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The unique structure of A-tracts and intrinsic DNA bending

Published online by Cambridge University Press:  10 June 2009

Tali E. Haran  and
Udayan Mohanty
Tali E. Haran*
Affiliation:
Department of Biology, Technion – Israel Institute of Technology, Technion, Haifa, Israel
Udayan Mohanty
Affiliation:
Department of Chemistry, Boston College, Chestnut Hill, MA, USA
*
*Author for correspondence: Dr. T. E. Haran, Department of Biology, Technion – Israel Institute of Technology, Technion, Haifa 32000, Israel. Tel.:972-4-8293767; Fax: 972-4-8225153; Email: [email protected]
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Abstract

Short runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 42 , Issue 1 , February 2009 , pp. 41 - 81
Copyright
Copyright © 2009 Cambridge University Press

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References

4. References

Abu-Daya, A. & Fox, K. R. (1997). Interaction of minor groove binding ligands with long AT tracts. Nucleic Acids Research 25, 4962–4969.CrossRefGoogle ScholarPubMed
Adachi, Y., Kas, E. & Laemmli, U. K. (1989). Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO Journal 8, 3997–4006.CrossRefGoogle ScholarPubMed
Adler, B., Sasakawa, C., Tobe, T., Makino, S., Komatsu, K. & Yoshikawa, M. (1989). A dual transcriptional activation system for the 230 kb plasmid genes coding for virulence-associated antigens of Shigella flexneri. Molecular Microbiology 3, 627–635.CrossRefGoogle ScholarPubMed
Aiyar, S. E., Gourse, R. L. & Ross, W. (1998). Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit. Proceedings of the National Academy of Sciences USA 95, 14652–14657.CrossRefGoogle ScholarPubMed
Albert, I., Mavrich, T. N., Tomsho, L. P., Qi, J., Zanton, S. J., Schuster, S. C. & Pugh, B. F. (2007). Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446, 572–576.CrossRefGoogle ScholarPubMed
Alexeev, D. G., Lipanov, A. A. & Skuratovskii, I. Y. (1987). Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove. Nature 325, 821–823.CrossRefGoogle ScholarPubMed
Anderson, J. D. & Widom, J. (2001). Poly(dA–dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Molecular and Cellular Biology 21, 3830–3839.CrossRefGoogle ScholarPubMed
Arnott, S., Chandrasekaran, R., Hall, I. H. & Puigjaner, L. C. (1983). Heteronomous DNA. Nucleic Acids Research 11, 4141–4155.CrossRefGoogle ScholarPubMed
Arnott, S. & Selsing, E. (1974). Structures of the polynucleotide complexes poly(dA).poly(dT) and poly(dT).poly(dA).poly(dT). Journal of Molecular Biology 88, 509–521.CrossRefGoogle ScholarPubMed
Atlung, T. & Ingmer, H. (1997). H-NS: a modulator of environmentally regulated gene expression. Molecular Microbiology 24, 7–17.CrossRefGoogle ScholarPubMed
Augustyn, K. E., Wojtuszewski, K., Hawkins, M. E., Knutson, J. R. & Mukerji, I. (2006). Examination of the premelting transition of DNA A-tracts using a fluorescent adenosine analogue. Biochemistry 45, 5039–5047.CrossRefGoogle ScholarPubMed
Bao, Y., White, C. L. & Luger, K. (2006). Nucleosome core particles containing a poly(dA⋅dT) sequence element exhibit a locally distorted DNA structure. Journal of Molecular Biology 361, 617–624.CrossRefGoogle Scholar
Barbic, A., Zimmer, D. P. & Crothers, D. M. (2003). Structural origins of adenine-tract bending. Proceedings of the National Academy of Sciences USA 100, 2369–2373.CrossRefGoogle ScholarPubMed
Bareket-Samish, A., Cohen, I. & Haran, T. E. (2000). Signals for TBP/TATA box recognition. Journal of Molecular Biology 299, 965–977.CrossRefGoogle ScholarPubMed
Bax, A., Kontaxis, G. & Tjandra, N. (2001). Dipolar couplings in macromolecular structure determination. Methods in Enzymology 339, 127–174.CrossRefGoogle ScholarPubMed
Behling, R. W. & Kearns, D. R. (1986). 1H two-dimensional nuclear Overhauser effect and relaxation studies of poly(dA).poly(dT). Biochemistry 25, 3335–3346.CrossRefGoogle ScholarPubMed
Benham, C., Kohwi-Shigematsu, T. & Bode, J. (1997). Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. Journal of Molecular Biology 274, 181–196.CrossRefGoogle ScholarPubMed
Berezney, R. & Coffey, D. S. (1974). Identification of a nuclear protein matrix. Biochemistry and Biophysics Research Communication 60, 1410–1417.CrossRefGoogle ScholarPubMed
Berman, H. M. & Schneider, B. (1999). Nucleic acid hydration. In Oxford Handbook of Nucleic Acids Structure (ed. Neidle, S.), pp. 295–312. Oxford: Oxford University Press.CrossRefGoogle Scholar
Beutel, B. A. & Gold, L. (1992). In vitro evolution of intrinsically bent DNA. Journal of Molecular Biology 228, 803–812.CrossRefGoogle ScholarPubMed
Beveridge, D. L., Dixit, S. B., Barreiro, G. & Thayer, K. M. (2004). Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting. Biopolymers 73, 380–403.CrossRefGoogle ScholarPubMed
Bloomfield, V. A., Crothers, D. M. & Tinoco, I. J. (2000). Nucleic Acids: Structures, Properties, and Functions. Sausalito: University Science Books.Google Scholar
Bode, J., Benham, C., Knopp, A. & Mielke, C. (2000). Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements). Critical Reviews in Eukaryotic Gene Expression 10, 73–90.CrossRefGoogle ScholarPubMed
Bode, J., Stengert-Iber, M., Kay, V., Schlake, T. & Dietz-Pfeilstetter, A. (1996). Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. Critical Reviews in Eukaryotic Gene Expression 6, 115–138.CrossRefGoogle ScholarPubMed
Bode, J., Winkelmann, S., Gotze, S., Spiker, S., Tsutsui, K., Bi, C., A, K. P. & Benham, C. (2006). Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy. Journal of Molecular Biology 358, 597–613.CrossRefGoogle Scholar
Bolshoy, A., McNamara, P., Harrington, R. E. & Trifonov, E. N. (1991). Curved DNA without A–A: experimental estimation of all 16 DNA wedge angles. Proceedings of the National Academy of Sciences USA 88, 2312–2316.CrossRefGoogle Scholar
Boulikas, T. (1993a). Homeodomain protein binding sites, inverted repeats, and nuclear matrix attachment regions along the human beta-globin gene complex. Journal of Cellular Biochemistry 52, 23–36.CrossRefGoogle ScholarPubMed
Boulikas, T. (1993b). Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. Journal of Cellular Biochemistry 52, 14–22.CrossRefGoogle ScholarPubMed
