, S. D. & Crothers, D. M. (1983). A computer graphics study of sequencedirected bending in DNA. J. Biomol. Struct. Dynam. 1, 429–435.CrossRefGoogle ScholarPubMed
Levene, S. D. & Zimm, B. H. (1989). Understanding the anomalous electrophoresis of bent DNA molecules: a reptation model. Science 245, 396–399.CrossRefGoogle ScholarPubMed
Li, Y. & Agrawal, S. (1995). Oligonucleotides containing G.A pairs: effect on flanking sequences on structure and stability. Biochemistry 34, 10056–10062.CrossRefGoogle ScholarPubMed
Li, Y., Zon, G. & Wilson, W. D. (1991). NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex. Proc. Natl. Acad. Sci. USA 88, 26–30.CrossRefGoogle Scholar
Liepinsh, E., Otting, G. & Wüthrich, K. (1992). NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res. 20, 6549–6553.CrossRefGoogle ScholarPubMed
Liepinsh, E., Leupin, W. & Otting, G. (1994 a). Hydration of DNA in aqueous solution: NMR evidence for a kinetic destabilization of the minor groove hydration of d-(TTAA)2 versus d-(AATT)2 segments. Nucleic Acids Res. 22, 2349–2254.CrossRefGoogle ScholarPubMed
Liepinsh, E., Leupin, W. & Otting, G., (1994 b). Hydration of DNA in aqueous solution: NMR evidence for a kinetic destabilisation of minor groove hydration of d(TTAA)2 versus d(AATT)2 segments. Nucleic Acids Res. 22, 2249–2254.CrossRefGoogle Scholar
Lipanov, A., Kopka, M. L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R. E. (1993). Structure of the B-DNA decamer CCAACITTGG in two different space groups: conformational flexibility of B-DNA. Biochemistry 32, 1373–1389.CrossRefGoogle ScholarPubMed
Liquiers, J., Taillandier, E., Peticolas, W. L. & Thomas, G. A. (1990). The infrared and Raman spectra of the duplex of d(GGTATACC) in the crystal show bands due to both the A-form and the B-form of DNA. J. Biomol. Struct. Dynam. 8, 295–302.CrossRefGoogle ScholarPubMed
Liu, H., Spielmann, H. P., Ulyanov, N. B., Wemmer, D. E. & James, T. L. (1995). Interproton distance bounds from 2D NOE intensities: effect of experimental noise and peak integration errors. J. Biomol. NMR. 6, 390–402.CrossRefGoogle ScholarPubMed
Loprete, D. M. & Hartman, K. A. (1993). Conditions for the stability of the B, C, and Z structural forms of poly(dG-dC) in the presence of lithium, potassium, magnesium, calcium and zinc cations. Biochemistry 32, 4077–4082.CrossRefGoogle Scholar
Lu, M., Guo, Q., Kallenbach, N. R. & Sheardy, R. D. (1992). Conformational properties of B-Z junctions in DNA. Biochemistry 31, 4712–4719.CrossRefGoogle ScholarPubMed
Lyubchenko, Y. L., Shlyakhtenko, L. S., Appelia, E. & Harrington, R. E. (1993). CA runs increase DNA flexibility in the complex of Cro protein with the OR3 site. Biochemistry 32, 4121–4127.CrossRefGoogle ScholarPubMed
Malfoy, B., Rousseau, N. & Leng, M. (1982). Interaction between antibodies to Z-form deoxyribonucleic acid and double-stranded polynucleotides. Biochemistry 21, 5463–5469.CrossRefGoogle ScholarPubMed
Maltseva, T. V., Agback, P. & Chattopadhyaya, J. (1993). How much hydration is necessary for the stabilisation of DNA-duplex Nucleic Acids Res. 21, 4246–4252.CrossRefGoogle ScholarPubMed
Maniatis, T., Jeffrey, A. & van der Sande, H. (1975). Chain length determination of small double and single stranded DNA molecules by polyacrilamide gel electrophoresis. Biochemistry 14, 3787–3794.CrossRefGoogle Scholar
Manning, G. S. (1983). Breathing and bending fluctuations in DNA modeled by an open-base-pair kink coupled to axial compression. Biopolymers 22, 689–703.CrossRefGoogle ScholarPubMed
Marini, J. C., Levene, S. D., Crothers, D. M. & Englund, P. T. (1983). A bent helix in kinetoplast DNA. Proc. Natl. Acad. Sci. USA 79, 7664–7683.CrossRefGoogle Scholar
Marini, J. C., Weisberg, R. & Landy, A. (1977). The isolation of the restriction fragments containing the primary and secondary (galT) bacterial att sires of phage lambda. Virology 83, 254–270.CrossRefGoogle Scholar
Marzec, C. J. & Day, L. A., (1993 a). An exact description of 5-membered ring conformations. 1. Parametrization via an amplitude-S, an angle-gamma, the pseudorotation amplitude-Q and phase angle-P, and the bond lengths. J. Biomol. Struct. Dyn. 10, 1091–1123.CrossRefGoogle Scholar
