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

Published online by Cambridge University Press:  17 April 2015

Anita C. Jones  and
Robert K. Neely
Anita C. Jones*
Affiliation:
EaStCHEM School of Chemistry, King's Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, UK
Robert K. Neely
Affiliation:
School of Chemistry, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
*
*Author for correspondence: A. C. Jones, EaStCHEM School of Chemistry, King's Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, UK. Tel: +44 131 6506449; Fax: +44 131 6506453; Email: [email protected]
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Abstract

Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 48 , Issue 2 , May 2015 , pp. 244 - 279
Copyright
Copyright © Cambridge University Press 2015 

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References

8. References

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.CrossRefGoogle Scholar
Allan, B. W. & Reich, N. O. (1996). Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35, 14757–14762.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Becker, W. (2005). Advanced Time-Correlated Single Photon Counting. Springer.CrossRefGoogle Scholar
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. Lakowicz, J.), pp. 241–305. US: Springer.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Bonnist, E. Y. & Jones, A. C. (2008). Long-wavelength fluorescence from 2-aminopurine-nucleobase dimers in DNA. Chemphyschem 9, 1121–1129.CrossRefGoogle ScholarPubMed
Bonnist, E. Y. M. (2008). Ph.D. thesis, University of Edinburgh.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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: NMR structure and UV-Vis spectroscopy characterization. Nucleic Acids Research 32, 5087–5095.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Genereux, J. C. & Barton, J. K. (2010). Mechanisms for DNA charge transport. Chemical Review 110, 1642–1662.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.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. & 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
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Harriman, A. (1987). Further comments on the redox potentials of tryptophan and tyrosine. The Journal of Physical Chemistry 91, 6102–6104.CrossRefGoogle Scholar
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.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
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Jean, J. M. & Hall, K. B. (2002). 2-aminopurine electronic structure and fluorescence properties in DNA. Biochemistry 41, 13152–13161.CrossRefGoogle ScholarPubMed
Jeltsch, A. (2002). Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBioChem 3, 274–293.3.0.CO;2-S>CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Jose, D., Datta, K., Johnson, N. P. & Von Hippel, P. H. (2009). Spectroscopic studies of position-specific DNA “breathing” fluctuations at replication forks and primer-template junctions. Proceedings of the National Academy of Sciences of the United States of America 106, 4231–4236.CrossRefGoogle ScholarPubMed
Kelley, S. O. (1999). Electron transfer between bases in double helical DNA. Science 283, 375–381.CrossRefGoogle ScholarPubMed
Kimura, T., Kawai, K., Fujitsuka, M. & Majima, T. (2004). Fluorescence properties of 2-aminopurine in human telomeric DNA. Chemical Communications (Cambridge) 1438–1439.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Lakowicz, J. R. (2006). Principles of Fluoresence Spectroscopy, 3rd edn. Springer.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Lenz, T., Bonnist, E. Y. M., Pljevaljčić, 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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Ma, L. (2012). Ph.D. thesis, University of Edinburgh.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Neely, R. K. (2005). Ph.D. thesis, University of Edinburgh.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Noé, M. S., Sinkeldam, R. W. & Tor, Y. (2013). Oligodeoxynucleotides containing multiple thiophene-modified isomorphic fluorescent nucleosides. The Journal of Organic Chemistry 78, 8123–8128.CrossRefGoogle ScholarPubMed
Nordlund, T. M. (2007). Sequence, structure and energy transfer in DNA. Photochemistry and Photobiology 83, 625–636.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Richardson, T. T., Wu, X., Keith, B. J., Heslop, P., Jones, A. C. & Connolly, B. A. (2013). Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil. Nucleic Acids Research 41, 2466–2478.CrossRefGoogle ScholarPubMed
Rist, M., Wagenknecht, H.-A. & Fiebig, T. (2002). Exciton and excimer formation in DNA at room temperature. ChemPhysChem 3, 704–707.3.0.CO;2-F>CrossRefGoogle ScholarPubMed
Sabir, T., Toulmin, A., Ma, L., Jones, A. C., Mcglynn, P., Schroder, G. F. & Magennis, S. W. (2012). Branchpoint expansion in a fully complementary three-way DNA junction. Journal of American Chemical Society 134, 6280–6285.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Sinkeldam, R. W., Greco, N. J. & Tor, Y. (2010). Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chemical Reviews 110, 2579–2619.CrossRefGoogle ScholarPubMed
Smirnov, S. (2002). Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Research 30, 5561–5569.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Somsen, O. J. G., Hoek, V. A. & Amerongen, V. H. (2005b). Fluorescence quenching of 2-aminopurine in dinucleotides. Chemical Physics Letters 402, 61–65.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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. (2010). Fluorescent nucleic acid base analogues. Quarterly Reviews of Biophysics 43, 159–183.CrossRefGoogle ScholarPubMed
Xia, T. (2008). Taking femtosecond snapshots of RNA conformational dynamics and complexity. Current Opinion in Chemical Biology 12, 604–611.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed