Density Functional Study of the Structure of Guanine Octets in Aqueous Medium

Mykola M. Ilchenko(1*), Igor Ya. Dubey(2)

(1) Institute of Molecular Biology and Genetics, National Academy of Sciences, 150 Zabolotnogo str., 03680 Kyiv, Ukraine, Ukraine
(2) Institute of Molecular Biology and Genetics, National Academy of Sciences, 150 Zabolotnogo str., 03680 Kyiv, Ukraine, Ukraine
(*) Corresponding author

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The structures and energies of guanine quartets and octets in water were determined by DFT (Density Functional Theory) calculations using M06-2X functional and 6-31G(d, p) basic set. Guanine quartets in vacuum were found to have not only the Hoogsteen or bifurcated, but also mixed system of hydrogen bonds; in water the latter two forms are transformed into the classic Hoogsteen-type structure. Four stable configurations of G-octets with D4, C4 and S4 symmetry formed by the pairs of guanine quartets with Hoogsteen, bifurcated or mixed system of H-bonds were identified. The most advantageous structure of the G-octet molecular system in aqueous medium was shown to be S4-symmetric structure consisting of the pair of mixed Hoogsteen-bifurcated type G-quartets
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DFT; G-Octets; G-Quartets; Guanine; H-Bonds

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H. J. Lipps, D. Rhodes, G-Quadruplex Structures: In Vivo Evidence and Function, Trends in Cell Biology, Volume 19, (Issue 8), August 2009, Pages 414-422.

Y. Wu, R. M. Brosh Jr., G-Quadruplex Nucleic Acids and Human Disease, FEBS Journal, Volume 277, (Issue 17), September 2010, Pages 3470-3488.

A. De Cian, L. Lacroix, C. Douarre, N. Temime-Smaali, C. Trentesaux, J.-F. Riou, J.-L. Mergny, Targeting Telomeres and Telomerase, Biochimie, Volume 90, (Issue 1), January 2008, Pages 131-155.

S. Neidle, Human Telomeric G-Quadruplex: The Current Status of Telomeric G-Quadruplexes as Therapeutic Targets in Human Cancer, FEBS Journal, Volume 277, (Issue 5), March 2010, Pages 1118-1125.

J. L.-Y. Chen, J. Sperry, N.Y. Ip, M.A. Brimble, Natural Products Targeting Telomere Maintenance, MedChemComm, Volume 2, (Issue 4), April 2011, Pages 229-245.

J. Gu, J. Leszczynski, M. Bansal, A New Insight into the Structure and Stability of Hoogsteen Hydrogen-Bonded G-Tetrad: an Ab Initio SCF Study, Chemical Physics Letters, V. 311, (Issue 3-4), September 1999, Pages 209-214.

M. Meyer, T. Steinke, M. Brandl, J. Sühnel, Density Functional Study of Guanine and Uracil Quartets and of Guanine Quartet/Metal Ion Complexes, Journal of Computational Chemistry, Volume 22, (Issue 1), January 2001, Pages 109-124.

T. van Mourik, A.J. Dingley, Characterization of the Monovalent Ion Position and Hydrogen-Bond Network in Guanine Quartets by DFT Calculations of NMR Parameters, Chemistry – A European Journal, Volume 11, (Issue 20), October 2005, Pages 6064-6079.

S. Mezzache, S. Alves, J.-P. Paumard, C. Pepe, J.-C. Tabet, Theoretical and Gas-Phase Studies of Specific Cationized Purine Base Quartet, Rapid Communications in Mass Spectrometry, Volume 21, (Issue 6), March 2007, Pages 1075-1082.

F. Meng, F. Wang, X. Zhao, A.F. Jalbout, Guanine Tetrad Interacting With Divalent Metal Ions (M = Fe2+, Co2+, Ni2+, Cu2+ and Zn 2+): A Density Functional Study, Journal of Molecular Structure: THEOCHEM, Volume 854, (Issue 1-3), April 2008, Pages 26-30.

