2-aminopurine as a fluorescent probe of DNA conformation and the DNA-enzyme interface

Quarterly Reviews of Biophysics

Volumn 48, Issue 2, 2015, Pages 244-279

  Jones, Anita C ^a   Neely, Robert K ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINOPURINE; DNA; ENZYME; FLUORESCENT DYE;

CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; SPECTROFLUOROMETRY;

2-AMINOPURINE; BASE SEQUENCE; DNA; ENZYMES; FLUORESCENT DYES; NUCLEIC ACID CONFORMATION; SPECTROMETRY, FLUORESCENCE;

EID: 84929272295     PISSN: 00335835     EISSN: 14698994     Source Type: Journal    
DOI: 10.1017/S0033583514000158     Document Type: Article

References (112)

1. ALEMAN, E. A., DE SILVA, C., PATRICK, E. M., MUSIER-FORSYTH, K., RUEDA, D. (2014). Single-molecule fluorescence using nucleotide analogs: a Proof-of-Principle. Journal of Physics Chemistry Letters 5, 777-781.
2. ALLAN, B.W., REICH, N. O. (1996). Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35, 14757-14762.
3. AVILOV, S. V., GODET, J., PIEMONT, E., MELY, Y. (2009). Site-specific characterization of HIV-1 nucleocapsid protein binding to oligonucleotides with two binding sites. Biochemistry 48, 2422-2430.
4. AVILOV, S. V., PIEMONT, E., SHVADCHAK, V., DE ROCQUIGNY, H., MELY, Y. (2008). Probing dynamics of HIV-1 nucleocapsid protein/target hexanucleotide complexes by 2-aminopurine. Nucleic Acids Research 36, 885-896.
5. BECKER, W. (2005). Advanced Time-Correlated Single Photon Counting. Springer.
6. BEECHEM, J., GRATTON, E., AMELOOT, M., KNUTSON, J., BRAND, L. (2002). The global analysis of fluorescence intensity and anisotropy decay data: second-generation theory and programs. In Topics in Fluorescence Spectroscopy, vol. 2 (ed. J. LAKOWICZ), pp. 241-305. US: Springer.
7. BEN GAIED, N., GLASSER, N., RAMALANJAONA, N., BELTZ, H., WOLFF, P., MARQUET, R., BURGER, A., MELY, Y. (2005). 8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2?-deoxyribosyl-2-aminopurine with improved properties. Nucleic Acids Research 33, 1031-1039.
8. BOCHTLER, M., SZCZEPANOWSKI, R. H., TAMULAITIS, G., GRAZULIS, S., CZAPINSKA, H., MANAKOVA, E., SIKSNYS, V. (2006). Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO Journal 25, 2219-2229.
9. BONNIST, E.Y., JONES, A. C. (2008). Long-wavelength fluorescence from 2-aminopurine-nucleobase dimers in DNA. Chemphyschem 9, 1121-1129.
10. BONNIST, E. Y.M. (2008). Ph.D. thesis, University of Edinburgh.
11. BONNIST, E. Y. M., LIEBERT, K., DRYDEN, D.T.F., JELTSCH, A., JONES, A. C. (2012). Using the fluorescence decay of 2-aminopurine to investigate conformational change in the recognition sequence of the EcoRV DNA-(adenine-N6)-methyltransferase on enzyme binding. Biophysical Chemistry 160, 28-34.
12. BUSCAGLIA, R., JAMESON, D.M., CHAIRES, J. B. (2012). G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots. Nucleic Acids Research 40, 4203-4215.
13. CAMPBELL, C. J., MOUNTFORD, C. P., STOQUERT, H. C., BUCK, A. H., DICKINSON, P., FERAPONTOVA, E., TERRY, J. G., BEATTIE, J. S., WALTON, A. J., CRAIN, J., GHAZAL, P., MOUNT, A. R. (2009). A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets. Analyst 134, 1873-1879.
14. DALLMANN, A., DEHMEL, L., PETERS, T., MÜGGE, C., GRIESINGER, C., TUMA, J., ERNSTING, N. P. (2010). 2-aminopurine incorporation perturbs the dynamics and structure of DNA. Angewandte Chemie International Edition in English 49, 5989-5992.