Boulikas, T. & Kong, C. F. (1993). Multitude of inverted repeats characterizes a class of anchorage sites of chromatin loops to the nuclear matrix. Journal of Cellular Biochemistry 53, 1–12.CrossRefGoogle ScholarPubMed
Bracco, L., Kotlarz, D., Kolb, A., Diekmann, S. & Buc, H. (1989). Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO Journal 8, 4289–4296.CrossRefGoogle ScholarPubMed
Brukner, I., Susic, S., Dlakic, M., Savic, A. & Pongor, S. (1994). Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. Journal of Molecular Biology 236, 26–32.CrossRefGoogle Scholar
Burkhoff, A. M. & Tullius, T. D. (1987). The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell 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. Nature 331, 455–457.CrossRefGoogle Scholar
Calladine, C. R., Drew, H. R. & McCall, M. J. (1988). The intrinsic curvature of DNA in solution. Journal of Molecular Biology 201, 127–137.CrossRefGoogle ScholarPubMed
Carmona, M., Claverie-Martin, F. & Magasanik, B. (1997). DNA bending and the initiation of transcription at sigma54-dependent bacterial promoters. Proceedings of the National Academy of Sciences USA 94, 9568–9572.CrossRefGoogle ScholarPubMed
Cellai, S., Mangiarotti, L., Vannini, N., Naryshkin, N., Kortkhonjia, E., Ebright, R. H. & Rivetti, C. (2007). Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex. EMBO Reports 8, 271–278.CrossRefGoogle ScholarPubMed
Chan, S. S., Austin, R. H., Mukerji, I. & Spiro, T. G. (1997). Temperature-Dependent Ultraviolet Resonance Raman Spectroscopy of the Premelting State of dA* dT DNA. Biophysical Journal 72, 1512–1520.CrossRefGoogle ScholarPubMed
Chan, S. S., Breslauer, K. J., Austin, R. H. & Hogan, M. E. (1993). Thermodynamics and premelting coformational changes of phased (dA)5 tracts. Biochemistry 32, 11776–11788.CrossRefGoogle Scholar
Chan, S. S., Breslauer, K. J., Hogan, M. E., Kessler, D. J., Austin, R. H., Ojemann, J., Passner, J. M. & Wiles, N. C. (1990). Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: correlations with DNA bending. Biochemistry 29, 6161–6171.CrossRefGoogle ScholarPubMed
Cheema, A. K., Choudhury, N. R. & Das, H. K. (1999). A- and T-tract-mediated intrinsic curvature in native DNA between the binding site of the upstream activator NtrC and the nifLA promoter of Klebsiella pneumoniae facilitates transcription. Journal of Bacteriology 181, 5296–5302.CrossRefGoogle ScholarPubMed
Chirico, G., Collini, M., Toth, K., Brun, N. & Langowski, J. (2001). Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy. Eur. Biophysical Journal 29, 597–606.CrossRefGoogle ScholarPubMed
Chiu, T. K. & Dickerson, R. E. (2000). 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. Journal of Molecular Biology 301, 915–945.CrossRefGoogle ScholarPubMed
Chiu, T. K., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1999). Absence of minor groove monovalent cations in the crosslinked dodecamer C–G–C–G–A–A–T–T–C–G–C–G. Journal of Molecular Biology 292, 589–608.CrossRefGoogle ScholarPubMed
Coll, M., Frederick, C. A., Wang, A. H. & 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. Proceedings of the National Academy of Sciences USA 84, 8385–8389.CrossRefGoogle Scholar
Crothers, D. M., Haran, T. E. & Nadeau, J. G. (1990). Intrinsically bent DNA. Journal of Biological Chemistry 265, 7093–7096.CrossRefGoogle ScholarPubMed
Crothers, D. M. & Shakked, Z. (1999). DNA bending by adenine–thymine tracts. In Oxford Handbook of Nucleic Acid Structure (ed. Neidle, S.), pp. 455–470. Oxford: Oxford University Press.CrossRefGoogle Scholar
De Santis, P., Palleschi, A., Savino, M. & Scipioni, A. (1990). Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry 29(39), 9269–9273.CrossRefGoogle ScholarPubMed
Denisov, V. P., Carlstrom, G., Kandadai, Venu K. & Halle, B. (1997). Kinetics of DNA Hydration. Journal of Molecular Biology 268, 118–136.CrossRefGoogle ScholarPubMed
Denisov, V. P. & Halle, B. (2000). Sequence-specific binding of counterions to B-DNA. Proceedings of the National Academy of Sciences USA 97, 629–633.CrossRefGoogle ScholarPubMed
Depew, R. E. & Wang, J. C. (1975). Conformational fluctuations of DNA helix. Proceedings of the National Academy of Sciences USA 72, 4275–4279.CrossRefGoogle ScholarPubMed
Dickerson, R. E. (1992). DNA structure from A to Z. Methods in Enzymology 211, 67–111.CrossRefGoogle ScholarPubMed
Dickerson, R. E. (1999). Helix structure and molecular recognition by B-DNA. In Oxford Handbook of Nucleic Acid Structure (ed. Neidle, S.), pp. 145–197. Oxford: Oxford University Press.CrossRefGoogle Scholar
Dickerson, R. E., Drew, H. R., Conner, B. N., Wing, R. M., Fratini, A. V. & Kopka, M. L. (1982). The anatomy of A-, B-, and Z-DNA. Science 216, 475–485.CrossRefGoogle Scholar
Dickerson, R. E., Goodsell, D. & Kopka, M. L. (1996). MPD and DNA bending in crystals and in solution. Journal of Molecular Biology 256, 108–125.CrossRefGoogle ScholarPubMed
Dickerson, R. E., Goodsell, D. S. & Neidle, S. (1994). “… the tyranny of the lattice …”. Proceedings of the National Academy of Sciences USA 91, 3579–3583.CrossRefGoogle Scholar
Diekmann, S. (1987). Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Research 15, 247–265.CrossRefGoogle ScholarPubMed
Diekmann, S. & Langowski, J. (1995). Supercoiling couples DNA curvature to the overall shape and the internal motion of the DNA molecule in solution. Journal of Molecular Structure (Theochem) 336, 227–234.CrossRefGoogle Scholar
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. Journal of Molecular Biology 225, 729–738.CrossRefGoogle ScholarPubMed
Diekmann, S., von Kitzing, E., McLaughlin, L., Ott, J. & Eckstein, F. (1987). The influence of exocyclic substituents of purine bases on DNA curvature. Proceedings of the National Academy of Sciences USA 84, 8257–8261.CrossRefGoogle ScholarPubMed
Diekmann, S. & Wang, J. C. (1985). On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. Journal of Molecular Biology 151, 1–11.CrossRefGoogle Scholar
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. Proceedings of the National Academy of Sciences USA 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. Journal of Molecular Biology 231, 1024–1039.CrossRefGoogle Scholar
Dlakic, M. & Harrington, R. E. (1996). The effects of sequence context on DNA curvature. Proceedings of the National Academy of Sciences USA 93, 3847–3852.CrossRefGoogle ScholarPubMed