Marzec, C. J. & Day, L. A. (1993 b). An exact description of 5-membered ring conformations. 2. Applications to furanose rings in DNA and RNA, analysis of errors, and bond angle bending energy. J. Biomol. Struct. Dyn. 10, 1125–1154.CrossRefGoogle Scholar
Maskos, K., Gunn, B. M., Leblanc, D. A. & Morden, K. M. (1993). NMR study of G-A and A-A pairing in (dGCGAATAAGCG)2. Biochemistry 32, 3583–3595.CrossRefGoogle Scholar
Mauffret, O., Hartmann, B., Convert, O., Lavery, R. & Fermandjian, S. (1992). The fine structure of two DNA dodecamers containing the cAMP responsive element sequence and its inverse. J. Mol. Biol. 227, 852–862.CrossRefGoogle ScholarPubMed
McCammon, J. A. & Harvey, S. C. (1987). Dynamics of proteins and nucleic acids. Cambridge University Press U. K.CrossRefGoogle Scholar
McCarthy, J. G., Frederick, C. A. & Nicolas, A. (1993). A structural analysis of the bent kinetoplast DNA from Crithidia Fasciculata by high resolution chemical probing. Nucleic Acids Res. 14, 3309–3317.CrossRefGoogle Scholar
McLean, M. J. & Wells, R. D., (1988 a). The role of sequence in the stabilisation of lefthanded DNA helices in vitro and in vivo. Biochim. Biophys. Ada 950, 243–248.CrossRefGoogle ScholarPubMed
McLean, M. J. & Wells, R. D. (1988 b). The role of DNA sequence in the formation of Z-DNA versus cruciforms in plasmids. J. Biol. Chem. 263, 7370–7377.CrossRefGoogle ScholarPubMed
McNamara, P. T., Bolshoy, A., Trifonov, E. N. & Harrington, R. E. (1990). Sequence dependent kinks induced in curved DNA. J. Biomol. Struct. Dynam. 8, 529–538.CrossRefGoogle ScholarPubMed
Mellema, J.-R., Hasnoot, C. A. G., van der Marel, G. A., Wille, G., van Boeckel, C. A. A., van Boom, J. H. & Altona, C. (1983). Proton NMR studies on the convalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Nucleic Acids Res. 11, 5717–5738.CrossRefGoogle Scholar
Metzler, W. J., Wang, C., Kitchen, D. B., Levy, R. M. & Pardi, A. (1990). Determining local conformation variations in DNA. J. Mol. Biol. 214, 711–736.CrossRefGoogle ScholarPubMed
Miaskiewicz, K., Osman, R. & Weinstein, H. (1993). Molecular dynamics simulation of the hydrated d(CGCGAATTCGCG)2 dodecamer. J. Am. Chem. Soc. 115, 1526–1537.CrossRefGoogle Scholar
Miller, M., Harrison, R. W., Wlodawer, A., Appella, E. & Sussman, J. L. (1988). Crystal structure of 15-mer DNA duplex containing unpaired bases. Nature 334, 85–86.CrossRefGoogle ScholarPubMed
Mills, J. B., Cooper, J. P. & Hagerman, P. J. (1994). Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry 33, 1797–1803.CrossRefGoogle ScholarPubMed
Milman, G., Langridge, R. & Chamberlin, M. J. (1966). The structure of a DNARNA hybrid. Proc. Natl. Acad. Sci. USA 57, 1804–1810.CrossRefGoogle Scholar
Milton, D. L., Casper, M. L., Wills, N. M. & Gesteland, R. F. (1990). Guanine tracts enhance sequence directed DNA bends. Nucleic Acids Res. 18, 817–820.CrossRefGoogle ScholarPubMed
Mlnchenkova, L. E., Schyolkina, A. K., Chernov, B. K. & Ivanov, V. I. (1986). CC/GG contacts facilitate the B to A transition of DNA in solution. J. Biomol. Struct. Dynam. 4, 463–476.CrossRefGoogle Scholar
Mishra, R. K., Latha, P. K. & Brahmachari, S. K. (1988). Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition insolution. Nucleic Acids Res. 16, 4651–4665.CrossRefGoogle ScholarPubMed
Miskovsky, P., Chinsky, L., Laigle, A. & Turpin, P. Y. (1989). The Z-conformation of poly(dA-dT).poly(dA-dT) in solution as studied by ultraviolet resonance Raman spectroscopy. J. Biomol. Struct. Dynam. 7, 623–637.CrossRefGoogle ScholarPubMed
Mitsui, Y., Langridge, R., Shortle, B. E., Cantor, C. R., Grant, R. C., Kodama, M. & Wells, R. D. (1970). Physical and enzymatic studies on Poly d(I-C).Poly d(I-C), and an unusual double helical DNA. Nature 228, 1166–1169.CrossRefGoogle Scholar
Moe, J. G. & Russu, I. M. (1990). Proton exchange and base-pair opening kinetics in 5′- d(CGCGAATTCGCG)-3′ and related dodecamers. Nucleic Acids Res. 18, 821–827.CrossRefGoogle ScholarPubMed
Moe, J. G. & Russu, I. M. (1992). Kinetics and energetics of base-pair opening in 5′- d(CGCGAATTCGCG)-3′ and a substitued dodecamer containing G-T mismatches. Biochemistry 31, 8421–8428.CrossRefGoogle Scholar
Morden, K. M. & Maskos, K. (1993). NMR Study of an extrahelical cytosine in an A.T rich region of a deoxyribodecanucleotide. Biopolymers 33, 27–36.CrossRefGoogle Scholar