C.F. Guerra, T. van der Wijst, J. Poater, M. Swart, F.M. Bickelhaupt, Adenine Versus Guanine Quartets in Aqueous Solution: Corrected DFT Study on the Differences in -Staking and Hydrogen-Bond Behavior, Theoretical Chemistry Accounts, Volume 125, (Issue 3-6), March 2010, Pages 245-252.

H. Liu, J.W. Gauld, Protonation of Guanine Quartets and Quartet Stacks: Insights from DFT Studies, Physical Chemistry Chemical Physics., Volume 11, (Issue 2), January 2009, Pages 278-287.

M. Meyer, T. Steinke, J. Sühnel, Density Functional Study of Isoguanine Tetrad and Pentad Sandwich Complexes With Alkali Metal Ions, Journal of Molecular Modeling, Volume 13, (Issue 2), February 2007, Pages 335-345.

J. Gu, J. Wang, J. Leszczynski, Isoguanine Octamer: From Bowl to Ball, Chemical Physics Letters, Volume 445, (Issue 4-6), September 2007, Pages 243-245.

Y. Zhao, D.G. Truhlar, Comparative DFT Study of van der Waals Complexes: Rare-Gas Dimers, Alkaline-Earth Dimers, Zinc Dimer, and Zinc-Rare-Gas Dimers, Journal of Physical Chemistry A, Volume 110, (Issue 15), March 2006, Pages 5121-5129.

Barone, M. Cossi, Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model, Journal of Physical Chemistry A, Volume 102, (Issue 11), February 1998, Pages 1995-2001.

Barone, M. Cossi, J. Tomasi, Geometry Optimization of Molecular Structures in Solution by the Polarizable Continuum Model, Journal of Computational Chemistry, Volume 19, (Issue 4), March 1998, Pages 404-417.

M. Cossi, G. Scalmani, N. Rega, V. Barone, New Developments in the Polarizable Continuum Model for Quantum Mechanical and Classical Calculations on Molecules in Solution, Journal of Chemical Physics, Volume 117, (Issue 1), July 2002, Pages 43-54.

Y. Zhao, D.G. Truhlar, The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, Theoretical Chemistry Accounts, Volume 120, (Issue 1-3), May 2008, Pages 215-241.

S. Grimme, Density Functional Theory with London Dispersion Corrections, Wiley Interdisciplinary Reviews: Computational Molecular Science, Volume 1, (Issue 2), March/April 2011, Pages 211-228.

E.G. Hohenstein, S.T. Chill, C.D. Sherrill, Assessment of the Performance of the M05-2X and M06-2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules, Journal of Chemical Theory and Computation, Volume 4, (Issue 12), December 2008, Pages 1996-2000.

M. Liu, M. Xu, J.K. Lee. The Acidity and Proton Affinity of the Damaged Base 1,N6-Ethenoadenine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications, Journal of Organic Chemistry, Volume 73, (Issue 15), August 2008, Pages 5907-5914.

Andrushchenko, H. Wieser, P. Bour, DNA Oligonucleotide-cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra, Journal of Physical Chemistry A, Volume 111, (Issue 39), October 2007, Pages 9714-9723.

Y. Paukku, G. Hill, Theoretical Determination of One-Electron Redox Potentials for DNA Bases, Base Pairs, and Stacks, Journal of Physical Chemistry A, Volume 115, (Issue 18), May 2011, Pages 4804-4810.

F.P. Pineda, J. Ortega-Castro, J.R. Alvarez-Idaboy, J. Frau, B.M. Cabrera, J.C. Ramrez, J. Donoso, F. Muoz, Hydrolysis of a Chlorambucil Analogue. A DFT Study, Journal of Physical Chemistry A, Volume 115, (Issue 11), March 2011, Pages 2359-2366.

V. Setnicka, J. Novy, S. Bohm, N. Sreenivasachary, M. Urbanova, K. Volka, Molecular Structure of Guanine-Quartet Supramolecular Assemblies in a Gel-State Based on a DFT Calculation of Infrared and Vibrational Circular Dichroism Spectra, Langmuir, Volume 24, (Issue 14), July 2008, Pages 7520-7527.


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