DNA complexes containing joined triplex and duplex motifs: melting behavior of intramolecular and bimolecular complexes with similar sequences

The Journal of Physical Chemistry. B
Hui-Ting LeeLuis A Marky

Abstract

Our laboratory is interested in predicting the thermal stability and melting behavior of nucleic acids from knowledge of their sequence. One focus is to understand how sequence, duplex and triplex stabilities, and solution conditions affect the melting behavior of complex DNA structures, such as intramolecular DNA complexes containing triplex and duplex motifs. Nucleic acid oligonucleotides (ODNs), as drugs, present an exquisite selectivity and affinity that can be used in antigene and antisense strategies for the control of gene expression. In this work, we try to answer the following question: How does the molecularity of a DNA complex affect its overall stability and melting behavior? We used a combination of temperature-dependent UV spectroscopy and calorimetric (DSC) techniques to investigate the melting behavior of DNA complexes with a similar helical stem sequence, TC(+)TC(+)TC(+)T/AGAGAGACGCG/CGCGTCTCTCT, but formed with different strand molecularity. We determined standard thermodynamic profiles, and the differential binding of protons and counterions accompanying their unfolding. The formation of a DNA complex is accompanied by a favorable free energy term resulting from the typical compensation of favorable enthalpy-...Continue Reading

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Citations

May 7, 2011·Analytical and Bioanalytical Chemistry·Mayurbhai PatelHaidong Huang
Feb 18, 2017·International Journal of Molecular Sciences·Václav Brázda, Jan Coufal
Nov 2, 2014·Chemical Communications : Chem Comm·Haidong Huang, Peter C Tlatelpa
Jul 19, 2012·Biopolymers·Chun-Ling ChangChin-Kun Hu
Jul 6, 2013·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Yuhao Du, Xiang Zhou
Feb 18, 2011·Journal of Biochemistry·Nikolai Vekshin
Feb 2, 2013·Chemical Communications : Chem Comm·Yan YuCheng Zhi Huang
Apr 29, 2011·RNA Biology·Fabian A BuskeTimothy L Bailey
Feb 2, 2018·Physical Chemistry Chemical Physics : PCCP·Carolyn E Carr, Luis A Marky
Aug 10, 2017·Biophysical Journal·Carolyn E Carr, Luis A Marky
Feb 22, 2013·The Journal of Physical Chemistry. B·Gennady V PalamarchukJerzy Leszczynski
Jan 15, 2015·The Journal of Physical Chemistry. B·Calliste ReilingLuis A Marky
Jul 29, 2011·Analytical Chemistry·Jing ZhengWeihong Tan
Sep 19, 2017·Journal of the American Chemical Society·Carolyn E Carr, Luis A Marky

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