DNA hairpins containing the cytidine analog pyrrolo-dC: Structural, thermodynamic, and spectroscopic studies

Biophysical Journal

Volumn 96, Issue 5, 2009, Pages 1884-1891

  Zhang, Xu ^a   Wadkins, Randy M ^a  

^a UNIVERSITY OF MISSISSIPPI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

7 AMINODACTINOMYCIN; CYTIDINE DERIVATIVE; DNA; DNA HAIRPIN; PYRROLO DEOXYCYTIDINE; UNCLASSIFIED DRUG; 7-AMINOACTINOMYCIN D; CYTIDINE; DACTINOMYCIN; DEOXYCYTIDINE; DRUG DERIVATIVE; PYRROLE DERIVATIVE; PYRROLO-DEOXYCYTIDINE;

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA STRAND; DNA STRUCTURE; DRUG DNA BINDING; FLUORESCENCE ANALYSIS; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN SECONDARY STRUCTURE; SPECTROFLUOROMETRY; STRUCTURE ANALYSIS; THERMOSTABILITY; THREE DIMENSIONAL IMAGING; ULTRAVIOLET SPECTROPHOTOMETRY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; FLUORESCENCE; INVERTED REPEAT; PROTEIN CONFORMATION; THERMODYNAMICS; TITRIMETRY; TRANSITION TEMPERATURE;

CYTIDINE; DACTINOMYCIN; DEOXYCYTIDINE; DNA; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; INVERTED REPEAT SEQUENCES; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PYRROLES; THERMODYNAMICS; TITRIMETRY; TRANSITION TEMPERATURE;

EID: 65549106053     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.12.3890     Document Type: Article

References (27)

1. Wadkins, R. M. 2000. Targeting DNA secondary structures. Curr. Med. Chem. 7:1-15.
2. Kouzine, F., and D. Levens. 2007. Supercoil-driven DNA structures regulate genetic transactions. Front. Biosci. 12:4409-4423.
3. Zannis-Hadjopoulos, M., W. Yahyaoui, and M. Callejo. 2007. 14-3-3 Cruciform-binding proteins as regulators of eukaryotic DNA replication. Trends Biochem. Sci. 33:44-49.
4. 1H NMR spectroscopy. J. Mol. Biol. 262:53-68.
5. Wadkins, R. M., and T. M. Jovin. 1991. Actinomycin D and 7-aminoactinomycin D binding to single-stranded DNA. Biochemistry. 30:9469-9478.
6. Wadkins, R. M., C. S. Tung, P. M. Vallone, and A. S. Benight. 2000. The role of the loop in binding of an actinomycinDanalog to hairpins formed by single-stranded DNA. Arch. Biochem. Biophys. 384:199-203.
7. Wadkins, R. M., B. Vladu, and C. -S. Tung. 1998. Actinomycin D binds to metastable hairpins in single-stranded DNA. Biochemistry. 37:11915-11923.
8. Vekshin, N., I. Savintsev, A. Kovalev, R. Yelemessov, and R. M. Wadkins. 2001. Solvatochromism of the excitation and emission spectra of 7-aminoactinomycin D: implications for drug recognition of DNA secondary structures. J. Phys. Chem. B. 105:8461-8467.
9. Kim, N. W., M. A. Piatyszek, K. R. Prowse, C. B. Harley, M. D. West, et al. 1994. Specific association of human telomerase activity with immortal cells and cancer. Science. 266:2011-2015.
10. Sharma, H. W., J. -Y. Maltese, X. Zhu, H. E. Kaiser, and R. Narayanan. 1996. Telomeres, telomerase and cancer: is the magic bullet real? Anticancer Res. 16:511-516.
11. Hurley, L. H., R. T. Wheelhouse, D. Sun, S. M. Kerwin, M. Salazar, et al. 2000. G-quadraplexes as targets for drug design. Pharmacol. Ther. 85:141-158.
12. Hurley, L. H. 2001. Secondary DNA structures as molecular targets for cancer therapeutics. Biochem. Soc. Trans. 29:692-696.
13. Seenisamy, J., E. M. Rezler, T. J. Powell, D. Tye, V. Gokhale, et al. 2004. The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. J. Am. Chem. Soc. 126:8702-8709.
14. Siddiqui-Jain, A., C. L. Grand, D. J. Bearss, and L. H. Hurley. 2002. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. USA. 99:11593-11598.
15. Grand, C. L., H. Han, R. M. Munoz, S. Weitman, D. D. Von Hoff, et al. 2002. The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo. Mol. Cancer Ther. 1:565-573.
16. Berry, D. A., K. -Y. Jung, D. S. Wise, A. D. Sercel, W. H. Pearson, et al. 2004. Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2′-deoxycytidine fo the study of oligonucleotides. Tetrahedron Lett. 45:2457-2461.
17. Liu, C., and C. T. Martin. 2002. Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence. J. Biol. Chem. 277:2725-2731.
18. Zang, H., Q. Fang, A. E. Pegg, and F. P. Guengerich. 2005. Kinetic analysis of steps in the repair of damaged DNA by human O6-alkylguanine-DNA alkyltransferase. J. Biol. Chem. 280:30873-30881.
19. Vallone, P. M., T. M. Paner, J. Hilario, M. J. Lane, B. D. Faldasz, et al. 1999. Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers. 50:425-442.
20. Jameson, D. M., and T. L. Hazlett. 1991. Time-resolved fluorescence in biology and biochemistry. In Biophysical and Biochemical Aspects of Fluorescence Spectroscopy. T. G. Dewey, editor. Plenum, New York. 105-133.
21. Goddard, T.D. and D.G. Kneller. SPARKY 3. San Francisco: University of California.
22. Thompson, K. C., and N. Miyake. 2005. Properties of a new fluorescent cytosine analogue, pyrrolocytosine. J. Phys. Chem. B. 109:6012-6019.
23. Marti, A. A., S. Jockusch, Z. Li, J. Ju, and N. J. Turro. 2006. Molecular beacons with intrinsically fluorescent nucleotides. Nucleic Acids Res. 34:e50.
24. Hardman, S. J. O., and K. C. Thompson. 2006. Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry. 45:9145-9155.
25. Dash, C., J. W. Rausch, and S. F. Le Grice. 2004. Using pyrrolo-deoxycytidine to probe RNA/DNA hybrids containing the human immuno-deficiency virus type-1 30 polypurine tract. Nucleic Acids Res. 32:1539-1547.
26. Kraulis, P. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:946-950.
27. Meritt, E. A., and D. J. Bacon. 1997. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:505-524.