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Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

E J Sambriski, V Ortiz and J J de Pablo

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The renaturation/denaturation of DNA oligonucleotides is characterized in the context of expanded ensemble (EXE) and transition path sampling (TPS) simulations. Free energy profiles have been determined from EXE for DNA sequences of varying composition, chain length, and ionic strength. TPS simulations within a Langevin dynamics formalism have been carried out to obtain further information of the transition state for renaturation. Simulation results reveal that free energy profiles are strikingly similar for the various DNA sequences considered in this work. Taking intact double-stranded DNA to have an extent of reaction ξ = 1.0, the maximum of the free energy profile appears at ξ≈0.15, corresponding to ~2 base pairs. In terms of chain length, the free energy barrier of longer oligonucleotides (30 versus 15 base pairs) is higher and slightly narrower, due to increased sharpness associated with the transition. Low ionic strength tends to decrease free energy barriers, whereby increasing strand rigidity facilitates reassociation. Two mechanisms for DNA reassociation emerge from our analysis of the transition state ensemble. Repetitive sequences tend to reassociate through a non-specific pathway involving molecular slithering. In contrast, random sequences associate through a more restrictive pathway involving the formation of specific contacts, which then leads to overall molecular zippering. In both random and repetitive sequences, the distribution of contacts suggests that nucleation is favored for sites located within the middle region of the chain. The prevalent extent of reaction for the transition state is ξ≈0.25, and the critical size of the nucleus as obtained from our analysis involves ~4 base pairs.


PACS

87.15.B- Structure of biomolecules

87.15.R- Reactions and kinetics

87.14.G- Nucleic acids

05.70.Ce Thermodynamic functions and equations of state

87.15.Vv Diffusion

82.39.Pj Nucleic acids, DNA and RNA bases

Subjects

Biological physics

Statistical physics and nonlinear systems

Chemical physics and physical chemistry

Dates

Issue 3 (21 January 2009)

Received 4 July 2008, in final form 28 August 2008

Published 17 December 2008



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