Fluorescent nucleic acid base analogues

Quarterly Reviews of Biophysics

Volumn 43, Issue 2, 2010, Pages 159-183

  Wilhelmsson, L Marcus ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE; NUCLEIC ACID;

ARTICLE; CHEMISTRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; STAINING;

FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; HUMANS; NUCLEIC ACIDS; STAINING AND LABELING;

EID: 77957167393     PISSN: 00335835     EISSN: 14698994     Source Type: Journal    
DOI: 10.1017/S0033583510000090     Document Type: Article

References (142)

1. 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.
2. ALDAYE, F.A. & SLEIMAN, H. F. (2006). Sequential selfassembly of a DNA hexagon as a template for the organization of gold nanoparticles. Angewandte Chemie International Edition 45, 2204-2209.
3. ALLAN, B.W. & REICH, N. O. (1996). Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35, 14757-14762.
4. ASSELINE, U. (2006). Development and applications of fluorescent oligonucleotides. Current Organic Chemistry 10, 491-518.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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 2k-deoxycytidine for the study of oligonucleotides. Tetrahedron Letters 45, 2457-2461.
11. BLOOM, L. B., OTTO, M. R., BEECHEM, J.M. & GOODMAN, M. F. (1993). Influence of 5k-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Biochemistry 32, 11247-11258.
12. 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.
13. BÖRJESSON, K., SANDIN, P. & WILHELMSSON, L. M. (2009b). Nucleic acid structure and sequence probing using fluorescent base analogue tCO. Biophysical Chemistry 139, 24-28.
14. 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.
15. 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 3k polypurine tract. Nucleic Acids Research 32, 1539-1547.
16. 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.
17. 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. (Pubitemid 27525790)
18. 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.
19. 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.
20. 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.
21. FREESE, E. (1959). Specific mutagenic effect of base analogues on phage-T4. Journal of Molecular Biology 1, 87-105.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. GRECO, N. J. & TOR, Y. (2007). Furan decorated nucleoside analogues as fluorescent probes: synthesis, photophysical evaluation, and site-specific incorporation. Tetrahedron 63, 3515-3527.
29. GUEST, C. R., HOCHSTRASSER, R. A., SOWERS, L.C. & MILLAR, D. P. (1991). Dynamics of mismatched basepairs in DNA. Biochemistry 30, 3271-3279.
30. 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.
31. HAWKINS, M. E. (2001). Fluorescent pteridine nucleoside analogs - a window on DNA interactions. Cell Biochemistry and Biophysics 34, 257-281.
32. 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.
33. 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. (Pubitemid 27030531)
34. 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.
35. 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 3k-processing reaction. Nucleic Acids Research 23, 2872-2880.
36. 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.
37. HOLMÉN, A., NORDÉN, B. & ALBINSSON, B. (1997). Electronic transition moments of 2-aminopurine. Journal of the American Chemical Society 119, 3114-3121.
38. 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.
39. HUDSON, R. H. E.&GHORBANI-CHOGHAMARANI, A. (2007). Oligodeoxynucleotides incorporating structurally simple 5-alkynyl-2k- deoxyuridines fluorometrically respond to hybridization. Organic and Biomolecular Chemistry 5, 1845-1848.
40. 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.
41. 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.
42. 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.
43. 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 doublestranded nucleic acids. Proceedings of the National Academy of Sciences of the United States of America 105, 11176-11181.
44. 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.
45. 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.
46. KELLEY, S.O. & BARTON, J. K. (1999). Electron transfer between bases in double helical DNA. Science 283, 375-381.
47. 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.
48. 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.
49. 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.
50. LIN, K., JONES, R. J. &MATTEUCCI, M. D. (1995). Tricyclic 2k-deoxycytidine analogs - syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. Journal of the American Chemical Society 117, 3873-3874.
51. 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.
52. 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.
53. 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.
54. 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.
55. MATRAY, T. J. & KOOL, E. T. (1999). A specific partner for abasic damage in DNA. Nature 399, 704-708.
56. 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.
57. 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.
58. MILLAR, D. P. (1996). Fluorescence studies of DNA and RNA structure and dynamics. Current Opinion in Structural Biology 6, 322-326.
59. 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.
60. 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.
61. 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.
62. 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.
63. 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.
64. 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.
65. NAKAGAWA, O., ONO, S., LI, Z., TSUJIMOTO, A. & SASAKI, S. (2007). Specific fluorescent probe for 8-oxoguanosine. Angewandte Chemie International Edition 46, 4500-4503.
66. 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.
67. NORMAN, D. G., GRAINGER, R. J., UHRIN, D. & LILLEY, D. M. J. (2000). Location of cyanine-3 on doublestranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39, 6317-6324.
68. 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.
69. 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.
70. OKAMOTO, A., SAITO, Y. & SAITO, I. (2005). Design of base-discriminating fluorescent nucleosides. Journal of Photochemistry and Photobiology C: Photochemistry Reviews 6, 108-122.
