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Fluorescent nucleic acid base analogues

Published online by Cambridge University Press:  18 May 2010

L. Marcus Wilhelmsson
L. Marcus Wilhelmsson*
Affiliation:
Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296Gothenburg, Sweden
*
*Author for correspondence: L. M. Wilhelmsson, Chalmers University of Technology, Department of Chemical Engineering/Physical Chemistry, SE-412 96Gothenburg, Sweden. Tel.: +46 31 7723051; Fax: +46 31 7723858; Email: [email protected]
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Abstract

The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tCO–tCnitro, and its possible future uses are discussed.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 43 , Issue 2 , May 2010 , pp. 159 - 183
Copyright
Copyright © Cambridge University Press 2010

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References

Albert, A. & Taguchi, H. (1973). Ultraviolet spectral correlation between cation of an amino-n-heteroaromatic compound and neutral species of correpsonding oxo-analog. Journal of the Chemical Society, Perkin Transactions 2 8, 1101–1103.CrossRefGoogle Scholar
Aldaye, F. A. & Sleiman, H. F. (2006). Sequential self-assembly of a DNA hexagon as a template for the organization of gold nanoparticles. Angewandte Chemie International Edition 45, 2204–2209.CrossRefGoogle ScholarPubMed
Allan, B. W. & Reich, N. O. (1996). Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35, 14757–14762.CrossRefGoogle ScholarPubMed
Asseline, U. (2006). Development and applications of fluorescent oligonucleotides. Current Organic Chemistry 10, 491–518.CrossRefGoogle Scholar
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
Bag, S. S., Saito, Y., Hanawa, K., Kodate, S., Suzuka, I. & Saito, I. (2006). Intelligent fluorescent nucleoside in sensing cytosine base: importance of hydrophobic nature of perylene fluorophore. Bioorganic and Medicinal Chemistry Letters 16, 6338–6341.CrossRefGoogle ScholarPubMed
Barhate, N., Cekan, P., Massey, A. P. & Sigurdsson, S. T. (2007). A nucleoside that contains a rigid nitroxide spin label: a fluorophore in disguise. Angewandte Chemie International Edition 46, 2655–2658.CrossRefGoogle ScholarPubMed
Berger, M., Ogawa, A. K., Mcminn, D. L., Wu, Y. Q., Schultz, P. G. & Romesberg, F. E. (2000). Stable and selective hybridization of oligonucleotides with unnatural hydrophobic bases. Angewandte Chemie International Edition 39, 2940–2942.3.0.CO;2-#>CrossRefGoogle ScholarPubMed
Bergstrom, D. E., Inoue, H. & Reddy, P. A. (1982). Pyrido[2,3-D]pyrimidine nucleosides – synthesis via cyclization of C-5-substituted cytidines. Journal of Organic Chemistry 47, 2174–2178.CrossRefGoogle Scholar
Berry, D. A., Jung, K. Y., Wise, D. S., Sercel, A. D., Pearson, W. H., Mackie, H., Randolph, J. B. & Somers, R. L. (2004). Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides. Tetrahedron Letters 45, 2457–2461.CrossRefGoogle Scholar
Bloom, L. B., Otto, M. R., Beechem, J. M. & Goodman, M. F. (1993). Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Biochemistry 32, 11247–11258.CrossRefGoogle Scholar
Börjesson, K., Preus, S., El-Sagheer, A. H., Brown, T., Albinsson, B. & Wilhelmsson, L. M. (2009a). Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid containing systems. Journal of the American Chemical Society 131, 4288–4293.CrossRefGoogle ScholarPubMed
Börjesson, K., Sandin, P. & Wilhelmsson, L. M. (2009b). Nucleic acid structure and sequence probing using fluorescent base analogue tCO. Biophysical Chemistry 139, 24–28.CrossRefGoogle ScholarPubMed
Cekan, P. & Sigurdsson, S. T. (2008). Single base interrogation by a fluorescent nucleotide: each of the four DNA bases identified by fluorescence spectroscopy. Chemical Communications 29, 3393–3395.CrossRefGoogle Scholar
Dash, C., Rausch, J. W. & Le Grice, S. F. J. (2004). Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3′ polypurine tract. Nucleic Acids Research 32, 1539–1547.CrossRefGoogle ScholarPubMed