Nadeau, J. G. & Crothers, D. M. (1989). Structural basis for DNA bending. Proc. Natl. Acad. Sci. USA 86, 2622–2626.CrossRefGoogle ScholarPubMed
Nagaich, A. K., Bhattacharyya, D., Bramachari, S. K. & Bansal, M. (1994). CA/TG sequence at the 5′ End of oligo(A)-tracts strongly modulates DNA curvature. J. Biol. Chem. 269, 7824–7833.CrossRefGoogle ScholarPubMed
Naylor, L. H. & Clark, E. M. (1990). d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. Nucleic Acids Res. 18, 1595–1601.CrossRefGoogle ScholarPubMed
Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987). The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature 330, 221–226.CrossRefGoogle ScholarPubMed
Niederweis, M., Lederer, T. & Hillen, W. (1994). Matrix effects suggest an important influence of DNA-polyacrilamide interactions on the electrophoretic mobility of DNA. J. Biol. Chem. 269, 10156–10162.CrossRefGoogle ScholarPubMed
Nlkonowicz, E., Roongta, V., Jones, C. R. & Gorenstein, D. G. (1989). Two dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelicoidal adenosine tridecamer oligodeoxyribonucleotide duplex. Biochemistry 28, 8714–8725.CrossRefGoogle Scholar
Nikonowicz, E. P. & Gorenstein, D. G. (1992). Comparison of the X-ray crystal, NMR solution and molecular dynamics calculated structures of a tandem G.A mismatched oligonucleotide duplex. J. Am. Chem. Soc. 114, 7494–7503.CrossRefGoogle Scholar
Nuutero, S., Fujimoto, B. S., Flynn, P. F., Reid, B. R., Ribeiro, N. S. & Schurr, J. M. (1994). The amplitude of local angular motion of purines in. DNA in solution. Biopolymers 34, 463–480.CrossRefGoogle ScholarPubMed
Oda, Y., Uesugi, S., Ikehara, M., Kawase, Y. & Ohtsuka, E. (1991). NMR studies for identification of dI:dG mismatch base-pairing structure in DNA. Nucleic Acids Res. 19, 5263–5267.CrossRefGoogle Scholar
Ogawa, T. & Okazaki, T. (1980). Discontinuous DNA replication. Annu. Rev. Biochem. 49, 421–457.CrossRefGoogle ScholarPubMed
Olson, W. K., Srinivavan, A. R., Maroun, R. C., Torres, R. & Clark, W. (1987). Base sequence effects in curved and rodlike DNA. Unusual DNA Structures eds. Wells, R. D. & Harvey, S. C., New York: Springer, 207–256.Google Scholar
Olson, W. K., Marky, N. L., Jernigan, R. L. & Zhurkin, V. B. (1993). Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232, 530–554.CrossRefGoogle ScholarPubMed
Park, Y.-W. & Breslauer, K. J. (1991). A spectroscopic and calorimetric study of the melting behaviors of a ‘bent’ and ‘normal’ DNA duplex: (d(GA4T4C))2 versus (d(GT4A4C))2. Proc. Natl. Acad. Set. USA 88, 1551–1555.CrossRefGoogle ScholarPubMed
Patel, D. J., Koslowski, S. A., Ikuta, S. & Itakura, K. (1984). Deoxyguanosinedeoxyadenosine pairing in the d(CGGAATTCGCG duplex: conformation and dynamics at and adjacent to the dG.dA mismatch site. Biochemistry 23, 3207–3215.CrossRefGoogle Scholar
Patel, D. J., Shapiro, L., Kozlowski, S. A., Gaffney, B. L. & Jones, R. A. (1986). Covalent carcinogenic O6-methylguanosine lesions in DNA structural studies of the O6meG.A and O6meG.G interactions in dodecanucleotide duplexes?. Mol. Biol. 188, 677–692.CrossRefGoogle Scholar
Pearlman, D. A. & Kollman, P. A. (1991). Are time-averaged restraints necessary for nuclear magnetic resonance refinement J. Mol. Biol. 220, 457–479.CrossRefGoogle ScholarPubMed
Peticolas, W. L., Wang, Y. & Thomas, G. A. (1988). Some rules for predicting the base-sequence dependence of DNA conformation. Proc. Natl. Acad. Set. USA 85, 2579–2583.CrossRefGoogle ScholarPubMed
Pohl, F. M. & Jovin, T. M. (1972). Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with Poly(dG-dC). J. Mol. Biol. 67, 375–396.CrossRefGoogle ScholarPubMed
Powers, P., Jones, C. R. & Gorenstein, D. G. (1990). Two-dimentional H and 31P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure. J. Biomol. Struct. Dynam. 8, 253–294.CrossRefGoogle Scholar
Price, M. A. & Tullius, T. D. (1993). How the structure of an adenine tract depends on sequence context: a new model for the structure of TNAN DNA sequences. Biochemistry 32, 127–136.CrossRefGoogle ScholarPubMed
Privé, G. G., Heinemann, U., Chandrasegaran, S., Kan, L. S., Kopta, M. L. & Dickerson, R. E. (1987). Helix geometry, hydration and G.A mismatch in a B-DNA decamer. Science 231, 498–504.CrossRefGoogle Scholar
Privé, G. G., Yanagi, K. & Dickerson, R. E. (1991). Structure of the B-DNA de camer CCAACGTTGG and comparison with isomorphous decamers CCAAGATTGG and CCAGGCCTGG. J. Mol. Biol. 217, 177–199.CrossRefGoogle Scholar