15. ENGMAN, K. C., SANDIN, P., OSBORNE, S., BROWN, T., BILLETER, M., LINCOLN, P., NORDEN, B., ALBINSSON, B., WILHELMSSON, L.M. (2004). DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC:NMRstructure andUV-Vis spectroscopy characterization. Nucleic Acids Research 32, 5087-5095.
16. ERITJA, R., KAPLAN, B. E., MHASKAR, D., SOWERS, L. C., PETRUSKA, J., GOODMAN, M. F. (1986). Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine. Nucleic Acids Research 14, 5869-5884.
17. EVANS, K., XU, D., KIM, Y., NORDLUND, T.M. (1992). 2-Aminopurine optical spectra: solvent, pentose ring, and DNA helix melting dependence. Journal of Fluorescence 2, 209-216.
18. FAZAKERLEY, G. V., SOWERS, L. C., ERITJA, R., KAPLAN, B.E., GOODMAN, M. F. (1987). NMR studies on an oligodeoxynucleotide containing 2-aminopurine opposite adenine. Biochemistry 26, 5641-5646.
19. FENG, K., ENGLER, G., SEEFELD, K., KLEINERMANNS, K. (2009). Dispersed fluorescence and delayed ionization of jet-cooled 2-aminopurine: relaxation to a dark state causes weak fluorescence. Chemphyschem 10, 886-889.
20. FINGER, L. D., PATEL, N., BEDDOWS, A., MA, L., EXELL, J. C., JARDINE, E., JONES, A.C., GRASBY, J.A. (2013). Observation of unpaired substrate DNA in the flap endonuclease-1 active site. Nucleic Acids Research 41, 9839-9847.
21. FOGARTY, A. C., JONES, A.C., CAMP, P. J. (2011). Extraction of lifetime distributions from fluorescence decays with application to DNA-base analogues. Physical Chemistry Chemical Physics 13, 3819-3830.
22. FREY, M.W., SOWERS, L. C., MILLAR, D.P., BENKOVIC, S. J. (1995). The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase. Biochemistry 34, 9185-9192.
23. GELOT, T., TOURON-TOUCEDA, P., CREGUT, O., LEONARD, J. & HAACKE, S. (2012). Ultrafast site-specific fluorescence quenching of 2-aminopurine in a DNA hairpin studied by femtosecond down-conversion. Journal of Physical Chemistry A 116, 2819-2825.
24. GENEREUX, J.C., BARTON, J. K. (2010). Mechanisms for DNA charge transport. Chemical Review 110, 1642-1662.
25. GODET, J., RAMALANJAONA, N., SHARMA, K. K., RICHERT, L., DE ROCQUIGNY, H., DARLIX, J. L., DUPORTAIL, G., MELY, Y. (2011). Specific implications of the HIV-1 nucleocapsid zinc fingers in the annealing of the primer binding site complementary sequences during the obligatory plus strand transfer. Nucleic Acids Research 39, 6633-6645.
26. GOEL, T., MUKHERJEE, T., RAO, B.J., KRISHNAMOORTHY, G. (2010). Fluorescence dynamics of double-and single-stranded DNA bound to histone and micellar surfaces. Journal of Physical Chemistry B 114, 8986-8993.
27. GOWHER, H., JELTSCH, A. (2000). Molecular enzymology of the Eco RV DNA-(adenine-N6)-methyltransferase: kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA. Journal of Molecular Biology 303, 93-110.
28. GUCKIAN, K. M., KRUGH, T.R., KOOL, E. T. (1998). Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair. Nature Structural Biology 5, 954-959.
29. GUCKIAN, K. M., KRUGH, T.R., KOOL, E. T. (2000). Solution structure of a nonpolar, non-hydrogen-bonded base pair surrogate in DNA. Journal of the American Chemical Society 122, 6841-6847.
30. GUEST, C. R., HOCHSTRASSER, R. A., SOWERS, L.C., MILLAR, D. P. (1991). Dynamics of mismatched base pairs in DNA. Biochemistry 30, 3271-3279.
31. HARDMAN, S. J., 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.
32. HARDMAN, S. J.O., THOMPSON, K. C. (2007). The fluorescence transition of 2-aminopurine in double-and single-stranded DNA. International Journal of Quantum Chemistry 107, 2092-2099.