Drak, J. & Crothers, D. M. (1991). Helical repeat and chirality effects on DNA gel electrophoretic mobility. Proceedings of the National Academy of Sciences USA 88, 3074–3078.CrossRefGoogle ScholarPubMed
Drew, H. R. & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer. III. Geometry of hydration. Journal of Molecular Biology 151, 535–556.CrossRefGoogle ScholarPubMed
Drew, H. R. & Travers, A. A. (1985). DNA bending and its relation to nucleosome positioning. Journal of Molecular Biology 186, 773–790.CrossRefGoogle ScholarPubMed
Edmonson, S. P. & Johnson, W. C. (1985). Base tilt of poly[d(A)]-poly[d(T)] and poly[d(AT)]-poly[d(AT)] in solution determined by linear dichroism. Biopolymers 24, 825–841.CrossRefGoogle Scholar
Edwards, K. J., Brown, D. G., Spink, N., Skelly, J. V. & Neidle, S. (1992). Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2·2 A resolution. Journal of Molecular Biology 226, 1161–1173.CrossRefGoogle ScholarPubMed
El Hassan, M. A. & Calladine, C. R. (1996). Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. Journal of Molecular Biology 259, 95–103.CrossRefGoogle ScholarPubMed
Estrem, S. T., Gaal, T., Ross, W. & Gourse, R. L. (1998). Identification of an UP element consensus sequence for bacterial promoters. Proceedings of the National Academy of Sciences USA 95, 9761–9766.CrossRefGoogle ScholarPubMed
Estrem, S. T., Ross, W., Gaal, T., Chen, Z. W., Niu, W., Ebright, R. H. & Gourse, R. L. (1999). Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes and Development 13, 2134–2147.CrossRefGoogle ScholarPubMed
Faiger, H., Ivanchenko, M., Cohen, I. & Haran, T. E. (2006). TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences. Nucleic Acids Research 34, 104–119.CrossRefGoogle ScholarPubMed
Faiger, H., Ivanchenko, M. & Haran, T. E. (2007). Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism. Nucleic Acids Research 35, 4409–4419.CrossRefGoogle ScholarPubMed
Falconi, M., Colonna, B., Prosseda, G., Micheli, G. & Gualerzi, C. O. (1998). Thermoregulation of Shigella and Escherichia coli EIEC pathogenicity. A temperature-dependent structural transition of DNA modulates accessibility of virF promoter to transcriptional repressor H-NS. EMBO Journal 17, 7033–7043.CrossRefGoogle ScholarPubMed
Falconi, M., Prosseda, G., Giangrossi, M., Beghetto, E. & Colonna, B. (2001). Involvement of FIS in the H-NS-mediated regulation of virF gene of Shigella and enteroinvasive Escherichia coli. Molecular Microbiology 42, 439–452.CrossRefGoogle ScholarPubMed
Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I. K., Sharon, E., Lubling, Y., Widom, J. & Segal, E. (2008). Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Computational Biology 4, e1000216.CrossRefGoogle ScholarPubMed
Fiorini, A., Gouveia, Fde S. & Fernandez, M. A. (2006). Scaffold/Matrix Attachment Regions and intrinsic DNA curvature. Biochemistry (Moscow) 71, 481–488.CrossRefGoogle ScholarPubMed
Fritsch, V., Ravishanker, G., Beveridge, D. L. & Westhof, E. (1993). Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations. Biopolymers 33, 1537–1552.CrossRefGoogle ScholarPubMed
Gaal, T., Rao, L., Estrem, S. T., Yang, J., Wartell, R. M. & Gourse, R. L. (1994). Localization of the intrinsically bent DNA region upstream of the E. coli rrnB P1 promoter. Nucleic Acids Research 22, 2344–2350.CrossRefGoogle Scholar
Ganunis, R. M., Guo, H. & Tullius, T. D. (1996). Effect of the crystallizing agent 2-methyl-2,4-pentanediol on the structure of adenine tract DNA in solution. Biochemistry 35, 13729–13732.CrossRefGoogle ScholarPubMed
Gartenberg, M. R. & Crothers, D. M. (1991). Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. Journal of Molecular Biology 219, 217–230.CrossRefGoogle ScholarPubMed
Gimenes, F., Takeda, K. I., Fiorini, A., Gouveia, F. S. & Fernandez, M. A. (2008). Intrinsically bent DNA in replication origins and gene promoters. Genetics and Molecular Research 7, 549–558.CrossRefGoogle ScholarPubMed
Goetze, S., Gluch, A., Benham, C. & Bode, J. (2003). Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: potential of predicting functional gene domains. Biochemistry 42, 154–166.CrossRefGoogle ScholarPubMed
Goodman, S. D. & Nash, H. A. (1989). Functional replacement of a protein-induced bend in a DNA recombination site. Nature 341, 251–254.CrossRefGoogle Scholar
Goodsell, D. S. & Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucleic Acids Research 22, 5497–5503.CrossRefGoogle ScholarPubMed
Goodsell, D. S., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1994). The crystal structure of C–C–A–T–T–A–A–T–G–G. Implications for bending of B-DNA at T–A steps. Journal of Molecular Biology 239, 79–96.CrossRefGoogle ScholarPubMed
Goodsell, D. S., Kopka, M. L., Cascio, D. & Dickerson, R. E. (1993). Crystal structure of CATGGCCATG and its implications for A-tract bending models. Proceedings of the National Academy of Sciences USA 90, 2930–2934.CrossRefGoogle ScholarPubMed
Gourse, R. L., Ross, W. & Gaal, T. (2000). UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Molecular Microbiology 37, 687–695.CrossRefGoogle ScholarPubMed
Griffith, J., Bleyman, M., Rauch, C. A., Kitchin, P. A. & Englund, P. T. (1986). Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell 46, 717–724.CrossRefGoogle ScholarPubMed
Guo, Z., Taubes, C. H., Oh, J. E., Maher, L. J. 3rd & Mohanty, U. (2008). DNA on a tube: electrostatic contribution to DNA stiffness. Journal of Physical Chemistry B 112, 16163–16169.CrossRefGoogle Scholar
Hagerman, P. J. (1985). Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry 24, 7033–7037.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1986). Sequence-directed curvature of DNA. Nature 321, 449–450.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1990a). Pyrimidine 5-methyl groups influence the magnitude of DNA curvature. Biochemistry 29, 1980–1983.CrossRefGoogle ScholarPubMed
Hagerman, P. J. (1990b). Sequence-directed curvature of DNA. Annual Reviews in Biochemistry 59, 755–781.CrossRefGoogle ScholarPubMed
Haran, T. E., Cohen, I., Spasic, A., Yang, K. & Mohanty, U. (2003). Dynamics of curved DNA molecules: prediction and experiment. Journal of the American Chemical Society 125, 11160–11161.CrossRefGoogle Scholar
Haran, T. E., Cohen, I., Spasic, A., Yang, K. & Mohanty, U. (2004). Characteristics of migration patterns of DNA oligomers in gels and its relationship to the question of intrinsic DNA bending. Journal of the American Chemical Society 126, 2372–2377.CrossRefGoogle Scholar
