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Nucleic Acids Research, 2003, Vol. 31, No. 15 4608-4615
© 2003 Oxford University Press

Controlling nucleic acid secondary structure by intercalation: effects of DNA strand length on coralyne-driven duplex disproportionation

Swapan S. Jain, Matjaz Polak and Nicholas V. Hud*

School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA

*To whom correspondence should be addressed. Tel: +1 404 385 1162; Fax: +1 404 894 2295; Email: hud{at}chemistry.gatech.edu
Present address:
Matjaz Polak, NMR Center, National Institute of Chemistry, Ljubljana, Slovenia

Small molecules that intercalate in DNA and RNA are powerful agents for controlling nucleic acid structural transitions. We recently demonstrated that coralyne, a small crescent-shaped molecule, can cause the complete and irreversible disproportionation of duplex poly(dA)·poly(dT) into triplex poly(dA)·poly(dT)·poly(dT) and a poly(dA) self- structure. Both DNA secondary structures that result from duplex disproportionation are stabilized by coralyne intercalation. In the present study, we show that the kinetics and thermodynamics of coralyne-driven duplex disproportionation strongly depend on oligonucleotide length. For example, disproportionation of duplex (dA)16·(dT)16 by coralyne reverts over the course of hours if the sample is maintained at 4°C. Coralyne-disproportioned (dA)32· (dT)32, on the other hand, only partially reverts to the duplex state over the course of days at the same temperature. Furthermore, the equilibrium state of a (dA)16·(dT)16 sample in the presence of coralyne at room temperature contains three different secondary structures [i.e. duplex, triplex and the (dA)16 self-structure]. Even the well-studied process of triplex stabilization by coralyne binding is found to be a length-dependent phenomenon and more complicated than previously appreciated. Together these observations indicate that at least one secondary structure in our nucleic acid system [i.e. duplex, triplex or (dA)n self-structure] binds coralyne in a length-dependent manner.


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