Puhl, H. L., Satyanarayana, R., Gudibande, R. & Behe, M. J. (1991). Polyd(A.T) and other synthetic polydeoxynucleotides containing oligoadenosine tracts form nucleosomes easily. J. Mol. Biol. 222, 1149–1160.CrossRefGoogle Scholar
Quignard, E., Fazakerley, G. V., van der Marel, G., van Boom, J. H. & Guschlbauer, W. (1987). Comparison of the conformation of an oligonucleotide containing a central G-T base pair with the non-mismatch sequence by proton NMR. Nucleic Adds Res. 15, 3397–3409.CrossRefGoogle ScholarPubMed
Quintana, J. R., Grzeskowiak, K., Yanagi, K. & Dickerson, R. E. (1992). Structure of a B-DNA decamer with a central T-A step: CGATTAATCG. J. Mol. Biol. 225, 379–395.CrossRefGoogle ScholarPubMed
Rabinovich, D., Haran, T., Eisenstein, M. & Sharked, Z. (1988). Structures of the mismatched duplex d(GGGTGCCC) and one of its Watson-Crick analogues d(GGGCGCCC). J. Mol. Biol. 200, 151–161.CrossRefGoogle ScholarPubMed
Radhakrishnan, I. & Patel, D. J. (1992). Three-dimensional homonuclear NOESYTOCSY of an intramolecular pyrimidine-purine-pyrimidine DNA triplex containing a central G.TA triple: Nonexchangeable proton assignments and structural implications. Biochemistry 31, 2514–2523.CrossRefGoogle ScholarPubMed
Rahmouni, A. R. (1992). Z-DNA as a probe for localized supercoiling in vivo. Mol. Microbiol. 6, 569–572.CrossRefGoogle ScholarPubMed
Rahmouni, A. R. & Wells, R. D. (1992). Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J. Mol. Biol. 223, 131–144.CrossRefGoogle ScholarPubMed
Ramakrishnan, B. & Sundaralingam, M. (1993). High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). J. Mol. Biol. 231, 431–444.CrossRefGoogle ScholarPubMed
Ramstein, J. & Lavery, R. (1988). Energetic coupling between DNA bending and basepair opening. Proc. Natl. Acad. Sci. USA 85, 7231–7235.CrossRefGoogle Scholar
Ramstein, J. & Lavery, R. (1990). Base-pair opening in B-DNA. J. Biomol. Struct. Dyn. 7, 915–933.CrossRefGoogle ScholarPubMed
Rao, S. N. & Kollman, P. A. (1990). Simulations of the B-DNA molecular dynamics of d(CGCGAATTCGCG)2 and d(GCGCGCGCGC)2: an analysis of the role of the initial geometry and a comparison of united and all-atom models. Biopolymers 29, 517–532.CrossRefGoogle Scholar
Rao, S. T., Westhof, E. & Sundaralingam, M. (1981). Exact method for the calculation of pseudorotation parameters P and Tm and their errors. Ada Crystal. A37, 421–425.Google Scholar
Ratmeyer, L., Vinayak, R., Zhong, Y. Y., Zon, G. & Wilson, W. D. (1994). Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. Biochemistry 33, 5298–5304.CrossRefGoogle ScholarPubMed
Reich, Z., Friedman, P., Scolnik, Y., Sussman, J. L. & Minsky, A. (1993). On the metastability of the left-handed DNA motifs. Biochemistry 32, 2116–2119.CrossRefGoogle ScholarPubMed
Rice, J. A. & Crothers, D. M. (1989). DNA bending by bulge defect. Biochemistry 28, 4512–4516.CrossRefGoogle ScholarPubMed
Roongta, V. A., Jones, C. R. & Gorenstein, D. G. (1990). Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecemers containing GT, GG, GA, AC, and GU base-pair mismatches on 31P NMR spectra. Biochemistry 29, 5245–5251.CrossRefGoogle ScholarPubMed
Rose, I. A., Hanson, K. R., Wilkinson, K. D. & Wimmer, M. J. (1980). A suggestion for naming faces of ring compounds. Proc. Natl. Acad. Sci. (USA) 77, 2439–2446.CrossRefGoogle ScholarPubMed
Rosen, M. A., Shapiro, L. & Patel, D. J., (1992 a). Solution structure of a trinucleotide A-T-A bulge loop within a DNA duplex. Biochemistry 31, 4015–4026.CrossRefGoogle ScholarPubMed
Rosen, M. A., Live, D. & Patel, D. J., (1992 b). Comparative NMR study of An-Bulge Loops in DNA duplexes: intrahelical stacking of A, A-A and A-A-A bulge loops. Biochemistry 31, 4004–4014.CrossRefGoogle Scholar
Rosenberg, J. M., Seeman, N. C., Day, R. O. & Rich, A. (1976). RNA double helices generated from crystal structures of double helical dinucleotide phosphates. Biochem. Biophys. Res. Commun. 69, 979–987.CrossRefGoogle Scholar
Saenger, W. (1984). Principles of Nucleic Acids Structures. New York: Springer.CrossRefGoogle Scholar
Saenger, W., Hunter, W. N. & Kennard, O. (1986). DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385–388.CrossRefGoogle ScholarPubMed