Haran, T. E. & Crothers, D. M. (1989). Cooperativity in A-tract structure and bending properties of composite TnAn blocks. Biochemistry 28, 2763–2767.CrossRefGoogle ScholarPubMed
Haran, T. E., Kahn, J. D. & Crothers, D. M. (1994). Sequence elements responsible for DNA curvature. Journal of Molecular Biology 244, 135–143.CrossRefGoogle ScholarPubMed
Herrera, J. E. & Chaires, J. B. (1989). A premelting conformational transition in poly(dA)-poly(dT) coupled to daunomycin binding. Biochemistry 28, 1993–2000.CrossRefGoogle ScholarPubMed
Hines, C. S., Meghoo, C., Shetty, S., Biburger, M., Brenowitz, M. & Hegde, R. S. (1998). DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins. Journal of Molecular Biology 276, 809–818.CrossRefGoogle ScholarPubMed
Hizver, J., Rozenberg, H., Frolow, F., Rabinovich, D. & Shakked, Z. (2001). DNA bending by an adenine–thymine tract and its role in gene regulation. Proceedings of the National Academy of Sciences USA 98, 8490–8495.CrossRefGoogle ScholarPubMed
Hosid, S. & Bolshoy, A. (2004). New elements of the termination of transcription in prokaryotes. Journal of Biomolecular Structure and Dynamics 22, 347–354.CrossRefGoogle ScholarPubMed
Hud, N. V. & Feigon, J. (1997). Localization of divalent ions in the minor groove of DNA A-tracts. Journal of the American Chemical Society 119, 5756–5757.CrossRefGoogle Scholar
Hud, N. V., Sklenar, V. & Feigon, J. (1999). Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. Journal of Molecular Biology 286, 651–660.CrossRefGoogle ScholarPubMed
Huth, J. R., Bewley, C. A., Nissen, M. S., Evans, J. N., Reeves, R., Gronenborn, A. M. & Clore, G. M. (1997). The solution structure of an HMG-I(Y)–DNA complex defines a new architectural minor groove binding motif. Nature Structural Biology 4, 657–665.CrossRefGoogle ScholarPubMed
Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M. & Trifonov, E. N. (1996). Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. Journal of Molecular Biology 262, 129–139.CrossRefGoogle ScholarPubMed
Ioshikhes, I. P., Albert, I., Zanton, S. J. & Pugh, B. F. (2006). Nucleosome positions predicted through comparative genomics. Nature Genetics 38, 1210–1215.CrossRefGoogle ScholarPubMed
Iyer, V. & Struhl, K. (1995). Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO Journal 14, 2570–2579.CrossRefGoogle ScholarPubMed
Izaurralde, E., Kas, E. & Laemmli, U. K. (1989). Highly preferential nucleation of histone H1 assembly on scaffold-associated regions. Journal of Molecular Biology 210, 573–585.CrossRefGoogle ScholarPubMed
Jerkovic, B. & Bolton, P. H. (2001). Magnesium increases the curvature of duplex DNA that contains dA tracts. Biochemistry 40, 9406–9411.CrossRefGoogle ScholarPubMed
Johannesson, H. & Halle, B. (1998). Minor groove hydration of DNA in solution: dependence on base composition and sequence. Journal of the American Chemical Society 120, 6859–6870.CrossRefGoogle Scholar
Johansson, E., Parkinson, G. & Neidle, S. (2000). A new crystal form for the dodecamer C–G–C–G–A–A–T–T–C–G–C–G: symmetry effects on sequence-dependent DNA structure. Journal of Molecular Biology 300, 551–561.CrossRefGoogle Scholar
Johnson, S. M., Tan, F. J., McCullough, H. L., Riordan, D. P. & Fire, A. Z. (2006). Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Research 16, 1505–1516.CrossRefGoogle ScholarPubMed
Joshi, R., Passner, J. M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M. A., Jacob, V., Aggarwal, A. K., Honig, B. & Mann, R. S. (2007). Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131, 530–543.CrossRefGoogle ScholarPubMed
Karlin, S., Blaisdell, B. E., Sapolsky, R. J., Cardon, L. & Burge, C. (1993). Assessments of DNA inhomogeneities in yeast chromosome III. Nucleic Acids Research 21, 703–711.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 Research 16, 8619–8632.CrossRefGoogle ScholarPubMed
Katayama, S., Matsushita, O., Tamai, E., Miyata, S. & Okabe, A. (2001). Phased A-tracts bind to the alpha subunit of RNA polymerase with increased affinity at low temperature. FEBS Letters 509, 235–238.CrossRefGoogle Scholar
Kintanar, A., Klevit, R. E. & Reid, B. R. (1987). Two-dimensional NMR investigation of a bent DNA fragment: assignment of the proton resonances and preliminary structure analysis. Nucleic Acids Research 15, 5845–5862.CrossRefGoogle ScholarPubMed
Kohwi-Shigematsu, T. & Kohwi, Y. (1990). Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer. Biochemistry 29, 9551–9560.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. Proceedings of the National Academy of Sciences USA 85, 1763–1767.CrossRefGoogle Scholar
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
Koo, H. S., Wu, H. M. & Crothers, D. M. (1986). DNA bending at adenine.thymine tracts. Nature 320, 501–506.CrossRefGoogle ScholarPubMed
Kopka, M. L., Fratini, A. V., Drew, H. R. & Dickerson, R. E. (1983). Ordered water structure around a B-DNA dodecamer, a quantitative study. Journal of Molecular Biology 163, 129–146.CrossRefGoogle ScholarPubMed
Kornberg, R. D. & Lorch, Y. (1999). Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285–294.CrossRefGoogle ScholarPubMed
Kozobay-Avraham, L., Hosid, S. & Bolshoy, A. (2006). Involvement of DNA curvature in intergenic regions of prokaryotes. Nucleic Acids Research 34, 2316–2327.CrossRefGoogle ScholarPubMed
Kremer, W., Klenin, K., Diekmann, S. & Langowski, J. (1993). DNA curvature influences the internal motions of supercoiled DNA. EMBO Journal 12, 4407–4412.CrossRefGoogle ScholarPubMed
Kubinec, M. G. & Wemmer, D. E. (1992). NMR Evidence for DNA Bound Water in Solution. Journal of the American Chemical Society 114, 8739–8740.CrossRefGoogle Scholar
Kunkel, G. R. & Martinson, H. G. (1981). Nucleosomes will not form on double-stranded RNA or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Research 9, 6869–6888.CrossRefGoogle ScholarPubMed
Laundon, C. H. & Griffith, J. D. (1987). Cationic metals promote sequence-directed DNA bending. Biochemistry 26, 3759–3762.CrossRefGoogle ScholarPubMed
Laundon, C. H. & Griffith, J. D. (1988). Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell 52, 545–549.CrossRefGoogle ScholarPubMed
