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Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

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Abstract

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

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Acknowledgments

The authors are thankful to DST, New Delhi for computational facility in the form of FIST scheme. We thankfully acknowledge the partial computational work at BRAF of C-DAC, Pune, India. KDD acknowledges CSIR for senior research fellowship.

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  1. Biophysics Unit, Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, Uttar Pradesh, India

    Amit Kumar Chaubey, Kshatresh Dutta Dubey & Rajendra Prasad Ojha

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  1. Amit Kumar Chaubey
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  2. Kshatresh Dutta Dubey
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  3. Rajendra Prasad Ojha
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Correspondence to Rajendra Prasad Ojha.

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Chaubey, A.K., Dubey, K.D. & Ojha, R.P. Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study. J Comput Aided Mol Des 26, 289–299 (2012). https://doi.org/10.1007/s10822-012-9548-z

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