Salazar, M., Champoux, J. J. & Reid, B. R. (1993). Sugar conformations at hybrid duplex junctions in HIV-i and Okasaki fragments. Biochemistry 32, 739–744.CrossRefGoogle Scholar
Salazar, M., Fedoroff, O. Y., Zhu, L. & Reid, B. R. (1994). The solution structure of the r(gcg)d(TATACCC):d(GGGTATACGC) Okasaki fragment contains two distinct duplex morphologies connected by a junction. J. Mol. Biol. 241, 440–455.CrossRefGoogle Scholar
Sanghani, S. R. & Lavery, R. (1994). Theoretical studies of DNA-RNA hybrid conformations. Nucleic Acids Res. 22, 1444–1449.CrossRefGoogle ScholarPubMed
Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659–675.CrossRefGoogle ScholarPubMed
Schleif, R. (1992). DNA looping. Ann. Rev. Biochetn. 61, 199–223.CrossRefGoogle ScholarPubMed
Schmitz, U., Zon, G. & James, T. L. (1990). Deoxyribose conformation in d(GTATATAC)2: evaluation of sugar pucker by simulation of double quantum filtered COSY cross-peaks. Biochemistry 29, 2357–2368.CrossRefGoogle Scholar
Schmitz, U., Pearlman, D. A. & James, T. L. (1991). Solution structure of d(GTATATAC)2 via restrained molecular dynamics simulations with NMR constraints derived from relaxation matrix analysis of two-dimensional NOE experiments. J. Mol. Biol. 221, 271–292.CrossRefGoogle Scholar
Schmitz, U., Sethson, I., Egan, W. M. & James, T. L. (1992). Solution stucture of a DNA octamer containing the Pribnow box via a restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectral fitting. J. Mol. Biol. 227, 510–531.CrossRefGoogle Scholar
Schmitz, U., Ulyanov, N. B., Kumar, A. & James, T. L. (1993). Molecular dynamics with time-averaged restraints for a DNA octamer. J. Mol. Biol. 234, 373–389.CrossRefGoogle ScholarPubMed
Schneider, B., Cohen, D. & Berman, H. M. (1992 a). Hydration of DNA bases: analysis of crystallographic data. Biopolymers 32, 725–750.CrossRefGoogle ScholarPubMed
Schneider, B., Ginell, S. L., Jones, R., Gaffney, B. & Berman, H. M. (1992 b). Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification. The relationship between conformation, packing, and hydratation in Z-DNA hexamers. Biochemistry 31, 9622–9628.CrossRefGoogle ScholarPubMed
Schneider, B., Cohen, D., Schleifer, L., Srinivasan, A. R., Olson, W. K. & Berman, H. M. (1993). A systemetic method for studying the spacial distribution of water molecules around nucleic acid bases. Biophys. J. 65, 2291–2303.CrossRefGoogle Scholar
Schroth, G. P., Chou, P.-J. & Ho, P. S. (1992). Mapping Z-DNA in the human genome. J. Biol. Chem. 267, 11846–11855.CrossRefGoogle ScholarPubMed
Schroth, G. P., Kagawa, T. F. & Ho, P. S. (1993). Structure and thermodynamics of nonalternating C.G base pair in Z-DNA: the crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG). Biochemistry 32, 13381–13392.CrossRefGoogle ScholarPubMed
Searle, M. S. & Wakelin, L. P. G. (1990). Sequence specific conformation of a DNA decamer containing an adenine tract studied in solution by 1H-NMR spectroscopy. Biochim. Biophys. Acta 1049, 69–77.CrossRefGoogle Scholar
Selsing, E., Wells, R. D., Early, T. A. & Kearns, D. R. (1978). Two contiguous conformations in a nucleic acid duplex. Nature 254, 249–250.CrossRefGoogle Scholar
Selsing, E. & Wells, R. D. (1979). Polynucleotide block polymers consisting of a DNA.RNA hybrid joined to a DNA.DNA duplex. J. Biol. Chem. 254, 5410–5418.CrossRefGoogle ScholarPubMed
Selsing, E., Wells, R. D., Alden, C. J. & Arnott, S. (1979). Polynucleotide block polymers consisting of a DNA.RNA hybrid joined to a DNA.DNA duplex. J. Biol. Chem. 254, 5410–5416.CrossRefGoogle ScholarPubMed
Shakked, Z. (1991). The influence of the environment on DNA structures determined by X-ray crystallography. Current Opinion in Structural Biology 1, 446–451.CrossRefGoogle Scholar
Sheardy, R. D. & Winkle, S. A. (1989). Temperature dependent CD and NMR studies on a synthetic oligonucleotide containing a B-Z junction at high salt. Biochemistry 28, 720–725.CrossRefGoogle ScholarPubMed
Sheardy, R. D., Suh, D., Kurzinsky, R., Doktycz, M. J., Benight, A. S. & Chaires, J. B. (1993). Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides. J. Mol. Biol.. 231, 475–488.CrossRefGoogle ScholarPubMed
Shindo, H. & Matsumoto, U. (1984). Direct evidence for a bimorphic structure of a DNA-RNA hybrid, poly(rA).poly(dT), at high relative humidity. J. Biol. Chem.. 259, 8682–8684.CrossRefGoogle Scholar
Shore, D., Langowski, J. & Baldwin, R. L. (1981). DNA flexibility studied by covalent closure of short fragments into circle. Proc. Natl. Acad. Sci. USA 78, 4833–4837.CrossRefGoogle Scholar
Shrader, T. E. & Crothers, D. M. (1989). Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86, 7418–7422.CrossRefGoogle ScholarPubMed
Simpson, L. (1979). Isolation of maxicircle component of kinetoplast DNA from hemoflagellate protozoa. Proc. Natl. Acad. Sci. USA 76, 1585–1588.CrossRefGoogle ScholarPubMed
Skelly, J. V., Edwards, K. J., Jenkins, T. C. & Neidle, S. (1993). Crystal structure of an oligonucleotide duplex containing G-G base pairs: influence of mispairing on DNA backbone conformation. Proc. Natl. Acad. Sci. USA 90, 804–808.CrossRefGoogle ScholarPubMed
Soumpasis, D. M. & Tung, C.-S., (1988). A rigorous bese pair oriented description of DNA structures, J. Biomol. Struct. Dynam. 6, 397.CrossRefGoogle Scholar
Sprous, D., Zacharias, W., Wood, Z. A. & Harvey, S. C. (1995). Dehydrating agents sharply reduce curvature in DNAs containing A tracts. Nucleic Acids Res. 23, 1816–1821.CrossRefGoogle ScholarPubMed
Stolarski, R., Egan, W. & James, T. L. (1992). Solution structure of the EcoRI DNA octamer containing 5-fluorouracil via restrained molecular dynamics using distance and torsion angle constraints extracted from NMR spectral simulations. Biochemistry 31, 7027–7042.CrossRefGoogle ScholarPubMed
Strobel, O. K., Keyes, R. S. & Bobst, A. M. (1990). Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogues. Biochemistry 29, 8522–8528.CrossRefGoogle ScholarPubMed
Suh, D., Sheardy, R. D. & Chaires, J. B. (1991). Unusual binding of Ethidium bromide to a deoxyoligonucleotide containing a B–Z junction. Biochemistry 30, 8722–8726.CrossRefGoogle ScholarPubMed
Sundaralingam, M. & Sekharudu, Y. C. (1988). Sequence directed bending and curvature. Structure and Expression Vol. 3 DNA Bending and Curvature eds. Olson, W. K., Sarma, M. H., Sarma, R. H. & Sundaralingam, M., New York: Adenine Press. 9–23.Google Scholar
Takeuchi, H., Hanamura, N. & Harada, I. (1994). Structural specificity of peptides in Z-DNA formation and energetics of the peptide induced B-Z transition of poly(dG-m5dC). J. Mol. Biol. 236, 610–617.CrossRefGoogle ScholarPubMed
Tao, N. J. (1994). Light scattering spectroscopy studies of the water molecules in DNA. Water and Biological Macromolecules Topics in Molecular and Structural Biology Vol. 17, London: Macmillan Press, London, 266–291.Google Scholar
Théveny, B., Coulaud, D., LeBret, M. & Revet, B. (1988). Local variations of curvature and flexibility along DNA molecules analyzed from electron micrographs. Structure and Expression Vol. 3 DNA Bending and Curvature eds. Olson, W. K., Sarma, M. H., Sarma, R. H. & Sundaralingam, M., New York: Adenine Press P39.Google Scholar
Timsit, Y. & Moras, D. (1992). Crystallization of DNA. Methods in Enzymology 211, 409–429.CrossRefGoogle ScholarPubMed
Torda, A. E., Scheek, R. M., & van Gunsteren, W. F.,(1989). Time-dependent distance restraints in molecular dynamics simulations. Chem. Phys. Lett. 157, 289–294.CrossRefGoogle Scholar
Travers, A. A. (1991). DNA bending and kinking. Sequence dependence and function. Curr. Op. Struct. Biol.. 1, 114–122.CrossRefGoogle Scholar
Trifonov, E. N. & Sussman, J. L. (1980). The pich of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816–3820.CrossRefGoogle Scholar
Tung, C. S. (1992). A reduced set of coordinates for modeling DNA structures: (1) A B-to-A transition pathway driven by pseudorotational angle. J. Biomol. Struct. Dynam.. 9, 1185–1194.CrossRefGoogle ScholarPubMed
Uesugi, S., Oda, Y., Ikehara, M., Kawase, Y. & Ohtsuka, E. (1987). Identification of I:A Mismatch base-pairing structure in DNA. J. Biol. Chem.. 262, 6965–6968.CrossRefGoogle Scholar
Ulanovsky, L. E. & Trifonov, E. N. (1987). Estimation of wedge components in curved DNA. Nature 326, 720–722.CrossRefGoogle ScholarPubMed
Ulyanov, N. B., Gorin, A. A., Zhurkin, V. B., Chen, B-C., Sarma, M. H. & Sarma, R. H. (1992). Systematic study of nuclear Overhauser effects vis-a-vis local helical parameters, sugar puckers, and glycosidic torsions in B-DNA: insensivity of NOE to local transitions in B-DNA oligonucleotides due to internal structural compensations. Biochemistry 31, 3918–3930.CrossRefGoogle Scholar