Lavery, R. & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. Journal of Biomolecular Structure and Dynamics 6, 63–91.CrossRefGoogle ScholarPubMed
Lavery, R. & Zakrzewska, K. (1999). Base and base pair morphologies, helical parameters, and definitions. In Oxford Handbook of Nucleic Acid Structure (ed. Neidle, S.). Oxford: Oxford University Press.Google Scholar
Lavigne, M. & Buc, H. (1999). Compression of the DNA minor groove is responsible for termination of DNA synthesis by HIV-1 reverse transcriptase. Journal of Molecular Biology 285, 977–995.CrossRefGoogle ScholarPubMed
Lavigne, M., Roux, P., Buc, H. & Schaeffer, F. (1997). DNA curvature controls termination of plus strand DNA synthesis at the centre of HIV-1 genome. Journal of Molecular Biology 266, 507–524.CrossRefGoogle ScholarPubMed
Lee, W., Tillo, D., Bray, N., Morse, R. H., Davis, R. W., Hughes, T. R. & Nislow, C. (2007). A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics 39, 1235–1244.CrossRefGoogle ScholarPubMed
Leroy, J. L., Charretier, E., Kochoyan, M. & Gueron, M. (1988). 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., Wu, H. M. & Crothers, D. M. (1986). Bending and flexibility of kinetoplast DNA. Biochemistry 25, 3988–3995.CrossRefGoogle ScholarPubMed
Levitt, M. (1978). How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proceedings of the National Academy of Sciences USA 75, 640–644.CrossRefGoogle ScholarPubMed
Liepinsh, E., Otting, G. & Wuthrich, 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 Research 20, 6549–6553.CrossRefGoogle ScholarPubMed
Lilja, A. E., Jenssen, J. R. & Kahn, J. D. (2004). Geometric and dynamic requirements for DNA looping, wrapping and unwrapping in the activation of E.coli glnAp2 transcription by NtrC. Journal of Molecular Biology 342, 467–478.CrossRefGoogle ScholarPubMed
Linial, M. & Shlomai, J. (1987a). Sequence-directed bent DNA helix is the specific binding site for Crithidia fasciculata nicking enzyme. Proceedings of the National Academy of Sciences USA 84, 8205–8209.CrossRefGoogle ScholarPubMed
Linial, M. & Shlomai, J. (1987b). The sequence-directed bent structure in kinetoplast DNA is recognized by an enzyme from Crithidia fasciculata. Journal of Biological Chemistry 262, 15194–15201.CrossRefGoogle ScholarPubMed
Lipanov, A. A. & Chuprina, V. P. (1987). The structure of poly(dA):poly(dT) in a condensed state and in solution. Nucleic Acids Research 15, 5833–5844.CrossRefGoogle Scholar
Lipanov, A. A., Chuprina, V. P., Alexeev, D. G. & Skuratovskii, I. (1990). Bh-DNA: variations of the poly[d(A)].poly[d(T)] structure within the framework of the fibre diffraction studies. Journal of Biomolecular Structure and Dynamics 7, 811–826.CrossRefGoogle Scholar
Liu, J. & Subirana, J. A. (1999). Structure of d(CGCGAATTCGCG) in the presence of Ca(2+) ions. Journal of Biological Chemistry 274, 24749–24752.CrossRefGoogle ScholarPubMed
Liu, Y., Bondarenko, V., Ninfa, A. & Studitsky, V. M. (2001). DNA supercoiling allows enhancer action over a large distance. Proceedings of the National Academy of Sciences USA 98, 14883–14888.CrossRefGoogle Scholar
Lowary, P. T. & Widom, J. (1998). New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology 276, 19–42.CrossRefGoogle ScholarPubMed
Lu, Q., Wallrath, L. L. & Elgin, S. C. (1994). Nucleosome positioning and gene regulation. Journal of Cellular Biochemistry 55, 83–92.CrossRefGoogle ScholarPubMed
Lu, Y. & Stellwagen, N. C. (2008). Monovalent cation binding by curved DNA molecules containing variable numbers of A-tracts. Biophysical Journal 94, 1719–1725.CrossRefGoogle ScholarPubMed
Lu, Y., Weers, B. D. & Stellwagen, N. C. (2005). Intrinsic curvature in the VP1 gene of SV40: comparison of solution and gel results. Biophysical Journal 88, 1191–1206.CrossRefGoogle ScholarPubMed
Luisi, B. (1995). DNA–protein interaction at high resolution. In DNA–Protein: Structural Interactions (ed. Lilley, D. M. J.), pp. 1–48. Oxford: IRL Press.Google Scholar
Lukes, J., Guilbride, D. L., Votypka, J., Zikova, A., Benne, R. & Englund, P. T. (2002). Kinetoplast DNA network: evolution of an improbable structure. Eukaryotic Cell 1, 495–502.CrossRefGoogle ScholarPubMed
Lukes, J., Hashimi, H. & Zikova, A. (2005). Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Current Genetics 48, 277–299.CrossRefGoogle ScholarPubMed
MacDonald, D., Herbert, K., Zhang, X., Polgruto, T. & Lu, P. (2001). Solution structure of an A-tract DNA bend. Journal of Molecular Biology 306, 1081–1098.CrossRefGoogle ScholarPubMed
Maki, A., Brownewell, F. E., Liu, D. & Kool, E. T. (2003). DNA curvature at A tracts containing a non-polar thymine mimic. Nucleic Acids Research 31, 1059–1066.CrossRefGoogle Scholar
Maki, A. S., Kim, T. & Kool, E. T. (2004). Direct comparison of A- and T-strand minor groove interactions in DNA curvature at A tracts. Biochemistry 43, 1102–1110.CrossRefGoogle ScholarPubMed
Manning, G. S. (1978). The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quarterly Reviews of Biophysics 11, 179–246.CrossRefGoogle Scholar
Manning, G. S. (2006). The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophysical Journal 91, 1–10.CrossRefGoogle ScholarPubMed
Marincola, F. C., Denisov, V. P. & Halle, B. (2004). Competitive Na+ and Rb+ Binding in the Minor Groove of DNA. Journal of the American Chemical Society 126, 6739–6750.CrossRefGoogle Scholar
Marini, J. C., Effron, P. N., Goodman, T. C., Singleton, C. K., Wells, R. D., Wartell, R. M. & Englund, P. T. (1984). Physical characterization of a kinetoplast DNA fragment with unusual properties. Journal of Biological Chemistry 259, 8974–8979.CrossRefGoogle ScholarPubMed
Marini, J. C., Levene, S. D., Crothers, D. M. & Englund, P. T. (1982). Bent helical strucutre in kinetoplast DNA. Proceedings of the National Academy of Sciences USA 79, 7664–7668.CrossRefGoogle Scholar
Mathew-Fenn, R. S., Das, R. & Harbury, P. A. (2008). Remeasuring the double helix. Science 322, 446–449.CrossRefGoogle ScholarPubMed
Matthews, K. S. (1992). DNA looping. Microbiology Reviews 56, 123–136.CrossRefGoogle ScholarPubMed
Maurelli, A. T. & Sansonetti, P. J. (1988). Identification of a chromosomal gene controlling temperature-regulated expression of Shigella virulence. Proceedings of the National Academy of Sciences USA 85, 2820–2824.CrossRefGoogle ScholarPubMed
Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I. & Pugh, B. F. (2008a). A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research 18, 1073–1083.CrossRefGoogle ScholarPubMed
Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I. & Pugh, B. F. (2008b). Nucleosome organization in the Drosophila genome. Nature 453, 358–362.CrossRefGoogle ScholarPubMed
McAlteer, K., Gaona, A. A., Michalczyk, R., Buchko, G. W., Isern, N. G., Silks, L. A., Miller, J. H. & Kennedy, M. A. (2004). Compensating ends in 16-base pair DNA oligomer containing a T3A3 segment: a NMR study of global DNA curvature. Biopolymers 75, 497–511.CrossRefGoogle Scholar
McConnell, K. J. & Beveridge, D. L. (2001). Molecular dynamics simulations of B0-DNA: sequence effects on A-tract-induced bending and flexibility. Journal of Molecular Biology 314, 23–40.CrossRefGoogle ScholarPubMed
McFail-Isom, L., Sines, C. C. & Williams, L. D. (1999). DNA structure: cations in charge? Current Opinion in Structural Biology 9, 298–304.CrossRefGoogle ScholarPubMed
Merling, A., Sagaydakova, N. & Haran, T. E. (2003). A-tract polarity dominate the curvature in flanking sequences. Biochemistry 42, 4978–4984.CrossRefGoogle ScholarPubMed
Mika, S. (2006). NMP-db. http://cubic.bioc.columbia.edu/db/nmpdb/.Google Scholar
Minasov, G., Tereshko, V. & Egli, M. (1999). Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing. Journal of Molecular Biology 291, 83–99.CrossRefGoogle ScholarPubMed
Mirkovitch, J., Mirault, M. E. & Laemmli, U. K. (1984). Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39, 223–232.CrossRefGoogle ScholarPubMed
Moe, J. G. & Russo, I. M. (1990). Proton exchange and base-pair opening kinetics in 5′-d(CGCGAATTCGCG)-3′ and related dodecamers. Nucleic Acids Research 18, 821–827.CrossRefGoogle ScholarPubMed
Mohanty, U., Searls, T. & McLaughlin, L. W. (1998). Anomalous migration of short sequences of nucleic acids in polyacrylamide gels: prediction and experiment. Journal of the American Chemical Society 120, 8275–8276.CrossRefGoogle Scholar
Mohanty, U. & Taubes, C. H. (2003). Dynamics of bent molecules in gels. Journal of Physical Chemsitry B 107, 6187–6193.CrossRefGoogle Scholar
Mollegaard, N. E., Bailly, C., Waring, M. J. & Nielsen, P. E. (1997). Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3′-A-tract junction. Nucleic Acids Research 25, 3497–3502.CrossRefGoogle ScholarPubMed
Mukerji, I. & Williams, A. P. (2002). UV resonance Raman and circular dichroism studies of a DNA duplex containing an A3T3 tract: evidence for a premelting transition and three-centered H-bonds. Biochemistry 41, 69–77.CrossRefGoogle ScholarPubMed
Nadeau, J. G. & Crothers, D. M. (1989). Structural basis for DNA bending. Proceedings of the National Academy of Sciences USA 86, 2622–2626.CrossRefGoogle ScholarPubMed
Nelson, H. C., 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
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. Journal of Molecular Biology 232, 530–554.CrossRefGoogle ScholarPubMed
Ozsolak, F., Song, J. S., Liu, X. S. & Fisher, D. E. (2007). High-throughput mapping of the chromatin structure of human promoters. Nature Biotechnology 25, 244–248.CrossRefGoogle ScholarPubMed
Park, Y. W. & Breslauer, K. J. (1991). A spectroscopic and calorimetric study of the melting behaviors of a ‘bent’ and a ‘normal’ DNA duplex: [d(GA4T4C)]2 versus [d(GT4A4C)]2. Proceedings of the National Academy of Sciences USA 88, 1551–1555.CrossRefGoogle Scholar
Pavlicek, J. W., Oussatcheva, E. A., Sinden, R. R., Potaman, V. N., Sankey, O. F. & Lyubchenko, Y. L. (2004). Supercoiling-induced DNA bending. Biochemistry 43, 10664–10668.CrossRefGoogle ScholarPubMed
Peckham, H. E., Thurman, R. E., Fu, Y., Stamatoyannopoulos, J. A., Noble, W. S., Struhl, K. & Weng, Z. (2007). Nucleosome positioning signals in genomic DNA. Genome Research 17, 1170–1177.CrossRefGoogle ScholarPubMed
Perez-Martin, J., Rojo, F. & De Lorenzo, V. (1994). Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiology Reviews 58, 268–290.CrossRefGoogle Scholar
Pfannschmidt, C. & Langowski, J. (1998). Superhelix organization by DNA curvature as measured through site-specific labeling. Journal of Molecular Biology 275, 601–611.CrossRefGoogle ScholarPubMed
Phan, A. T., Leroy, J. L. & Gueron, M. (1999). Determination of the residence time of water molecules hydrating B′-DNA and B-DNA by one-dimensional zero-enhancement nuclear Overhauser effect spectroscopy. Journal of Molecular Biology 286, 505–519.CrossRefGoogle ScholarPubMed
Platts, A. E., Quayle, A. K. & Krawetz, S. A. (2006). In-silico prediction and observations of nuclear matrix attachment. Cellular & Molecular Biology Letters 11, 191–213.CrossRefGoogle ScholarPubMed
Premilat, S. & Albiser, G. (1997). X-ray fibre diffraction study of an elevated temperature structure of poly(dA).poly(dT). Journal of Molecular Biology 274, 64–71.CrossRefGoogle ScholarPubMed
Prosseda, G., Falconi, M., Giangrossi, M., Gualerzi, C. O., Micheli, G. & Colonna, B. (2004). The virF promoter in Shigella: more than just a curved DNA stretch. Molecular Microbiology 51, 523–537.CrossRefGoogle ScholarPubMed
Prunell, A. (1982). Nucleosome reconstitution on plasmid-inserted poly(dA).poly(dT). EMBO Journal 1, 173–179.CrossRefGoogle ScholarPubMed
Puhl, H. L., Gudibande, S. R. & Behe, M. J. (1991). Poly[d(A.T)] and other synthetic polydeoxynucleotides containing oligoadenosine tracts form nucleosomes easily. Journal of Molecular Biology 222, 1149–1160.CrossRefGoogle Scholar
Rauch, C. A., Perez-Morga, D., Cozzarelli, N. R. & Englund, P. T. (1993). The absence of supercoiling in kinetoplast DNA minicircles. EMBO Journal 12, 403–411.CrossRefGoogle ScholarPubMed
Reeves, R. & Nissen, M. S. (1990). The A⋅T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. Journal of Biological Chemistry 265, 8573–8582.CrossRefGoogle Scholar
Rhodes, D. (1979). Nucleosome cores reconstituted from poly (dA–dT) and the octamer of histones. Nucleic Acids Research 6, 1805–1816.CrossRefGoogle ScholarPubMed
Rippe, K., Schrader, A., Riede, P., Strohner, R., Lehmann, E. & Langst, G. (2007). DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proceedings of the National Academy of Sciences USA 104, 15635–15640.CrossRefGoogle ScholarPubMed
Rohs, R., Sklenar, H. & Shakked, Z. (2005). Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. Structure 13, 1499–1509.CrossRefGoogle ScholarPubMed
