Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Comparative Analysis of the Structural and Dynamical Characteristics of AT and GC Base-pair Sequences in DNA Molecule

For the better understanding of the physical mechanism of structure-functional organization of DNA molecule, studies of differences in structural-dynamic peculiarities of AT and GC sequences are important (1, 2). In this work, we analyzed three groups of data on studies of physical-chemical properties of AT and GC base-pair sequences.

The first group consisted of a set of optimization quantum-chemical conformational calculations to clarify the peculiarities of H-bonding geometry in single AT and GC nucleotide pairs and short oligonucleotide duplexes (3). They showed multiplicity of the forms of hydrogen bonding in AT and GC complementary pairing. Twofold structural polymorphism of AT pairs and fourfold polymorphism of GC pairs with dramatically substantial differences in geometry of H-bonding have been demonstrated.

Another was the group of data on quantum-chemical semi-empirical PM3 calculations of normal modes spectra of nucleotide pairs and of short oligonucleotide duplexes (4, 5). Analysis of harmonic frequencies showed quit definite differences in the intensities of normal modes in the middle- and high-frequency region of IR-spectra of these compounds, caused by differences in the geometry of packing of AT and GC pairs.

And the third group was the data obtained by the method of mathematical modeling of the internal DNA dynamics to study propagation of conformational distortions along long AT- and GC base-pair sequences (6, 7). Results of the analysis showed noticeable differences in dynamical characteristics, such as the size, velocity, energy, and life time of the distortions.

Comparing the differences found in the three groups permits us to suggest that the first group data, which showed heightened fourfold polymorphism of the complementary GC bases pairing, can be physical reason of the heightened lability of GC pairs in comparison with the lability of AT pairs when organizing double helix structure. As a consequence, the DNA secondary structure consisting preferably of GC pairs should experience a larger uncertainty in sequence dependence of the helix form, than the DNA-helixes consisting preferably of AT pairs. Thus, in accordance with this sign the heightened frequency of appearance of AT complementary nucleotide pairs in the cell genome looks evidently more preferable with respect to frequency of appearance of GC base pairs.

References and Footnotes
  1. J. D. Watson. Molecular Biology of the Gene. W. A. Benjamin, Inc. New York (1965).
  2. W. Saenger. Principles of Nucleic Acid Structure. Springer-Verlag, New York, Berlin, Heidelberg, Tokyo (1984).
  3. A. V. Kabanov, V. M. Komarov. Intern J Quant Chem 88, 579-587 (2002).
  4. A. V. Kabanov, V. M. Komarov, L. V. Yakushevich, A. V. Teplukhin. Intern J Quant Chem 100, 595-609 (2004).
  5. V. M. Komarov. J Biol Phys 24, 167-184 (1999).
  6. L. V. Yakushevich, L. A. Krasnobaeva, A. V. Shapovalov, N. R. Quintero. Biophysics 50, 404-409 (2005).
  7. N. A. Kovaleva, A. V. Savin, L. I. Manevich, A. V. Kabanov, V. M. Komarov, L. V. Yakushevich. Polymer Science 48-A, 278-293 (2006).

A. V. Kabanov1, *
V. M. Komarov1
L. A. Krasnobaeva2
L. V. Yakushevich1

1Institue of Cell Biophysics
Russian Academy of Sciences
Pushchino, Moscow Region, Russia
2Tomsk State University
Tomsk, Russia

*Phone: +7 4967 739 484
Fax: +7 4967 330 509
Email: kabanov@mail.ru