Ulyanov, N. B., Sarma, M. H., Zhurkin, V. B. & Sarma, R. H. (1993). Decreased interstrand H2-H1′ distance in the GC-rich part of the duplex d(CCTCAAACTCC).d(GGAGTTTGAGG) in solution at low temperature: proton NMR investigation. Biochemistry 32, 6875–6883.CrossRefGoogle Scholar
Ulyanov, N. B., Schmitz, U., Kumar, A. & James, T. L. (1995). Probability assessment of conformational ensembles: sugar repuckering in a DNA duplex in solution. Biophysical J. 68, 13–24.CrossRefGoogle Scholar
Usman, N., Egli, M. & Rich, A. (1992). Large scale chemical synthesis, purification and crystallisation of RNA-DNA chimeras. Nucleic Acids Res.. 20, 6695–6699.CrossRefGoogle ScholarPubMed
van de Ven, F. J. M. & Hilbers, C. W. (1988). Nucleic acids and nuclear magnetic resonance. Eur. J. Biochem.. 178, 1–38.CrossRefGoogle ScholarPubMed
van Gunsteren, W. F. & Berendsen, H. J. C. (1986). GROMOS86: Groningen Molecular Simulation System, University of Groningen.Google Scholar
Venable, R. M., Widmalm, G., Brooks, B. R., Egan, W. & Pastor, R. W. (1992). Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGATTCGCG). Biopolymers 32, 783–794.CrossRefGoogle ScholarPubMed
Verdaguer, N., Aymami, J., Fernandez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J. & Subirana, J. A. (1991). Molecular structure of a complete turn of A-DNA. J. Mol. Biol. 221, 623–635.CrossRefGoogle ScholarPubMed
Vogt, N., Rousseau, N., Leng, M. & Malfoy, B. (1988). A study of the B-Z transition of the AC-rich region of the repeat unit of a satellite DNA from Cebus by means of chemical probes. J. Biol. Chem. 263, 11826–11832.CrossRefGoogle ScholarPubMed
von Kitzing, E. & Diekmann, S. (1987). Molecular mechanics calculations of dA12-dT12 and of the curved molecule d(GCTCGAAAAA)4.d(TTTTTCGAGC)4. Eur. Biophys J. 15, 13–26.CrossRefGoogle ScholarPubMed
Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. & Rich, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680–686.CrossRefGoogle ScholarPubMed
Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., van der Marel, G., van Boom, J. H. & Rich, A. (1981). Left-handed double helical DNA: variations in the backbone conformation. Science 211, 171–186.CrossRefGoogle ScholarPubMed
Wang, A. H.-J., Fujii, S., van Boom, J. H., van der Marel, G. A., van Boeckel, C. A. A. & Rich, A. (1982). Molecular structure of r(GCG)d(TATACGC): a DNA-RNA hybrid helix joined to double helical DNA. Nature 299, 601–612.CrossRefGoogle ScholarPubMed
Wang, A. H. J., Hakoshima, T., Marel, G. A., van Boom, J. H. & Rich, A., (1984 a). AT base pairs are less stable than GC base pairs in z-DNA: the crystal structure of d(m5CGTAm5CG). Cell 37, 321–331.CrossRefGoogle ScholarPubMed
Wang, A. J. H. & Rich, A., (1984 b). Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. Cell 37, 321–327.CrossRefGoogle Scholar
Wang, A. H.-J., Gessner, R. V., van der Marel, G., van Boom, J. H. & Rich, A. (1985). Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. Proc. Natl. Acad. Sci. USA 82, 3611–3615.CrossRefGoogle ScholarPubMed
Wang, Y. & Griffith, J. (1991). Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases. Biochemistry 30, 1358–1363.CrossRefGoogle ScholarPubMed
Wang, Y., Thomas, G. A. & Peticolas, W. L., (1987 a). Sequence dependent conformation of oligomeric DNA's in aqueous solutions and in crystals. J. Biomol. Struct. Dynam. 5, 249–274.CrossRefGoogle ScholarPubMed
Wang, Y., Thomas, G. A. & Peticolas, W. L., (1987 b). Sequence dependence of the B to Z transition in crystals and aqueous NaCl solutions for deoxyoligonucleotides containing all four canonical DNA bases. Biochemistry 26, 5178–5186.CrossRefGoogle Scholar
Wang, Y., Thomas, G. A. & Peticolas, W. L. (1989). A Duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions. J. Biomol. Struct. Dynam. 6, 1177–1187.CrossRefGoogle Scholar
Webster, G. D., Sanderson, M. R., Skelly, J. V., Neidle, S., Swann, P. F., Li, B. F. & Tickle, I. J. (1990). Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG). Proc. Natl. Acad. Sci. USA 87, 6693–6697.CrossRefGoogle ScholarPubMed
Westhof, E. (1992). Westhof's rule. Nature 358, 450–460.CrossRefGoogle Scholar
Westhof, E. (1994). Structural water bridges in nucleic acids. Water and Biological Macromolecules, Topics in Molecular and Structural Biology, London: Macmillan Press, 17, P226–306.Google Scholar