Rombel, I., North, A., Hwang, I., Wyman, C. & Kustu, S. (1998). The bacterial enhancer-binding protein NtrC as a molecular machine. Cold Spring Harbor Symposium in Quantitative Biology 63, 157–166.CrossRefGoogle ScholarPubMed
Roque, A., Orrego, M., Ponte, I. & Suau, P. (2004). The preferential binding of histone H1 to DNA scaffold-associated regions is determined by its C-terminal domain. Nucleic Acids Research 32, 6111–6119.CrossRefGoogle ScholarPubMed
Ross, E. D., Keating, A. M. & Maher, L. J. 3rd (2000). DNA constraints on transcription activation in vitro. Journal of Molecular Biology 297, 321–334.CrossRefGoogle ScholarPubMed
Ross, W., Gosink, K. K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K. & Gourse, R. L. (1993). A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262, 1407–1413.CrossRefGoogle ScholarPubMed
Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302.CrossRefGoogle ScholarPubMed
Rozenberg, H., Rabinovich, D., Frolow, F., Hegde, R. S. & Shakked, Z. (1998). Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proceedings of the National Academy of Sciences USA 95, 15194–15199.CrossRefGoogle ScholarPubMed
Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag.CrossRefGoogle Scholar
Sanghani, S. R., Zakrzewska, K., Harvey, S. C. & Lavery, R. (1996). Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature. Nucleic Acids Research 24, 1632–1637.CrossRefGoogle ScholarPubMed
Sarai, A., Mazur, J., Nussinov, R. & Jernigan, R. L. (1989). Sequence dependence of DNA conformational flexibility. Biochemistry 28, 7842–7849.CrossRefGoogle ScholarPubMed
Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology 191, 659–675.CrossRefGoogle ScholarPubMed
Schleif, R. (1992). DNA looping. Annual Reviews in Biochemistry 61, 199–223.CrossRefGoogle ScholarPubMed
Schnitzler, G. R. (2008). Control of nucleosome positions by DNA sequence and remodeling machines. Cellular Biochemistry and Biophysics 51, 67–80.CrossRefGoogle ScholarPubMed
Schulz, A., Langowski, J. & Rippe, K. (2000). The effect of the DNA conformation on the rate of NtrC activated transcription of Escherichia coli RNA polymerase.sigma(54) holoenzyme. Journal of Molecular Biology 300, 709–725.CrossRefGoogle ScholarPubMed
Schurr, J. M., Fujimoto, B. S., Wu, P. & Song, L. (1992). Fluorescence studies of nucleic acids: dynamics, rigidities and structures. In Topics in Fluorescence Spectroscopy, vol. 3 (ed. Lakowicz, J. R.), pp. 137–229. New York: Plenum Press.CrossRefGoogle Scholar
Seela, F. & Grein, T. (1992). 7-Deaza-2′-deoxyadenosine and 3-deaza-2′-deoxyadenosine replacing dA within d(A6) -tracts: differential bending at 3′- and 5′-junctions of d(A6).d(T6) and B-DNA. Nucleic Acids Research 20, 2297–2306.CrossRefGoogle ScholarPubMed
Seeman, N. C. (2003). DNA in a material world. Nature 421, 427–431.CrossRefGoogle Scholar
Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, I. K., Wang, J. P. & Widom, J. (2006). A genomic code for nucleosome positioning. Nature 442, 772–778.CrossRefGoogle ScholarPubMed
Shatzky-Schwartz, M., Arbuckle, N. D., Eisenstein, M., Rabinovich, D., Bareket-Samish, A., Haran, T. E., Luisi, B. F. & Shakked, Z. (1997). X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. Journal of Molecular Biology 267, 595–623.CrossRefGoogle ScholarPubMed
Shimizu, M., Mori, T., Sakurai, T. & Shindo, H. (2000). Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA) small middle dotpoly(dT) tracts in vivo. EMBO Journal 19, 3358–3365.CrossRefGoogle ScholarPubMed
Shui, X., McFail-Isom, L., Hu, G. G. & Williams, L. D. (1998a). The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37, 8341–8355.CrossRefGoogle ScholarPubMed
Shui, X., Sines, C. C., McFail-Isom, L., Vanderveer, D. & Williams, L. D. (1998b). Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 37, 16877–16887.CrossRefGoogle ScholarPubMed
Sinden, R. S. (1994). DNA Structure and Function. San Diego, CA: Academic Press.Google Scholar
Snoussi, K. & Leroy, J. L. (2002). Alteration of A⋅T base-pair opening kinetics by the ammonium cation in DNA A-tracts. Biochemistry 41, 12467–12474.CrossRefGoogle ScholarPubMed
Soler-Lopez, M., Malinina, L., Liu, J., Huynh-Dinh, T. & Subirana, J. A. (1999). Water and ions in a high resolution structure of B-DNA. Journal of Biological Chemistry 274, 23683–23686.CrossRefGoogle Scholar
Song, J. S., Liu, X., Liu, X. S. & He, X. (2008). A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Research 18, 1064–1072.CrossRefGoogle ScholarPubMed
Sprous, D., Young, M. A. & Beveridge, D. L. (1999). Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature. Journal of Molecular Biology 285, 1623–1632.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 Research 23, 1816–1821.CrossRefGoogle ScholarPubMed
Stefl, R., Wu, H., Ravindranathan, S., Sklenar, V. & Feigon, J. (2004). DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum. Proceedings of the National Academy of Sciences USA 101, 1177–1182.CrossRefGoogle ScholarPubMed
Steitz, T. A. (1990). Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding. Quarterly Reviews of Biophysics 23, 205–280.CrossRefGoogle ScholarPubMed
Stellwagen, E., Lu, Y. & Stellwagen, N. C. (2005). Curved DNA molecules migrate anomalously slowly in free solution. Nucleic Acids Research 33, 4425–4432.CrossRefGoogle ScholarPubMed
Stellwagen, N. C. (2006). Curved DNA molecules migrate anomalously slowly in polyacrylamide gels even at zero gel concentration. Electrophoresis 27, 1163–1168.CrossRefGoogle ScholarPubMed
Stellwagen, N. C., Magnusdottir, S., Gelfi, C. & Righetti, P. G. (2001). Preferential counterion binding to A-tract DNA oligomers. Journal of Molecular Biology 305, 1025–1033.CrossRefGoogle ScholarPubMed
Stofer, E. & Lavery, R. (1994). Measuring the geometry of DNA grooves. Biopolymers 34, 337–346.CrossRefGoogle ScholarPubMed
Strahs, D. & Schlick, T. (2000). A-tract bending: insights into experimental structures by computational models. Journal of Molecular Biology 301, 643–663.CrossRefGoogle ScholarPubMed
Struhl, K. (1985). Naturally occurring poly(dA–dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proceedings of the National Academy of Sciences USA 82, 8419–8423.CrossRefGoogle ScholarPubMed
Sun, Z. M., Mulligan, C. & McLaughlin, L. W. (2006). Removal of a single minor-groove functional group eliminates A-tract curvature. Journal of the American Chemical Society 128, 11756–11757.Google Scholar