71. 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.
72. OKAMOTO, A., TAINAKA, K. & SAITO, I. (2003b). Synthesis and properties of a novel fluorescent nucleobase, naphthopyridopyrimidine. Tetrahedron Letters 44, 6871-6874.
73. 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.
74. 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.
75. 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 sequencedependent. Organic Letters 9, 4503-4506.
76. 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.
77. PORTERFIELD, W. & TAHMASSEBI, D. C. (2009). Synthesis of a fluorescent 2(3k-dideoxycytosine analog, tCdd. Bioorganic and Medicinal Chemistry Letters 19, 111-113.
78. PREUS, S., BÖRJESSON, K., KILSA?, K., ALBINSSON, B. & WILHELMSSON, L. M. (2010). Characterization of nucleobase analogue FRET acceptor tCnitro. Journal of Physical Chemistry B 114, 1050-1056.
79. 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.
80. 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.
81. 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.
82. 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.
83. 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.
84. 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.
85. 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.
86. 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.
87. 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.
88. 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.
89. 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.
90. SANDIN, P., BÖRJESSON, K., LI, H., MA?RTENSSON, 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.
91. 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.
92. 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.
93. 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.
94. 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.
95. SCHNEIDER, K.C. & BENNER, S. A. (1990). Oligonucleotides containing flexible nucleoside analogs. Journal of the American Chemical Society 112, 453-455.
96. SECRIST, J. A., BARRIO, J.R. & LEONARD, N. J. (1972). Fluorescent modification of adenosine triphosphate with activity in enzyme systems: 1,N6-ethenoadenosine triphosphate. Science 175, 646-647.
97. 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.
98. 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.
99. SEELA, F., ZULAUF, M., SAUER, M. & DEIMEL, M. (2000). 7-substituted 7-deaza-2k-deoxyadenosines and 8-aza-7- deaza-2k-deoxyadenosines : fluorescence of DNA-base analogues induced by the 7-alkynyl side chain. Helvetica Chimica Acta 83, 910-927.
100. SEEMAN, N. C. (2003). DNA in a material world. Nature 421(6921), 427-431.
101. 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.
102. 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.
103. SINKELDAM, R. W., GRECO, N. J. & TOR, Y. (2008). Polarity of major grooves explored by using an isosteric emissive nucleoside. ChemBioChem 9, 706-709.
104. SOWERS, L. C., BOULARD, Y. & FAZAKERLEY, G. V. (2000). Multiple structures for the 2-aminopurine-cytosine mispair. Biochemistry 39, 7613-7620.
105. 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.
106. 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.
107. SRIVATSAN, S.G. & TOR, Y. (2007a). Fluorescent pyrimidine ribonucleotide: Synthesis, enzymatic incorporation, and utilization. Journal of the American Chemical Society 129, 2044-2053.
108. SRIVATSAN, S.G. & TOR, Y. (2007b). Using an emissive uridine analogue for assembling fluorescent HIV-1 TAR constructs. Tetrahedron 63, 3601-3607.
109. SRIVATSAN, S.G. & TOR, Y. (2009). Enzymatic incorporation of emissive pyrimidine ribonucleotides. Chemistry - An Asian Journal 4, 419-427.
110. 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.
111. 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.
112. 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.
113. 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.
114. 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.
115. 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.
116. 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.
117. 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.
118. STRÄSSLER, C., DAVIS, N. E. & KOOL, E. T. (1999). Novel nucleoside analogues with fluorophores replacing the DNA base. Helvetica Chimica Acta 82, 2160-2171.
119. 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.
120. 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.
121. SWITZER, C. Y., MORONEY, S.E. & BENNER, S. A. (1993). Enzymatic recognition of the base-pair between isocytidine and isoguanine. Biochemistry 32, 10489-10496.
122. 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.
123. 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.
124. 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.
125. 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.
126. VARGHESE, R.&WAGENKNECHT, H. A. (2009). White-lightemitting DNA (WED). Chemistry - A European Journal 15, 9307-9310.
127. 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.
128. 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.
129. 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.
130. 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.
131. WILSON, J.N. & KOOL, E. T. (2006). Fluorescent DNA base replacements: reporters and sensors for biological systems. Organic and Biomolecular Chemistry 4, 4265-4274.
132. 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.
133. 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.
134. 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.
135. WOO, J. S., MEYER, R. B. & GAMPER, H. B. (1996). G/Cmodified oligodeoxynucleotides with selective complementarity: synthesis and hybridization properties. Nucleic Acids Research 24, 2470-2475.
136. 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.
137. 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.
138. 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.
139. 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.
140. 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.
141. 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.
142. ZHANG, X. & WADKINS, R. M. (2009). DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies. Biophysical Journal 96, 1884-1891.