33. HARIHARAN, C., REHA-KRANTZ, L. J. (2005). Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions. Biochemistry 44, 15674-15684.
34. HARRIMAN, A. (1987). Further comments on the redox potentials of tryptophan and tyrosine. The Journal of Physical Chemistry 91, 6102-6104.
35. HE, R. X., DUAN, X.H., LI, X. Y. (2006). Theoretical investigation of spectral properties and tautomerization mechanism of 2-aminopurine. Physical Chemistry Chemical Physics 8, 587-591.
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. HOLZ, B., KLIMASAUSKAS, S., SERVA, S., WEINHOLD, E. (1998). 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases. Nucleic Acids Research 26, 1076-1083.
39. JAMES, D. R., SIEMIARCZUK, A., WARE, W. R. (1992). Stroboscopic optical boxcar technique for the determination of fluorescence lifetimes. Review of Scientific Instruments 63, 1710.
40. JEAN, J.M., HALL, K. B. (2001). 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proceedings of the National Academy of Sciences 98, 37-41.
41. JEAN, J.M., HALL, K. B. (2002). 2-aminopurine electronic structure and fluorescence properties in DNA. Biochemistry 41, 13152-13161.
42. JELTSCH, A. (2002). Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBioChem 3, 274-293.
43. JOHNSON, N. P., BAASE, W.A., VON HIPPEL, P. H. (2004). Low-energy circular dichroism of 2-aminopurine dinucleotide as a probe of local conformation of DNA and RNA. Proceedings of the National Academy of Sciences of the United States of America 101, 3426-3431.
44. JOSE, D., DATTA, K., JOHNSON, N.P., VON HIPPEL, P.H. (2009). Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primertemplate junctions. Proceedings of the National Academy of Sciences of the United States of America 106, 4231-4236.
45. KELLEY, S.O. (1999). Electron transfer between bases in double helical DNA. Science 283, 375-381.
46. KIMURA, T., KAWAI, K., FUJITSUKA, M., MAJIMA, T. (2004). Fluorescence properties of 2-aminopurine in human telomeric DNA. Chemical Communications (Cambridge) 1438-1439.
47. KIMURA, T., KAWAI, K., FUJITSUKA, M., MAJIMA, T. (2007). Monitoring G-quadruplex structures and G-quadruplex-ligand complex using 2-aminopurine modified oligonucleotides. Tetrahedron 63, 3585-3590.
48. LAKOWICZ, J. R. (2006). Principles of Fluoresence Spectroscopy, 3rd edn. Springer.
49. LARSEN, O. F. A., VAN STOKKUM, I. H. M., DE WEERD, F. L., VENGRIS, M., ARAVINDAKUMAR, C.T., VAN GRONDELLE, R., GEACINTOV, N.E., VAN AMERONGEN, H. (2004). Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA duplexes. Physical Chemistry Chemical Physics 6, 154.
50. LAW, S. M., ERITJA, R., GOODMAN, M.F., BRESLAUER, K. J. (1996). Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry 35, 12329-12337.
51. LEE, B. J., BARCH, M., CASTNER, E.W. Jr., VOLKER, J., BRESLAUER, K. J. (2007). Structure and dynamics in DNA looped domains: CAG triplet repeat sequence dynamics probed by 2-aminopurine fluorescence. Biochemistry 46, 10756-10766.
52. LENZ, T., BONNIST, E. Y. M., PLJEVALJI, G., NEELY, R. K., DRYDEN, D. T. F., SCHEIDIG, A. J., JONES, A.C., WEINHOLD, E. (2007). 2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence. Journal of the American Chemical Society 129, 6240-6248.
53. LIANG, J., MATSIKA, S. (2011). Pathways for fluorescence quenching in 2-aminopurine pi-stacked with pyrimidine nucleobases. Journal of the American Chemical Society 133, 6799-6808.
54. LIANG, J., NGUYEN, Q.L., MATSIKA, S. (2013). Exciplexes and conical intersections lead to fluorescence quenching in pi-stacked dimers of 2-aminopurine with natural purine nucleobases. Photochemical & Photobiological Sciences 12, 1387-1400.