Suter, B., Schnappauf, G. & Thoma, F. (2000). Poly (dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Research 28, 4083–4089.CrossRefGoogle ScholarPubMed
Tchernaenko, V., Halvorson, H. R. & Lutter, L. C. (2004). Topological measurement of an A-tract bend angle: effect of magnesium. Journal of Molecular Biology 341, 55–63.CrossRefGoogle ScholarPubMed
Tereshko, V., Minasov, G. & Egli, M. (1999a). The Dickerson–Drew B-DNA dodecamer revisited at atomic resolution. Journal of the American Chemical Society 121, 470–471.CrossRefGoogle Scholar
Tereshko, V., Minasov, G. & Egli, M. (1999b). A ‘hydrate-ion’ spine in a B-DNA minor groove. Journal of the American Chemical Society 121, 3590–3595.CrossRefGoogle Scholar
Thompson, J. F. & Landy, A. (1988). Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Research 16, 9687–9705.CrossRefGoogle ScholarPubMed
Timasheff, S. N. (1993). The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annual Reviews of Biophysics and Biomolecular Structure 22, 67–97.CrossRefGoogle ScholarPubMed
Toth, K., Sauermann, V. & Langowski, J. (1998). DNA curvature in solution measured by fluorescence resonance energy transfer. Biochemistry 37, 8173–8179.CrossRefGoogle ScholarPubMed
Travers, A. A. (1989). DNA conformation and protein binding. Annual Reviews in Biochemistry 58, 427–452.CrossRefGoogle ScholarPubMed
Travers, A. A. (1995). DNA bending by sequence and proteins. In DNA–Protein: Structural Interactions (ed. Lilley, D. M. J.), pp. 49–75. Oxford: IRL Press.CrossRefGoogle Scholar
Travers, A. A. & Klug, A. (1990). Bending of DNA in nucleoprotein complexes. In DNA Topology and Its Biological Effects (eds. Cozzarelli, N. R. and Wang, J. C.), pp. 57–106. Cold Spring Harbor, NY: Cold Spring Harbor Press.Google Scholar
Tsen, H. & Levene, S. D. (1997). Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method. Proceedings of the National Academy of Sciences USA 94, 2817–2822.CrossRefGoogle ScholarPubMed
Ulanovsky, L., Bodner, M., Trifonov, E. N. & Choder, M. (1986). Curved DNA: design, synthesis, and circularization. Proceedings of the National Academy of Sciences USA 83, 862–866.CrossRefGoogle ScholarPubMed
Ulanovsky, L. E. & Trifonov, E. N. (1987). Estimation of wedge components in curved DNA. Nature 326, 720–722.CrossRefGoogle ScholarPubMed
Ussery, D. W., Hinton, J. C., Jordi, B. J., Granum, P. E., Seirafi, A., Stephen, R. J., Tupper, A. E., Berridge, G., Sidebotham, J. M. & Higgins, C. F. (1994). The chromatin-associated protein H-NS. Biochimie 76, 968–980.CrossRefGoogle ScholarPubMed
Vologodskii, A. & Cozzarelli, N. R. (1996). Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophysical Journal 70, 2548–2556.CrossRefGoogle ScholarPubMed
Vologodskii, A. V. & Cozzarelli, N. R. (1994). Conformational and thermodynamic properties of supercoiled DNA. Annual Reviews of Biophysics and Biomolecular Structure 23, 609–643.CrossRefGoogle ScholarPubMed
Warmlander, S., Sponer, J. E., Sponer, J. & Leijon, M. (2002). The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA. Journal of Biological Chemistry 277, 28491–28497.CrossRefGoogle Scholar
Whitehouse, I. & Tsukiyama, T. (2006). Antagonistic forces that position nucleosomes in vivo. Nature Structural & Molecular Biology 13, 633–640.CrossRefGoogle ScholarPubMed
Widlund, H. R., Cao, H., Simonsson, S., Magnusson, E., Simonsson, T., Nielsen, P. E., Kahn, J. D., Crothers, D. M. & Kubista, M. (1997). Identification and characterization of genomic nucleosome-positioning sequences. Journal of Molecular Biology 267, 807–817.CrossRefGoogle ScholarPubMed
Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature 287, 755–758.CrossRefGoogle ScholarPubMed
Wolffe, A. P. (1994). Nucleosome positioning and modification: chromatin structures that potentiate transcription. Trends in Biochemical Sciences 19, 240–244.CrossRefGoogle ScholarPubMed
Wu, H.-M. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509–513.CrossRefGoogle ScholarPubMed
Xu, Y. C. & Bremer, H. (1997). Winding of the DNA helix by divalent metal ions. Nucleic Acids Research 25, 4067–4071.CrossRefGoogle ScholarPubMed
Yasuno, K., Yamazaki, T., Tanaka, Y., Kodama, T. S., Matsugami, A., Katahira, M., Ishihama, A. & Kyogoku, Y. (2001). Interaction of the C-terminal domain of the E. coli RNA polymerase alpha subunit with the UP element: recognizing the backbone structure in the minor groove surface. Journal of Molecular Biology 306, 213–225.CrossRefGoogle Scholar
Yoon, C., Prive, G. G., Goodsell, D. S. & Dickerson, R. E. (1988). Structure of an alternating-B DNA helix and its relationship to A-tract DNA. Proceedings of the National Academy of Sciences USA 85, 6332–6336.CrossRefGoogle ScholarPubMed
Young, M. A. & Beveridge, D. L. (1998). Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. Journal of Molecular Biology 281, 675–687.CrossRefGoogle ScholarPubMed
Yuan, G. C. & Liu, J. S. (2008). Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology 4, e13.CrossRefGoogle ScholarPubMed
Yuan, G. C., Liu, Y. J., Dion, M. F., Slack, M. D., Wu, L. F., Altschuler, S. J. & Rando, O. J. (2005). Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626–630.CrossRefGoogle ScholarPubMed
Zhang, Y., XI, Z., Hegde, R. S., Shakked, Z. & Crothers, D. M. (2004). Predicting indirect readout effects in protein–DNA interactions. Proceedings of the National Academy of Sciences USA 101, 8337–8341.CrossRefGoogle ScholarPubMed
Zhao, K., Kas, E., Gonzalez, E. & Laemmli, U. K. (1993). SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO Journal 12, 3237–3247.CrossRefGoogle ScholarPubMed
Zhurkin, V. B., Ulyanov, N. B., Gorin, A. A. & Jernigan, R. L. (1991). Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proceedings of the National Academy of Sciences USA 88, 7046–7050.CrossRefGoogle ScholarPubMed
Zimmer, C. & Wähnert, U. (1986). Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Progress in Biophysics and Molecular Biology 47, 31–112.CrossRefGoogle ScholarPubMed
Zinkel, S. S. & Crothers, D. M. (1987). DNA bend direction by phase sensitive detection. Nature 328, 178–181.CrossRefGoogle ScholarPubMed
Zinkel, S. S. & Crothers, D. M. (1990). Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers 29, 29–38.CrossRefGoogle ScholarPubMed