Dolghih, E., Roitberg, A. E. & Krause, J. L. (2007). Fluorescence resonance energy transfer in dye-labeled DNA. Journal of Photochemistry and Photobiology A: Chemistry 190, 321–327.CrossRefGoogle Scholar
Driscoll, S. L., Hawkins, M. E., Balis, F. M., Pfleiderer, W. & Laws, W. R. (1997). Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides. Biophysical Journal 73, 3277–3286.CrossRefGoogle ScholarPubMed
Dyrager, C., Börjesson, K., Diner, P., Elf, A., Albinsson, B., Wilhelmsson, L. M. & Grøtli, M. (2009). Synthesis and photophysical characterisation of fluorescent 8-(1H-1,2,3-Triazol-4-yl)adenosine derivatives. European Journal of Organic Chemistry 10, 1515–1521.CrossRefGoogle Scholar
Eldrup, A. B., Nielsen, B. B., Haaima, G., Rasmussen, H., Kastrup, J. S., Christensen, C. & Nielsen, P. E. (2001). 1,8-Naphthyridin-2(1H)-ones – novel bicyclic and tricyclic analogues of thymine in peptide nucleic acids (PNAs). European Journal of Organic Chemistry 9, 1781–1790.3.0.CO;2-K>CrossRefGoogle Scholar
Engman, K. C., Sandin, P., Osborne, S., Brown, T., Billeter, M., Lincoln, P., Nordén, B., Albinsson, B. & Wilhelmsson, L. M. (2004). DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization. Nucleic Acids Research 32, 5087–5095.CrossRefGoogle ScholarPubMed
Freese, E. (1959). Specific mutagenic effect of base analogues on phage-T4. Journal of Molecular Biology 1, 87–105.CrossRefGoogle Scholar
Gao, J. M., Strassler, C., Tahmassebi, D. & Kool, E. T. (2002). Libraries of composite polyfluors built from fluorescent deoxyribosides. Journal of the American Chemical Society 124, 11590–11591.CrossRefGoogle ScholarPubMed
Gilbert, S. D., Stoddard, C. D., Wise, S. J. & Batey, R. T. (2006). Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. Journal of Molecular Biology 359, 754–768.CrossRefGoogle Scholar
Godde, F., Toulme, J. J. & Moreau, S. (1998). Benzoquinazoline derivatives as substitutes for thymine in nucleic acid complexes. Use of fluorescence emission of benzo[g]quinazoline-2,4-(1H,3H)-dione in probing duplex and triplex formation. Biochemistry 37, 13765–13775.CrossRefGoogle Scholar
Godde, F., Toulme, J. J. & Moreau, S. (2000). 4-amino-1H-benzo[g]quinazoline-2-one: a fluorescent analog of cytosine to probe protonation sites in triplex forming oligonucleotides. Nucleic Acids Research 28, 2977–2985.CrossRefGoogle ScholarPubMed
Greco, N. J., Sinkeldam, R. W. & Tor, Y. (2009). An emissive C analog distinguishes between G, 8-oxoG, and T. Organic Letters 11, 1115–1118.CrossRefGoogle ScholarPubMed
Greco, N. J. & Tor, Y. (2005). Simple fluorescent pyrimidine analogues detect the presence of DNA abasic sites. Journal of the American Chemical Society 127, 10784–10785.CrossRefGoogle ScholarPubMed
Greco, N. J. & Tor, Y. (2007). Furan decorated nucleoside analogues as fluorescent probes: synthesis, photophysical evaluation, and site-specific incorporation. Tetrahedron 63, 3515–3527.CrossRefGoogle ScholarPubMed
Guest, C. R., Hochstrasser, R. A., Sowers, L. C. & Millar, D. P. (1991). Dynamics of mismatched base-pairs in DNA. Biochemistry 30, 3271–3279.CrossRefGoogle ScholarPubMed
Hardman, S. J. O. & Thompson, K. C. (2006). Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry 45, 9145–9155.CrossRefGoogle ScholarPubMed
Hawkins, M. E. (2001). Fluorescent pteridine nucleoside analogs – a window on DNA interactions. Cell Biochemistry and Biophysics 34, 257–281.CrossRefGoogle ScholarPubMed
Hawkins, M. E. & Balis, F. M. (2004). Use of pteridine nucleoside analogs as hybridization probes. Nucleic Acids Research 32, e62, doi:10.1093/nar/gnh060.CrossRefGoogle ScholarPubMed
Hawkins, M. E., Pfleiderer, W., Balis, F. M., Porter, D. & Knutson, J. R. (1997). Fluorescence properties of pteridine nucleoside analogs as monomers and incorporated into oligonucleotides. Analytical Biochemistry 244, 86–95.CrossRefGoogle ScholarPubMed