55. LOBSIGER, S., BLASER, S., SINHA, R. K., FREY, H.M., LEUTWYLER, S. (2014). Switching on the fluorescence of 2-aminopurine by site-selective microhydration. Nature Chemistry 6, 989-993.
56. LOBSIGER, S., SINHA, R.K., LEUTWYLER, S. (2013). Building up water-wire clusters: isomer-selective ultraviolet and infrared spectra of jet-cooled 2-aminopurine (H2O)n, n = 2 and 3. Journal of Physical Chemistry B 117, 12410-12421.
57. LOBSIGER, S., SINHA, R. K., TRACHSEL, M., LEUTWYLER, S. (2011). Low-lying excited states and nonradiative processes of the adenine analogues 7H-and 9H-2-aminopurine. Journal of Chemical Physics 134, 114307.
58. LUDWIG, V., AMARAL, M. S. D., DA COSTA, Z. M., BORIN, A. C., CANUTO, S., SERRANO-ANDRÉS, L. (2008). 2-Aminopurine non-radiative decay and emission in aqueous solution: a theoretical study. Chemical Physics Letters 463, 201-205.
59. LYCKSELL, P. O., GRÄSLUND, A., CLAESENS, F., MCLAUGHLIN, L.W., LARSSON, U., RIGLER, R. (1987). Base pair opening dynamics of a 2-aminopurine substituted Eco RI restricion sequence and its unsubstituted counterpart in oligonucleotides. Nucleic Acids Research 15, 9011-9025.
60. MA, L. (2012). Ph.D. thesis, University of Edinburgh.
61. MA, L., WU, X., WILSON, G.G., JONES, A.C. & DRYDEN, D.T. (2014). Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction-modification enzyme. Biochemical and Biophysical Research Communications 449, 120-125.
62. MANOJ, P., MIN, C.-K., ARAVINDAKUMAR, C.T., JOO, T. (2008). Ultrafast charge transfer dynamics in 2-aminopurine modified double helical DNA. Chemical Physics 352, 333-338.
63. NADLER, A., STROHMEIER, J., DIEDERICHSEN, U. (2011). 8-Vinyl-2-deoxyguanosine as a fluorescent 2-deoxyguanosine mimic for investigating DNA hybridization and topology. Angewandte Chemie International Edition in English 50, 5392-5396.
64. NARAYANAN, M., KODALI, G., XING, Y., STANLEY, R. J. (2010). Photoinduced electron transfer occurs between 2-aminopurine and the DNA nucleic acid monophosphates: results from cyclic voltammetry and fluorescence quenching. The Journal of Physical Chemistry B 114, 10573-10580.
65. NEELY, R. K. (2005). Ph.D. thesis, University of Edinburgh.
66. NEELY, R. K., DAUJOTYTE, D., GRAZULIS, S., MAGENNIS, S.W., DRYDEN, D. T., KLIMASAUSKAS, S., JONES, A. C. (2005). Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M. HhaI-DNA complexes. Nucleic Acids Research 33, 6953-6960.
67. NEELY, R.K., JONES, A. C. (2006). Influence of base dynamics on the conformational properties of DNA: observation of static conformational states in rigid duplexes at 77 K. Journal of the American Chemical Society 128, 15952-15953.
68. NEELY, R. K., MAGENNIS, S.W., DRYDEN, D.T.F., JONES, A. C. (2004). Evidence of tautomerism in 2-aminopurine from fluorescence lifetime measurements. The Journal of Physical Chemistry B 108, 17606-17610.
69. NEELY, R. K., MAGENNIS, S.W., PARSONS, S., JONES, A.C. (2007). Photophysics and X-ray structure of crystalline 2-aminopurine. Chemphyschem 8, 1095-1102.
70. NEELY, R. K., TAMULAITIS, G., CHEN, K., KUBALA, M., SIKSNYS, V., JONES, A. C. (2009). Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes. Nucleic Acids Research 37, 6859-6870.
71. NOÉ, M. S., SINKELDAM, R.W., TOR, Y. (2013). Oligodeoxynucleotides containing multiple thiophenemodified isomorphic fluorescent nucleosides. The Journal of Organic Chemistry 78, 8123-8128.
72. NORDLUND, T.M. (2007). Sequence, structure and energy transfer in DNA. Photochemistry and Photobiology 83, 625-636.
73. NORDLUND, T. M., ANDERSSON, S., NILSSON, L., RIGLER, R., GRAESLUND, 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.