Westhof, E. & Beveridge, D. L. (1990). Water Science Reviews 5, (ed. Franks, F.) Cambridge: Cambridge Univ. Press.Google Scholar
Westhof, E. & Chevrier, B. (1986). Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer. J. Mol. Biol. 190, 699–712.CrossRefGoogle Scholar
Wijmenja, S. S., Mooren, M. M. W. & Hilbers, C. W. (1993). NMR of nucleic acids. NMR of Macromolecules. ed. Roberts, G. C. K., Oxford: IRL Press, 217–283.CrossRefGoogle Scholar
Wilkins, M. H. F., Stokes, A. R., Wilson, H. R. (1953). Molecular structure of deoxypentose nucleic acids. Nature 171, 738–740.CrossRefGoogle ScholarPubMed
Wing, R., Drew, H., Takano, T., Broca, C., Itakura, K. & Dickerson, R. E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature 287, 755–757.CrossRefGoogle ScholarPubMed
Winkle, S. A. & Sheardy, R. D. (1990). Anomalous gel migration of DNA oligomers containing multiple conformational junctions. Biochemistry 29, 6514–6521.CrossRefGoogle ScholarPubMed
Withka, J. M., Wilde, J. A., Bolton, P. H., Mazumder, A. & Gerlt, J. A. (1991). Characterization of conformational features of DNA heteroduplexes containing aldehyde abasic sites. Biochemistry 30, 9931–9940.CrossRefGoogle Scholar
Woodson, S. A. & Crothers, D. M. (1989). Conformation of a bulge-containing oligomer from a hot-spot sequence by NMR and energy minimization. Biopolymers 28, 1149–1177.CrossRefGoogle ScholarPubMed
Wu, H.-Y. & Behe, M. J. (1984). Salt-induced Z-A-Z transition sequence in the mixed ribo-deoxyribocopolymer poly(rG-dC).poly(rC-dG). Proc. Natl. Acad. Sci. USA 81, 7284–7287.CrossRefGoogle Scholar
Wu, H.-M. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509–513.CrossRefGoogle ScholarPubMed
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. New York: Wiley.CrossRefGoogle Scholar
Xodo, L. E., Manzini, G., Quadrifoglio, F., Yathindra, N., van der Marel, G. A. & van Boom, J. H. (1989). The left handed Z-DNA conformation in oligodeoxynucleotides containing different amounts of AT base pairs: a far UV circular dichroism study. J. Biomol. Struct. Dynam. 6, 1217–1231.CrossRefGoogle ScholarPubMed
Yuan, H., Quintana, J. & Dickerson, R. E. (1992). Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer CGTATATCG. Biochemistry 31, 8009–8021.CrossRefGoogle Scholar
Zakrzewska, K. (1992). Static and dynamic conformational properties of AT sequences in B-DNA. J. Biomol. Struct. Dynam. 9, 681–693.CrossRefGoogle ScholarPubMed
Zarling, D. A., Diekmann, S. & Calhoun, C. J. (1988). Protein recognition of B:d(A)n.d(T)n sequences and kinetoplast DNA. Structure and Expression Vol. 3 DNA Bending and Curvature eds. Olson, W. K., Sarma, M. H., Sarma, R. H. & Sundaralingam, M.. New York: Adenine Press. P87.Google Scholar
Zhou, G. & Ho, P. S. (1990). Stabilization of Z-DNA by demethylation of thymine bases: 1·3 A single-crystal structure of d(m5CGUAm5CG). Biochemistry 29, 7229–7236.CrossRefGoogle ScholarPubMed
Zhurkin, V. B., Lysov, Y. P. & Ivanov, V. I. (1979). Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 6, 1081–1096.CrossRefGoogle ScholarPubMed
Zhurkin, V. B. (1985). Sequence dependent bending of DNA andphasing of nucleosomes. J. Biomol. Struct. Dynam. 2, 785–794.CrossRefGoogle ScholarPubMed
Zhurkin, V. B., Shlyakhtenko, L. S., Lyubchenko, Yu. L., Harrington, R. E., Appella, E., Teplukin, A. V., Poltev, V. I. & Jernigan, R. L. (1995). Curvature and twist of DNA with An:Tn trancts as a function of temperature and hydration. J. Biomol. Struct. Dynam. 12, 8274.Google Scholar
Zieba, K., Chu, T. M., Kupte, D. W. & Marky, L. A. (1991). Differential hydration of dA-dT base pairing and dA and dT bulges in deoxyoligonucleotides. Biochemistry 30, 8018–8026.CrossRefGoogle ScholarPubMed
Zimm, B. H. (1993). Mechanism of gel electrophoresis of DNA: unexpected findings. Curr. Op. Struct. Biol. 3, 373–376.CrossRefGoogle Scholar
Zimmer, D. P. & Crothers, D. M. (1995). NMR of enzymatically synthesized uniformly 13C-13N-labeled DNA oligonucleotides. Proc. Natl Acad. Sci. USA 92, 3091–3095.CrossRefGoogle ScholarPubMed
Zimmerman, S. B. & Pheiffer, B. H. (1981). A RNA.DNA hybrid that can adopt two conformations: an X-ray diffraction study of poly(rA).poly(dT) in concentrated solution or in fibers. Nucleic Acids Res. 78, 78–82.Google ScholarPubMed