Hawkins, M. E., Pfleiderer, W., Jungmann, O. & Balis, F. M. (2001). Synthesis and fluorescence characterization of pteridine adenosine nucleoside analogs for DNA incorporation. Analytical Biochemistry 298, 231–240.CrossRefGoogle ScholarPubMed
Hawkins, M. E., Pfleiderer, W., Mazumder, A., Pommier, Y. G. & Falls, F. M. (1995). Incorporation of a fluorescent guanosine analog into oligonucleotides and its application to a real-time assay for the Hiv-1 integrase 3′-processing reaction. Nucleic Acids Research 23, 2872–2880.CrossRefGoogle ScholarPubMed
Hochstrasser, R. A., Carver, T. E., Sowers, L. C. & Millar, D. P. (1994). Melting of a DNA helix terminus within the active-site of a DNA-polymerase. Biochemistry 33, 11971–11979.CrossRefGoogle ScholarPubMed
Holmén, A., Nordén, B. & Albinsson, B. (1997). Electronic transition moments of 2-aminopurine. Journal of the American Chemical Society 119, 3114–3121.CrossRefGoogle Scholar
Hu, J., Dodd, D. W., Hudson, R. H. E. & Corey, D. R. (2009). Cellular localization and allele-selective inhibition of mutant huntingtin protein by peptide nucleic acid oligomers containing the fluorescent nucleobase [bis-o-(aminoethoxy)phenyl]pyrrolocytosine. Bioorganic and Medicinal Chemistry Letters 19, 6181–6184.CrossRefGoogle ScholarPubMed
Hudson, R. H. E. & Ghorbani-Choghamarani, A. (2007). Oligodeoxynucleotides incorporating structurally simple 5-alkynyl-2′-deoxyuridines fluorometrically respond to hybridization. Organic and Biomolecular Chemistry 5, 1845–1848.CrossRefGoogle ScholarPubMed
Hudson, R. H. E., Viirre, R. D., Liu, Y. H., Wojciechowski, F. & Dambenieks, A. K. (2003). Chemistry for the synthesis of nucleobase-modified peptide nucleic acid. In 39th IUPAC Congress/86th Conference of the Canadian Society for Chemistry, Ottawa, Canada, p. 1591–1598.Google Scholar
Hurley, D. J. & Tor, Y. (2002). Donor/acceptor interactions in systematically modified Ru-II-Os-II oligonucleotides. Journal of the American Chemical Society 124, 13231–13241.CrossRefGoogle ScholarPubMed
Inoue, H., Imura, A. & Ohtsuka, E. (1987). Synthesis of dodecadeoxyribonucleotides containing pyrrolo[2,3-d]pyrimidine nucleoside and their base-pairing ability. Nippon Kagaku Kaishi 7, 1214–1220.CrossRefGoogle Scholar
Iqbal, A., Arslan, S., Okumus, B., Wilson, T. J., Giraud, G., Norman, D. G., Ha, T. & Lilley, D. M. J. (2008a). Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. Proceedings of the National Academy of Sciences of the United States of America 105, 11176–11181.CrossRefGoogle ScholarPubMed
Iqbal, A., Wang, L., Thompson, K. C., Lilley, D. M. J. & Norman, D. G. (2008b). The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies. Biochemistry 47, 7857–7862.CrossRefGoogle ScholarPubMed
Joyce, C. M., Potapova, O., Delucia, A. M., Huang, X. W., Basu, V. P. & Grindley, N. D. F. (2008). Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry 47, 6103–6116.CrossRefGoogle ScholarPubMed
Kelley, S. O. & Barton, J. K. (1999). Electron transfer between bases in double helical DNA. Science 283, 375–381.CrossRefGoogle ScholarPubMed
Laland, S. G. & Serckhanssen, G. (1964). Synthesis of pyrimidin-2-1 deoxyribosides and their ability to support growth of deoxyriboside-requiring organism lactobacillus acidophilus R26. Biochemical Journal 90, 76–81.CrossRefGoogle Scholar
Lemay, J. F., Penedo, J. C., Tremblay, R., Lilley, D. M. J. & Lafontaine, D. A. (2006). Folding of the adenine riboswitch. Chemistry & Biology 13, 857–868.CrossRefGoogle ScholarPubMed
Lewis, F. D., Zhang, L. G. & Zuo, X. B. (2005). Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold. Journal of the American Chemical Society 127, 10002–10003.CrossRefGoogle Scholar
Lin, K., Jones, R. J. & Matteucci, M. D. (1995). Tricyclic 2′-deoxycytidine analogs – syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. Journal of the American Chemical Society 117, 3873–3874.CrossRefGoogle Scholar