74. O'NEIL, M.A., BARTON, J. K. (2002). 2-aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids. Journal of the American Chemical Society 124, 13053-13066.
75. O'NEILL, M.A., BARTON, J. K. (2002). Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA. Proceedings of the National Academy of Sciences of the United States of America 99, 16543-16550.
76. O'NEILL, M.A., BARTON, J. K. (2004a). DNA-mediated charge transport requires conformational motion of the DNA bases: elimination of charge transport in rigid glasses at 77 K. Journal of the American Chemical Society 126, 13234-13235.
77. O'NEILL, M.A., BARTON, J. K. (2004b). DNA charge transport: conformationally gated hopping through stacked domains. Journal of the American Chemical Society 126, 11471-11483.
78. O'NEILL, M. A., BECKER, H. C., WAN, C., BARTON, J.K., ZEWAIL, A. H. (2003). Ultrafast dynamics in DNA-mediated electron transfer: base gating and the role of temperature. Angewandte Chemie International Edition in English 42, 5896-5900.
79. O'NEILL, M. A., DOHNO, C., BARTON, J. K. (2004). Direct chemical evidence for charge transfer between photoexcited 2-aminopurine and guanine in duplex DNA. Journal of the American Chemical Society 126, 1316-1317.
80. RACHOFSKY, E. L., OSMAN, R., ROSS, J. B. A. (2001a). Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence†. Biochemistry 40, 946-956.
81. RACHOFSKY, E. L., ROSS, J. B. A., KRAUSS, M., OSMAN, R. (2001b). CASSCF investigation of electronic excited states of 2-aminopurine. The Journal of Physical Chemistry A 105, 190-197.
82. RACHOFSKY, E. L., SEIBERT, E., STIVERS, J. T., OSMAN, R., ROSS, J. B. A. (2001c). Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine†. Biochemistry 40, 957-967.
83. RACHOFSKY, E. L., SOWERS, L. C., HAWKINS, M. E., BALIS, F. M., LAWS, W.R., ROSS, J. B. A. (1998). Emission kinetics of fluorescent nucleoside analogs, 3256, 68-75.
84. RAMREDDY, T., KOMBRABAIL, M., KRISHNAMOORTHY, G., RAO, B. J. (2009). Site-specific dynamics in TAT triplex DNA as revealed by time-domain fluorescence of 2-aminopurine. Journal of Physical Chemistry B 113, 6840-6846.
85. RAMREDDY, T., RAO, B. J., KRISHNAMOORTHY, G. (2007). Site-specific dynamics of strands in ss-and dsDNA as revealed by time-domain fluorescence of 2-aminopurine. Journal of Physical Chemistry B 111, 5757-5766.
86. RANEY, K. D., SOWERS, L. C., MILLAR, D.P., BENKOVIC, S. J. (1994). A fluorescence-based assay for monitoring helicase activity. Proceedings of the National Academy of Sciences 91, 6644-6648.
87. REDDY, Y.V., RAO, D. N. (2000). Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence. Journal of Molecular Biology 298, 597-610.
88. REHA-KRANTZ, L. J. (2009). The use of 2-aminopurine fluorescence to study DNA polymerase function. Methods in Molecular. Biology. (Totowa, NJ, U. S.) 521 (DNA Replication), 381-396.
89. REICHARDT, C., WEN, C., VOGT, R.A., CRESPO-HERNANDEZ, C. E. (2013). Role of intersystem crossing in the fluorescence quenching of 2-aminopurine 2-deoxyriboside in solution. Photochemical & Photobiological Sciences 12, 1341-1350.
90. RICHARDSON, T. T., WU, X., KEITH, B. J., HESLOP, P., JONES, A.C., CONNOLLY, B. A. (2013). Unwinding of primerlates by archaeal family-B DNA polymerases in response to template-strand uracil. Nucleic Acids Research 41, 2466-2478.
91. RIST, M., WAGENKNECHT, H.-A., FIEBIG, T. (2002). Exciton and excimer formation in DNA at room temperature. ChemPhysChem 3, 704-707.
