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Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2′-fluoro-ANA/RNA and DNA/RNA hybrids

Oxford University Press
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  • Article
  • Medicine


Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Peter Yakovchuk, Ekaterina Protozanova and Maxim D. Frank-Kamenetskii* Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA Received October 28, 2005; Revised and Accepted January 4, 2006 ABSTRACT Two factors are mainly responsible for the stability of the DNA double helix: base pairing between com- plementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking paramet- ers are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na1. From stacking parameters of individual contacts, we calculate base-stacking con- tribution to the stability of A�T- and G�C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA sta- bility parameters. For all temperatures and salt con- centrationsemployed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A�T pairing is always destabilizing and G�C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence. INTRODUCTION Stability of the DNA double helix with respect to separation of complementary strands is known to depend on the base com- position of the duplex (1–4). A classical study of Marmur and Doty (1) on DNA polymer stability gives a linear relationship between the G�C content of the polymer and its melting tem- perature. The simplest explan

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