Lin, K. Y. & Matteucci, M. D. (1998). A cytosine analogue capable of clamp-like binding to a guanine in helical nucleic acids. Journal of the American Chemical Society 120, 8531–8532.CrossRefGoogle Scholar
Liu, C. H. & Martin, C. T. (2001). Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase. Journal of Molecular Biology 308, 465–475.CrossRefGoogle ScholarPubMed
Lycksell, P. O., Gräslund, A., Claesens, F., Mclaughlin, L. W., Larsson, U. & Rigler, R. (1987). Base pair opening dynamics of a 2-aminopurine substituted EcoRI restriction sequence and its unsubstituted counterpart in oligonucleotides. Nucleic Acids Research 15, 9011–9025.CrossRefGoogle ScholarPubMed
Marti, A. A., Jockusch, S., Li, Z. M., Ju, J. Y. & Turro, N. J. (2006). Molecular beacons with intrinsically fluorescent nucleotides. Nucleic Acids Research 34, e50.CrossRefGoogle ScholarPubMed
Matray, T. J. & Kool, E. T. (1999). A specific partner for abasic damage in DNA. Nature 399, 704–708.CrossRefGoogle ScholarPubMed
Matsuda, S. & Romesberg, F. E. (2004). Optimization of interstrand hydrophobic packing interactions within unnatural DNA base pairs. Journal of the American Chemical Society 126 14419–14427.CrossRefGoogle ScholarPubMed
Mayer, E., Valis, L., Wagner, C., Rist, M., Amann, N. & Wagenknecht, H. A. (2004). 1-ethynylpyrene as a tunable and versatile molecular beacon for DNA. ChemBioChem 5, 865–868.CrossRefGoogle ScholarPubMed
Millar, D. P. (1996). Fluorescence studies of DNA and RNA structure and dynamics. Current Opinion in Structural Biology 6, 322–326.CrossRefGoogle ScholarPubMed
Miyata, K., Mineo, R., Tamamushi, R., Mizuta, M., Ohkubo, A., Taguchi, H., Seio, K., Santa, T. & Sekine, M. (2007). Synthesis and fluorescent properties of bi- and tricyclic 4-N-carbamoyldeoxycytidine derivatives. Journal of Organic Chemistry 72, 102–108.CrossRefGoogle ScholarPubMed
Miyata, K., Tamamushi, R., Ohkubo, A., Taguchi, H., Seio, K., Santa, T. & Sekine, M. (2006). Synthesis and properties of a new fluorescent bicyclic 4-N-carbamoyldeoxycytidine derivative. Organic Letters 8, 1545–1548.CrossRefGoogle ScholarPubMed
Mizuta, M., Banba, J. I., Kanamori, T., Tawarada, R., Ohkubo, A., Sekine, M. & Seio, K. (2008). New nucleotide pairs for stable DNA triplexes stabilized by stacking interaction. Journal of the American Chemical Society 130, 9622–9623.CrossRefGoogle ScholarPubMed
Mizuta, M., Seio, K., Miyata, K. & Sekine, M. (2007). Fluorescent pyrimidopyrimidoindole nucleosides: Control of photophysical characterizations by substituent effects. Journal of Organic Chemistry 72, 5046–5055.CrossRefGoogle ScholarPubMed
Mizuta, M., Seio, K., Ohkubo, A. & Sekine, M. (2009). Fluorescence properties of pyrimidopyrimidoindole nucleoside dC(PPI) incorporated into oligodeoxynucleotides. Journal of Physical Chemistry B 113, 9562–9569.CrossRefGoogle ScholarPubMed
Moser, A. M., Patel, M., Yoo, H., Balis, F. M. & Hawkins, M. E. (2000). Real-time fluorescence assay for O-6-alkylguanine-DNA alkyltransferase. Analytical Biochemistry 281, 216–222.CrossRefGoogle Scholar
Nakagawa, O., Ono, S., Li, Z., Tsujimoto, A. & Sasaki, S. (2007). Specific fluorescent probe for 8-oxoguanosine. Angewandte Chemie International Edition 46, 4500–4503.CrossRefGoogle ScholarPubMed
Nordlund, T. M., Andersson, S., Nilsson, L., Rigler, R., Gräslund, A. & Mclaughlin, L. W. (1989). Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry 28, 9095–9103.CrossRefGoogle ScholarPubMed
Norman, D. G., Grainger, R. J., Uhrin, D. & Lilley, D. M. J. (2000). Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39, 6317–6324.CrossRefGoogle ScholarPubMed
Ogawa, A. K., Wu, Y. Q., Berger, M., Schultz, P. G. & Romesberg, F. E. (2000a). Rational design of an unnatural base pair with increased kinetic selectivity. Journal of the American Chemical Society 122, 8803–8804.CrossRefGoogle Scholar
Ogawa, A. K., Wu, Y. Q., Mcminn, D. L., Liu, J. Q., Schultz, P. G. & Romesberg, F. E. (2000b). Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs. Journal of the American Chemical Society 122, 3274–3287.CrossRefGoogle Scholar