92. SABIR, T., TOULMIN, A., MA, L., JONES, A. C., MCGLYNN, P., SCHRODER, G.F., MAGENNIS, S.W. (2012). Branchpoint expansion in a fully complementary threeway DNA junction. Journal of American Chemical Society 134, 6280-6285.
93. SERRANO-ANDRES, L., MERCHAN, M., BORIN, A. C. (2006). Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry. Proceedings of the National Academy of Sciences of the United States of America 103, 8691-8696.
94. SINHA, R. K., LOBSIGER, S., TRACHSEL, M., LEUTWYLER, S. (2011). Vibronic spectra of jet-cooled 2-aminopurine. H2O clusters studied by UV resonant two-photon ionization spectroscopy and quantum chemical calculations. Journal of Physical Chemistry A 115, 6208-6217.
95. SINKELDAM, R.W., GRECO, N.J., TOR, Y. (2010). Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chemical Reviews 110, 2579-2619.
96. SMIRNOV, S. (2002). Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Research 30, 5561-5569.
97. SOMSEN, O. J., KEUKENS, L. B., DE KEIJZER, M. N., VAN HOEK, A., VAN AMERONGEN, H. (2005a). Structural heterogeneity in DNA: temperature dependence of 2-aminopurine fluorescence in dinucleotides. Chemphyschem 6, 1622-1627.
98. SOMSEN, O. J. G., HOEK, V.A., AMERONGEN, V.H. (2005b). Fluorescence quenching of 2-aminopurine in dinucleotides. Chemical Physics Letters 402, 61-65.
99. SOMSEN, O. J. G., TRINKUNAS, G., KEIJZER, M. N. D., HOEK, A.V., AMERONGEN, H. V. (2006). Local diffusive dynamics in DNA. Journal of Luminescence 119-120, 100-104.
100. SOWERS, L. C., BOULARD, Y., FAZAKERLEY, G. V. (2000). Multiple structures for the 2-aminopurinecytosine mispair†. Biochemistry 39, 7613-7620.
101. 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.
102. SU, T.-J., CONNOLLY, B. A., DARLINGTON, C., MALLIN, R., DRYDEN, D. T. F. (2004). Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase. Nucleic Acids Research 32, 2223-2230.
103. SUBUDDHI, U., HOGG, M., REHA-KRANTZ, L. J. (2008). Use of 2-aminopurine fluorescence to study the role of the beta hairpin in the proofreading pathway catalyzed by the phage T4 and RB69 DNA polymerases. Biochemistry 47, 6130-6137.
104. TLEUGABULOVA, D., REHA-KRANTZ, L. J. (2007). Probing DNA polymerase-DNA interactions: examining the template strand in exonuclease complexes using 2-aminopurine fluorescence and acrylamide quenching. Biochemistry 46, 6559-6569.
105. WAN, C., FIEBIG, T., SCHIEMANN, O., BARTON, J.K., ZEWAIL, A.H. (2000). Femtosecond direct observation of charge transfer between bases in DNA. Proceedings of the National Academy of Sciences of the United States of America 97, 14052-14055.
106. WAN, C., XIA, T., BECKER, H.-C., ZEWAIL, A. H. (2005). Ultrafast unequilibrated charge transfer: a new channel in the quenching of fluorescent biological probes. Chemical Physics Letters 412, 158-163.
107. 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.
108. WILHELMSSON, L.M. (2010). Fluorescent nucleic acid base analogues. Quarterly Reviews of Biophysics 43, 159-183.
109. XIA, T. (2008). Taking femtosecond snapshots of RNA conformational dynamics and complexity. Current Opinion in Chemical Biology 12, 604-611.
110. XIA, T., BECKER, H. C., WAN, C., FRANKEL, A., ROBERTS, R.W., ZEWAIL, A. H. (2003). The RNA-protein complex: direct probing of the interfacial recognition dynamics and its correlation with biological functions. Proceedings of the National Academy of Sciences of the United States of America 100, 8119-8123.
111. XU, D., EVANS, K.O., NORDLUND, T.M. (1994). Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption. Biochemistry 33, 9592-9599.
112. YOUNGBLOOD, B., BONNIST, E., DRYDEN, D.T.F., JONES, A.C., REICH, N. O. (2008). Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies. Nucleic Acids Research 36, 2917-2925.