Structure of guanine octamers d(G)₈ determined by combination of VCD spectroscopy and theoretical computations

V. Andruchshenko¹, D. Tsankov², M. Krasteva³, H. Wieser³, and P. Bouř¹

¹Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Praha 6, Czech Republic

²Institute of Organic Chemistry, Bulgarian Academy of Sciences, BG-1113 Sofia, Bulgaria

³Department of Chemistry, University of Calgary, Calgary, AB , T2N 1N4, Canada

andrushchenko@uochb.cas.cz

Despite the vast amount of spectroscopic data available up to date, the solution structure of polynucleotides and oligonucleotides rich in guanine bases remains ambiguous. Different geometries have been proposed, ranging from single- to multiple-stranded arrangements depending on the experimental conditions [1-4]. Being relatively simple and widely available, IR spectroscopy is a convenient method to study the structural organization of nucleic acids in solutions. Later, a more sensitive chiroptical derivative of IR spectroscopy, vibrational circular dichroism (VCD), was successfully employed for such studies [1, 5]. However, the results obtained by these methods for polyG and similar systems significantly varied even at comparable experimental conditions. Fairly different IR and VCD spectra have been ascribed to four-stranded structures [1-4, 6, 7]. In some cases no explanation has been given for such discrepancies, while in the others the observed differences have been attributed to metastable polyG quadruplex structures [3, 4], or to a quadruplex-duplex transition [4].

To shed some light on the ambiguity exhibiting by the G-rich nucleic acid systems, we performed a combined experimental and computational study of the d(G)₈ octamer. Experimental IR and VCD spectra were measured for the octamer at standard conditions, used also in other studies devoted to G-quadruplexes. Theoretical IR and VCD spectra were calculated for single-, double- and quadruple-stranded d(G)₈ systems employing a multi-scale approach. The computational methodology included initial molecular dynamics (MD) simulations for each proposed structure, followed by ab initio calculations of force fields and atomic tensors for smaller fragments obtained from the octamers, and a subsequent transfer of those properties to the original octamers according to the Cartesian coordinate tensor (CCT) techniques [8]. On the basis of a comparison of the computed spectra with experiment the most probable structures could be determined.

References

1. A. Annamalai, T. A. Keiderling, J. Am. Chem. Soc., 109, (1987), 3125.

2. T. Xiang, D. J. Goss, M. Diem, Biophys. J., 65, (1993), 1255.

3. F. B. Howard, J. Frazier, H. T. Miles, Biopolymers, 16, (1977), 791.

4. A. G. Petrovic, P.L. Polavarapu, J. Phys. Chem. B, 112, (2008), 2245.

5. V. Andrushchenko, Y. Blagoi, J. H. van de Sande, H. Wieser, J. Biomol. Struct. Dyn., 19, (2002), 889.

6. M. R. Guzman, J. Liquier, S. K. Brahmachari, E. Taillandier, Spectrochim. Acta, Part A, 64, (2006), 495.

7. J. Nový, S. Bohm, J. Králová, V. Král, M. Urbanová, Biopolymers, 89, (2008), 144.

8. P. Bouř, J. Sopková, L. Bednárová, P. Maloň, T. A. Keiderling, J. Comput. Chem., 18, (1997), 646.

Acknowledgements.

This work was supported by the Grant Agency of the Czech Republic (grant P208/10/0559 (VA)), Grant Agency of the Academy of Sciences (grants A400550702 and M200550902 (PB)), and Natural Sciences and Engineering Research Council of Canada (NSERC) (HW).