Okamoto, A., Saito, Y. & Saito, I. (2005). Design of base-discriminating fluorescent nucleosides. Journal of Photochemistry and Photobiology C: Photochemistry Reviews 6, 108–122.CrossRefGoogle Scholar
Okamoto, A., Tainaka, K. & Saito, I. (2003a). Clear distinction of purine bases on the complementary strand by a fluorescence change of a novel fluorescent nucleoside. Journal of the American Chemical Society 125, 4972–4973.CrossRefGoogle ScholarPubMed
Okamoto, A., Tainaka, K. & Saito, I. (2003b). Synthesis and properties of a novel fluorescent nucleobase, naphthopyridopyrimidine. Tetrahedron Letters 44, 6871–6874.CrossRefGoogle Scholar
Okamoto, A., Tanaka, K., Fukuta, T. & Saito, I. (2003c). Design of base-discriminating fluorescent nucleoside and its application to T/C SNP typing. Journal of the American Chemical Society 125, 9296–9297.CrossRefGoogle Scholar
Okamoto, A., Tanaka, K., Fukuta, T. & Saito, I. (2004). Cytosine detection by a fluorescein-labeled probe containing base-discriminating fluorescent nucleobase. ChemBioChem 5, 958–963.CrossRefGoogle ScholarPubMed
Ortega, J. A., Blas, J. R., Orozco, M., Grandas, A., Pedroso, E. & Robles, J. (2007). Binding affinities of oligonucleotides and PNAs containing phenoxazine and g-clamp cytosine analogues are unusually sequence-dependent. Organic Letters 9, 4503–4506.CrossRefGoogle ScholarPubMed
Piccirilli, J. A., Krauch, T., Moroney, S. E. & Benner, S. A. (1990). Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343, 33–37.CrossRefGoogle ScholarPubMed
Porterfield, W. & Tahmassebi, D. C. (2009). Synthesis of a fluorescent 2(3′-dideoxycytosine analog, tCdd. Bioorganic and Medicinal Chemistry Letters 19, 111–113.CrossRefGoogle Scholar
Preus, S., Börjesson, K., Kilså, K., Albinsson, B. & Wilhelmsson, L. M. (2010). Characterization of nucleobase analogue FRET acceptor tCnitro. Journal of Physical Chemistry B 114, 1050–1056.CrossRefGoogle ScholarPubMed
Rachofsky, E. L., Osman, R. & Ross, J. B. A. (2001). Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. Biochemistry 40, 946–956.CrossRefGoogle Scholar
Rajeev, K. G., Maier, M. A., Lesnik, E. A. & Manoharan, M. (2001). High-affinity peptide nucleic acid oligomers containing tricyclic cytosine analogues. In 222nd National Meeting of the American Chemical Society, Chicago, Illinois, p. 4395–4398.Google Scholar
Ranasinghe, R. T., Rusling, D. A., Powers, V. E. C., Fox, K. R. & Brown, T. (2005). Recognition of CG inversions in DNA triple helices by methylated 3H-pyrrolo[2,3-d] pyrimidin-2(7H)-one nucleoside analogues. Chemical Communications 20, 2555–2557.CrossRefGoogle Scholar
Ren, R. X. F., Chaudhuri, N. C., Paris, P. L., Rumney, S. & Kool, E. T. (1996). Naphthalene, phenanthrene, and pyrene as DNA base analogues: Synthesis, structure, and fluorescence in DNA. Journal of the American Chemical Society 118, 7671–7678.CrossRefGoogle ScholarPubMed
Rist, M. J. & Marino, J. P. (2002). Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Current Organic Chemistry 6, 775–793.CrossRefGoogle Scholar
Roca, A. I. & Singleton, S. F. (2003). Direct evaluation of a mechanism for activation of the RecA nucleoprotein filament. Journal of the American Chemical Society 125, 15366–15375.CrossRefGoogle ScholarPubMed
Saito, Y., Bag, S. S., Kusakabe, Y., Nagai, C., Matsumoto, K., Mizuno, E., Kodate, S., Suzuka, I. & Saito, I. (2007). Dual-labeled oligonucleotide probe for sensing adenosine via FRET: A novel alternative to SNPs genotyping. Chemical Communications 21, 2133–2135.CrossRefGoogle Scholar
Saito, Y., Hanawa, K., Kawasaki, N., Bag, S. S. & Saito, I. (2006). Acridone-labeled base-discriminating fluorescence (BDF) nucleoside: Synthesis and their photophysical properties. Chemistry Letters 35, 1182–1183.CrossRefGoogle Scholar
