Structure and dynamics of a DNA duplex containing single a-anomeric deoxyadenosine residue.

• Authors: Łukasz Bielecki , Ryszard W Adamiak
• Languages of publication: EN

Abstracts

EN

Structure and dynamics of an undecamer DNA duplex containing a single α-anomeric deoxyadenosine residue placed in opposition to a thymidine unit have been studied using simulation of molecular dynamics in aqueous solution. Despite several noticeable deviations from the B-DNA duplex structure caused by the anomerisation, such as: West type puckering of the α-anomeric sugar, disrupted base stacking pattern and unstable duplex bending, the formation of a non-classical α-dA-T pair was observed. A novel way of visual presentation of trajectory data allowing high throughput screening of the conformational parameters is presented.

Keywords

EN

structure; base stacking; bending; α-anomers; dynamics; DNA

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2001
• Volume: 48
• Issue: 1
• Pages: 103-111

Dates

published

2001

received

2000-10-4

revised

2000-12-20

accepted

2001-01-10

Contributors

author

Łukasz Bielecki

• Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Ryszard W Adamiak

• Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• 1. Post, M.L., Birnbaum, G.I., Huber, C.P. & Shugar, D. (1977) α-Nucleosides in biological systems. Crystal structure and conformation of α-cytidine. Biochim. Biophys. Acta 479, 133-142.
• 2. Bielecki, L., Skalski, B., Zagorowska, I., Verrall, R.E. & Adamiak, R.W. (2000) Fluorescent α-anomeric 1,N(6)ethenodeoxyadenosine in DNA duplexes. The α-εdA/dA pair. Nucleosides, Nucleotides & Nucleic Acids 19, 1735-1750.
• 3. Séquin, U. (1973) Nucleosides and Nucleotides. Part 5. The stereochemistry of oligonucleotides consisting of 2'-deoxy-α-D-riboses, a study with DREIDING stereomodels. Experientia 29, 1059- 1062.
• 4. Morvan, F., Rayner, B., Imbach, J.-L., Lee, M., Hartley, J.A., Chang, D.-K. & Lown, J.W. (1987) α-DNA-V. Parallel annealing, handedness and conformation of the duplex of the unnatural α- hexadeoxyribonucleotide α-[d(CpApTpGpCpG)] with its β-complement β-[d(GpTpApCpGpC)] deduced from high field 1H-NMR. Nucleic Acids Res. 15, 3421-3437.
• 5. Aramini, J.A., van de Sande, J.H. & Germann, M.W.(1996) Structure of a DNA duplex that contains α-anomeric nucleosides and 3'-3' and 5'-5' phosphodiester linkages: Coexistence of parallel and antiparallel DNA. Biochemistry 35, 9355- 9365.
• 6. Aramini, J.A., Kalisch, B.W., Pon, R.T., van de Sande, J.H. & Germann, M.W. (1997) Spectroscopic, thermodynamic studies of DNA duplexes containing α-anomeric C, A and G nucleotides and polarity reversals: Coexistence of localized parallel and antiparallel DNA. Biochemistry 36, 9715- 9725.
• 7. Gagnor, C., Rayner, B., Leonetti, J.-P., Imbach, J.-L. & Lebleu, B. (1989) α-DNA IX: Parallel annealing of alpha-anomeric oligodeoxyribonucleotides to natural mRNA is required for interference in RNase H mediated hydrolysis and reverse transcription. Nucleic Acids Res. 17, 5107-5114.
• 8. Boiziau, C., Thuong, N.T. & Toulmé, J.J. (1992) Mechanisms of the inhibition of reverse transcription by antisense oligonucleotides. Proc. Natl. Acad. Sci. U.S.A. 89, 768-772.
• 9. Périgaud, C., Gosselin, G. & Imbach, J.-L. (1992) Nucleoside analogues as chemotherapeutic agents: A review. Nucleosides & Nucleotides 11, 903-945.
• 10. Morvan, F., Porumb, H., Degols, G., Lefebvre, I., Pompon, A., Sproat, B.S., Rayner, B., Malvy, C., Lebleu, B. & Imbach, J.-L. (1993) Comparative evaluation of seven oligonucleotide analogues as potential antisense agents. J. Med. Chem. 36, 280-287.
• 11. Debart, F., Rayner, B., Degols, G. & Imbach, J.-L. (1992) Synthesis and base-pairing properties of the nuclease-resistant α-anomeric dodecaribonucleotide α-[r(UCUUAACCCACA)]. Nucleic Acids Res. 20, 1193-1200.
• 12. Noonberg, S.B., Francois, J.-C., Praseuth, D., Guieysse-Peugeot, A.-L., Lacoste, J., Garestier, T. & Hélene, C. (1995) Triplex formation with α anomers of purine-rich and pyrimidine-rich oligodeoxynucleotides. Nucleic Acids Res. 23, 4042-4049.
• 13. Ide, H., Shimizu, H., Kimura, Y., Sakamoto, S., Makino, K., Glackin, M., Wallace, S.S., Nakamuta, H., Sasaki, M. & Sugimoto, N. (1995) Influence of α-deoxyadenosine on the stability and structure of DNA. Thermodynamic and molecular mechanics studies. Biochemistry 34, 6947-6955.
• 14. Bates, P.J, Laughton, C.A., Jenkins, T.C., Capaldi, D.C., Roselt, P.D., Reese, C.B. & Neidle, S. (1996) Efficient triple helix formation by oligodeoxyribonucleotides containing α- or β-2-amino-5-(2- deoxy-D-ribofuranosyl)pyridine residues. Nucleic Acids Res. 24, 4176-4184.
• 15. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P. & Kollman, P.A. (1995) AMBER Version 4.1. University of California.
• 16. Gaussian 94, Revision C.3. Gaussian Inc., Pittsburgh 1995.
• 17. Bayly, C.I., Cieplak, P., Cornell, W.D. & Kollman, P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model. J. Phys. Chem. 97, 10269-10280.
• 18. Cheatham, T.E. & Kollman, P.A. (1997) Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119, 4805-4825.
• 19. Lavery, R. & Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91.
• 20. Bielecki, L., Kulinski, T. & Adamiak, R.W. (1999) Structure and dynamics of adenosine loops in RNA bulge duplexes. RNA hydration at the bulge site; in RNA Biochemistry and Biotechnology (Barciszewski, J. & Clark, B.F.C., eds.) pp. 73-87, NATO ASI Series, Kluwer Academic Publishers.
• 21. Young, M.A., Ravishanker, G., Beveridge, D.L. & Berman, H.M. (1995) Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68, 2454-2468.
• 22. Dickerson, R.E. (1998) DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906-1926.