Single-molecule fluorescence using nucleotide analogs: A proof-of-principle

Journal of Physical Chemistry Letters

Volumn 5, Issue 5, 2014, Pages 777-781

  Alemán, Elvin A ^a,e   De Silva, Chamaree ^b,f   Patrick, Eric M ^a   Musier Forsyth, Karin ^b   Rueda, David ^a,c,d  

^a WAYNE STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c Section of Virology   (United Kingdom)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

^e CALIFORNIA STATE UNIVERSITY   (United States)

^f MERCER UNIVERSITY   (United States)

Author keywords

2 aminopurine; DNA dynamics; fluorescent base nucleotide analogues; pyrrolo C; single molecule fluorescence

Indexed keywords

2-AMINOPURINE; DNA DYNAMICS; NUCLEOTIDE ANALOGUES; PYRROLO-C; SINGLE-MOLECULE FLUORESCENCES;

DNA; DYNAMICS; MOLECULES; NUCLEOTIDES; PROTEINS; RNA;

FLUORESCENCE;

EID: 84897785322     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz4025832     Document Type: Article

References (33)

1. Michalet, X.; Weiss, S.; Jager, M. Single-Molecule Fluorescence Studies of Protein Folding and Conformational Dynamics Chem. Rev. 2006, 106 (5) 1785-1813
2. Lu, H. P.; Xun, L.; Xie, X. S. Single-Molecule Enzymatic Dynamics Science 1998, 282 (5395) 1877-1882
3. Joo, C.; Balci, H.; Ishitsuka, Y.; Buranachai, C.; Ha, T. Advances in Single-Molecule Fluorescence Methods for Molecular Biology Annu. Rev. Biochem. 2008, 77, 51-76
4. Ditzler, M. A.; Alemán, E. A.; Rueda, D.; Walter, N. G. Focus on Function: Single Molecule RNA Enzymology Biopolymers 2007, 87 (5-6) 302-316
5. Karunatilaka, K. S.; Rueda, D. Single-Molecule Fluorescence Studies of RNA: A Decade's Progress Chem. Phys. Lett. 2009, 476 (1) 1-10
6. Ulrich, N. G. Single-Molecule Fluorescence Studies of Protein Folding Methods Mol. Biol. 2009, 490, 311-337
7. Kapanidis, A. N.; Weiss, S. Fluorescent Probes and Bioconjugation Chemistries for Single-Molecule fluorescence analysis of biomolecules J. Chem. Phys. 2002, 117 (24) 10953-10964
8. Shi, J.; Dertouzos, J.; Gafni, A.; Steel, D.; Palfey, B. A. Single-Molecule Kinetics Reveals Signatures of Half-Sites Reactivity in Dihydroorotate Dehydrogenase A Catalysis Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (15) 5775-5780
9. Xue, Q.; Yeung, E. S. Differences in the Chemical Reactivity of Individual Molecules of an Enzyme Nature 1995, 373 (6516) 681-683
10. Ward, D. C.; Reich, E.; Stryer, L. Fluorescence Studies of Nucleotides and Polynucleotides. I. Formycin, 2-Aminopurine Riboside, 2,6-Diaminopurine Riboside, and their Derivatives J. Biol. Chem. 1969, 244 (5) 1228-1237
11. Serrano-Andres, L.; Merchan, M.; Borin, A. C. Adenine and 2-Aminopurine: Paradigms of Modern Theoretical Photochemistry Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (23) 8691-8696
12. Hall, K. B. 2-Aminopurine as a Probe of RNA Conformational Transitions Methods Enzymol. 2009, 469, 269-285
13. Roberts, R. J.; Cheng, X. Base Flipping Annu. Rev. Biochem. 1998, 67, 181-198
14. Buscaglia, R.; Jameson, D. M.; Chaires, J. B. G-Quadruplex Structure and Stability Illuminated by 2-Aminopurine Phasor Plots Nucleic Acids Res. 2012, 40 (9) 4203-4215
15. Ballin, J. D.; Bharill, S.; Fialcowitz-White, E. J.; Gryczynski, I.; Gryczynski, Z.; Wilson, G. M. Site-Specific Variations in RNA Folding Thermodynamics Visualized by 2-Aminopurine Fluorescence Biochemistry 2007, 46 (49) 13948-13960