Saito, Y., Hanawa, K., Motegi, K., Omoto, K., Okamoto, A. & Saito, I. (2005). Synthesis and properties of purine-type base-discriminating fluorescent (BDF) nucleosides: distinction of thymine by fluorescence-labeled deoxyadenosine derivatives. Tetrahedron Letters 46, 7605–7608.CrossRefGoogle Scholar
Saito, Y., Motegi, K., Bag, S. S. & Saito, I. (2008). Anthracene based base-discriminating fluorescent oligonucleotide probes for SNPs typing: Synthesis and photophysical properties. Bioorganic and Medicinal Chemistry 16, 107–113.CrossRefGoogle ScholarPubMed
Sanabia, J. E., Goldner, L. S., Lacaze, P. A. & Hawkins, M. E. (2004). On the feasibility of single-molecule detection of the guanosine-analogue 3-MI. Journal of Physical Chemistry B 108, 15293–15300.CrossRefGoogle Scholar
Sandin, P., Börjesson, K., Li, H., Mårtensson, J., Brown, T., Wilhelmsson, L. M. & Albinsson, B. (2008). Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue. Nucleic Acids Research 36, 157–167.CrossRefGoogle Scholar
Sandin, P., Lincoln, P., Brown, T. & Wilhelmsson, L. M. (2007). Synthesis and oligonucleotide incorporation of fluorescent cytosine analogue tC: a promising nucleic acid probe. Nature Protocols 2, 615–623.CrossRefGoogle Scholar
Sandin, P., Stengel, G., Ljungdahl, T., Börjesson, K., Macao, B. & Wilhelmsson, L. M. (2009a). Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment. Nucleic Acids Research 37, 3924–3933.CrossRefGoogle ScholarPubMed
Sandin, P., Tumpane, J., Börjesson, K., Wilhelmsson, L. M., Brown, T., Nordén, B., Albinsson, B. & Lincoln, P. (2009b). Thermodynamic aspects of DNA nanoconstruct stability and design. Journal of Physical Chemistry C 113, 5941–5946.CrossRefGoogle Scholar
Sandin, P., Wilhelmsson, L. M., Lincoln, P., Powers, V. E. C., Brown, T. & Albinsson, B. (2005). Fluorescent properties of DNA base analogue tC upon incorporation into DNA – negligible influence of neighbouring bases on fluorescence quantum yield. Nucleic Acids Research 33, 5019–5025.CrossRefGoogle ScholarPubMed
Schneider, K. C. & Benner, S. A. (1990). Oligonucleotides containing flexible nucleoside analogs. Journal of the American Chemical Society 112, 453–455.CrossRefGoogle Scholar
Secrist, J. A., Barrio, J. R. & Leonard, N. J. (1972). Fluorescent modification of adenosine triphosphate with activity in enzyme systems: 1,N 6-ethenoadenosine triphosphate. Science 175, 646–647.CrossRefGoogle Scholar
Seela, F. & Sirivolu, V. R. (2008). Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azide-alkyne “click” reaction. Organic and Biomolecular Chemistry 6, 1674–1687.Google Scholar
Seela, F. & Zulauf, M. (1998). 7-deazaadenine-DNA: Bulky 7-iodo substituents or hydrophobic 7-hexynyl chains are well accommodated in the major groove of oligonucleotide duplexes. Chemistry – A European Journal 4, 1781–1790.3.0.CO;2-K>CrossRefGoogle Scholar
Seela, F., Zulauf, M., Sauer, M. & Deimel, M. (2000). 7-substituted 7-deaza-2′-deoxyadenosines and 8-aza-7-deaza-2′-deoxyadenosines: fluorescence of DNA-base analogues induced by the 7-alkynyl side chain. Helvetica Chimica Acta 83, 910–927.3.0.CO;2-4>CrossRefGoogle Scholar
Seeman, N. C. (2003). DNA in a material world. Nature 421(6921), 427–431.CrossRefGoogle Scholar
Singleton, S. F., Roca, A. I., Lee, A. M. & Xiao, J. (2007). Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog. Tetrahedron 63, 3553–3566.CrossRefGoogle ScholarPubMed
Singleton, S. F., Shan, F., Kanan, M. W., Mcintosh, C. M., Stearman, C. J., Helm, J. S. & Webb, K. J. (2001). Facile synthesis of a fluorescent deoxycytidine analogue suitable for probing the RecA nucleoprotein filament. Organic Letters 3, 3919–3922.CrossRefGoogle ScholarPubMed
Sinkeldam, R. W., Greco, N. J. & Tor, Y. (2008). Polarity of major grooves explored by using an isosteric emissive nucleoside. ChemBioChem 9, 706–709.CrossRefGoogle ScholarPubMed
Sowers, L. C., Boulard, Y. & Fazakerley, G. V. (2000). Multiple structures for the 2-aminopurine-cytosine mispair. Biochemistry 39, 7613–7620.CrossRefGoogle ScholarPubMed
Sowers, L. C., Fazakerley, G. V., Eritja, R., Kaplan, B. E. & Goodman, M. F. (1986). Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proceedings of the National Academy of Sciences of the United States of America 83, 5434–5438.CrossRefGoogle Scholar
Srivatsan, S. G., Greco, N. J. & Tor, Y. (2008a). A highly emissive fluorescent nucleoside that signals the activity of toxic ribosome-inactivating proteins. Angewandte Chemie International Edition 47, 6661–6665.CrossRefGoogle ScholarPubMed
Srivatsan, S. G. & Tor, Y. (2007a). Fluorescent pyrimidine ribonucleotide: Synthesis, enzymatic incorporation, and utilization. Journal of the American Chemical Society 129, 2044–2053.CrossRefGoogle ScholarPubMed
Srivatsan, S. G. & Tor, Y. (2007b). Using an emissive uridine analogue for assembling fluorescent HIV-1 TAR constructs. Tetrahedron 63, 3601–3607.CrossRefGoogle ScholarPubMed
Srivatsan, S. G. & Tor, Y. (2009). Enzymatic incorporation of emissive pyrimidine ribonucleotides. Chemistry – An Asian Journal 4, 419–427.CrossRefGoogle ScholarPubMed
Srivatsan, S. G., Weizman, H. & Tor, Y. (2008b). A highly fluorescent nucleoside analog based on thieno[3,4-d] pyrimidine senses mismatched pairing. Organic and Biomolecular Chemistry 6, 1334–1338.CrossRefGoogle ScholarPubMed
Stanley, R. J., Hou, Z. J., Yang, A. P. & Hawkins, M. E. (2005). The two-photon excitation cross section of 6MAP, a fluorescent adenine analogue. Journal of Physical Chemistry B 109, 3690–3695.CrossRefGoogle ScholarPubMed
Stengel, G., Gill, J. P., Sandin, P., Wilhelmsson, L. M., Albinsson, B., Nordén, B. & Millar, D. P. (2007). Conformational dynamics of DNA polymerase probed with a novel fluorescent DNA base analog. Biochemistry 46, 12289–12297.Google Scholar
Stengel, G., Purse, B. W., Wilhelmsson, L. M., Urban, M. & Kuchta, R. D. (2009a). Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment. Biochemistry 48, 7547–7555.CrossRefGoogle ScholarPubMed
Stengel, G., Urban, M., Purse, B. W. & Kuchta, R. D. (2009b). High density labeling of polymerase chain reaction products with the fluorescent base analogue tCo. Analytical Chemistry 81, 9079–9085.CrossRefGoogle ScholarPubMed
Stengel, G., Urban, M., Purse, B. W. & Kuchta, R. D. (2010). Incorporation of the fluorescent ribonucleotide analogue tCTP by T7 RNA polymerase. Analytical Chemistry 82, 1082–1089.CrossRefGoogle ScholarPubMed
Stivers, J. T. (1998). 2-aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Research 26, 3837–3844.CrossRefGoogle ScholarPubMed
Stivers, J. T., Pankiewicz, K. W. & Watanabe, K. A. (1999). Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry 38, 952–963.CrossRefGoogle ScholarPubMed
Strässler, C., Davis, N. E. & Kool, E. T. (1999). Novel nucleoside analogues with fluorophores replacing the DNA base. Helvetica Chimica Acta 82, 2160–2171.3.0.CO;2-4>CrossRefGoogle ScholarPubMed
Svanvik, N., Westman, G., Wang, D. Y. & Kubista, M. (2000). Light-up probes: Thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution. Analytical Biochemistry 281, 26–35.CrossRefGoogle ScholarPubMed
Switzer, C., Moroney, S. E. & Benner, S. A. (1989). Enzymatic incorporation of a new base pair into DNA and RNA. Journal of the American Chemical Society 111, 8322–8323.CrossRefGoogle Scholar
Switzer, C. Y., Moroney, S. E. & Benner, S. A. (1993). Enzymatic recognition of the base-pair between isocytidine and isoguanine. Biochemistry 32, 10489–10496.CrossRefGoogle Scholar
Tainaka, K., Tanaka, K., Ikeda, S., Nishiza, K., Unzai, T., Fujiwara, Y., Saito, I. & Okamoto, A. (2007). PRODAN-conjugated DNA: synthesis and photochemical properties. Journal of the American Chemical Society 129, 4776–4784.CrossRefGoogle ScholarPubMed
Tinsley, R. A. & Walter, N. G. (2006). Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA – A Publication of the RNA Society 12, 522–529.CrossRefGoogle ScholarPubMed
Tor, Y., Del Valle, S., Jaramillo, D., Srivatsan, S. G., Rios, A. & Weizman, H. (2007). Designing new isomorphic fluorescent nucleobase analogues: the thieno[3,2-d]pyrimidine core. Tetrahedron 63, 3608–3614.CrossRefGoogle Scholar
Tumpane, J., Kumar, R., Lundberg, E. P., Sandin, P., Gale, N., Nandhakumar, I. S., Albinsson, B., Lincoln, P., Wilhelmsson, L. M., Brown, T. & Nordén, B. (2007). Triplex addressability as a basis for functional DNA nanostructures. Nano Letters 7, 3832–3839.CrossRefGoogle ScholarPubMed
Varghese, R. & Wagenknecht, H. A. (2009). White-light-emitting DNA (WED). Chemistry – A European Journal 15, 9307–9310.CrossRefGoogle ScholarPubMed
Urban, M., Joubert, N., Purse, B. W., Hocek, M. & Kuchta, R. D. (2010). Mechanisms by which human DNA primase chooses to polymerize a nucleoside triphosphate. Biochemistry 49, 727–735.CrossRefGoogle ScholarPubMed
Ward, D. C., Reich, E. & Stryer, L. (1969). Fluorescence studies of nucleotides and polynucleotides I. Formycin 2-aminopurine riboside 2,6-diaminopurine riboside and their derivatives. Journal of Biological Chemistry 244, 1228–1237.CrossRefGoogle Scholar
Wilhelmsson, L. M., Holmén, A., Lincoln, P., Nielsen, P. E. & Nordén, B. (2001). A highly fluorescent DNA base analogue that forms Watson–Crick base pairs with guanine. Journal of the American Chemical Society 123, 2434–2435.CrossRefGoogle ScholarPubMed
Wilhelmsson, L. M., Sandin, P., Holmén, A., Albinsson, B., Lincoln, P. & Nordén, B. (2003). Photophysical characterization of fluorescent DNA base analogue, tC. Journal of Physical Chemistry B 107, 9094–9101.CrossRefGoogle Scholar
Wilson, J. N. & Kool, E. T. (2006). Fluorescent DNA base replacements: reporters and sensors for biological systems. Organic and Biomolecular Chemistry 4, 4265–4274.CrossRefGoogle ScholarPubMed
Wojciechowski, F. & Hudson, R. H. E. (2008). Fluorescence and hybridization properties of peptide nucleic acid containing a substituted phenylpyrrolocytosine designed to engage guanine with an additional H-bond. Journal of the American Chemical Society 130, 12574–12575.CrossRefGoogle ScholarPubMed
Wojciechowski, F. & Hudson, R. H. E. (2009). Peptide nucleic acid containing a meta-substituted phenylpyrrolocytosine exhibits a fluorescence response and increased binding affinity toward RNA. Organic Letters 11, 4878–4881.CrossRefGoogle ScholarPubMed
Wojtuszewski, K., Hawkins, M. E., Cole, J. L. & Mukerji, I. (2001). HU binding to DNA: Evidence for multiple complex formation and DNA bending. Biochemistry 40, 2588–2598.CrossRefGoogle Scholar
Woo, J. S., Meyer, R. B. & Gamper, H. B. (1996). G/C-modified oligodeoxynucleotides with selective complementarity: synthesis and hybridization properties. Nucleic Acids Research 24, 2470–2475.CrossRefGoogle ScholarPubMed
Wu, P. G., Nordlund, T. M., Gildea, B. & Mclaughlin, L. W. (1990). Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base. Biochemistry 29, 6508–6514.CrossRefGoogle ScholarPubMed
Xiao, J., Lee, A. M. & Singleton, S. F. (2006). Construction and evaluation of a kinetic scheme for RecA-mediated DNA strand exchange. Biopolymers 81, 473–496.CrossRefGoogle ScholarPubMed
Xie, Y., Dix, A. V. & Tor, Y. (2009). FRET enabled real time detection of RNA-small molecule binding. Journal of the American Chemical Society 131, 17605–17614.CrossRefGoogle ScholarPubMed
Yang, K. S., Matsika, S. & Stanley, R. J. (2007). 6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase. Journal of Physical Chemistry B 111, 10615–10625.CrossRefGoogle ScholarPubMed
Yang, K. S. & Stanley, R. J. (2008). The extent of DNA deformation in DNA photolyase-substrate complexes: A solution state fluorescence study. Photochemistry and Photobiology 84, 741–749.Google Scholar
Zang, Z., Fang, Q. M., Pegg, A. E. & Guengerich, F. P. (2005). Kinetic analysis of steps in the repair of damaged DNA by human O-6-alkylguanine-DNA alkyltransferase. Journal of Biological Chemistry 280 30873–30881.CrossRefGoogle Scholar
Zhang, X. & Wadkins, R. M. (2009). DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies. Biophysical Journal 96, 1884–1891.CrossRefGoogle ScholarPubMed