16. Sarkar, K.; Nguyen, D. A.; Gruebele, M. Loop and Stem Dynamics During RNA Hairpin Folding and Unfolding RNA 2010, 16 (12) 2427-2434
17. Larsen, O. F. A.; van Stokkum, I. H. M.; Groot, M. L.; Kennis, J. T. M.; van Grondelle, R.; van Amerongen, H. Electronic States in 2-Aminopurine Revealed by Ultrafast Transient Absorption and Target Analysis Chem. Phys. Lett. 2003, 371 (1-2) 157-163
18. Hardman, S. J.; Thompson, K. C. Influence of Base Stacking and Hydrogen Bonding on the Fluorescence of 2-Aminopurine and Pyrrolocytosine in Nucleic Acids Biochemistry 2006, 45 (30) 9145-9155
19. Jean, J. M.; Hall, K. B. 2-Aminopurine Electronic Structure and Fluorescence Properties in DNA Biochemistry 2002, 41 (44) 13152-13161
20. Somsen, O. J. G.; Hoek, v. A.; Amerongen, v. H. Fluorescence Quenching of 2-Aminopurine in Dinucleotides ChemPhysChem 2005, 402, 61-65
21. Nguyen, H. N.; Zhao, L.; Gray, C. W.; Gray, D. M.; Xia, T. Ultrafast Fluorescence Decay Profiles Reveal Differential Unstacking of 2-Aminopurine from Neighboring Bases in Single-Stranded DNA-Binding Protein Subsites Biochemistry 2011, 50 (42) 8989-9001
22. Somsen, O. J.; Keukens, L. B.; de Keijzer, M. N.; van Hoek, A.; van Amerongen, H. Structural Heterogeneity in DNA: Temperature Dependence of 2-Aminopurine Fluorescence in Dinucleotides ChemPhysChem 2005, 6 (8) 1622-1627
23. Alemán, E. A.; Pedini, H. S.; Rueda, D. Covalent-Bond-Based Immobilization Approaches for Single-Molecule Fluorescence ChemBioChem 2009, 10 (18) 2862-2866
24. Tatischeff, I.; Klein, R.; Duquesne, M. A New Fluorescent Photoproduct of Tryptophan Evidenced by Long Wavelength Excitation of Fluorescence Photochem. Photobiol. 1976, 24 (5) 413-416
25. Fazio, T.; Visnapuu, M. L.; Wind, S.; Greene, E. C. DNA Curtains and Nanoscale Curtain Rods: High-Throughput Tools for Single Molecule Imaging Langmuir 2008, 24 (18) 10524-10531
26. Guest, C. R.; Hochstrasser, R. A.; Sowers, L. C.; Millar, D. P. Dynamics of Mismatched Base Pairs in DNA Biochemistry 1991, 30 (13) 3271-3279
27. Garo, F.; Haner, R. Influence of a GC Base Pair on Excitation Energy Transfer in DNA-Assembled Phenanthrene pi-Stacks Bioconjugate Chem. 2012, 23 (10) 2105-2113
28. Rachofsky, E. L.; Seibert, E.; Stivers, J. T.; Osman, R.; Ross, J. B. Conformation and Dynamics of Abasic Sites in DNA Investigated by Time-Resolved Fluorescence of 2-Aminopurine Biochemistry 2001, 40 (4) 957-967
29. Stivers, J. T. 2-Aminopurine Fluorescence Studies of Base Stacking Interactions at Abasic Sites in DNA: Metal-Ion and Base Sequence Effects Nucleic Acids Res. 1998, 26 (16) 3837-3844
30. Szczepanowski, R. H.; Carpenter, M. A.; Czapinska, H.; Zaremba, M.; Tamulaitis, G.; Siksnys, V.; Bhagwat, A. S.; Bochtler, M. Central Base Pair Flipping and Discrimination by Psp GI Nucleic Acids Res. 2008, 36 (19) 6109-6117
31. Carpenter, M. A.; Bhagwat, A. S. DNA Base Flipping by Both Members of the PspGI Restriction-Modification System Nucleic Acids Res. 2008, 36 (16) 5417-5425
32. Yap, L. P.; Stehlin, C.; Musier-Forsyth, K. Use of Semi-Synthetic Transfer RNAs to Probe Molecular Recognition by Escherichia coli Proline-tRNA synthetase Chem. Biol. 1995, 2 (10) 661-666
33. Tinsley, R. A.; Walter, N. G. Pyrrolo-C As a Fluorescent Probe for Monitoring RNA Secondary Structure Formation RNA 2006, 12 (3) 522-529