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Originally published as Biophys J. BioFAST on November 11, 2005.
doi:10.1529/biophysj.105.059535
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Biophysical Journal 90:1000-1008 (2006)
© 2006 The Biophysical Society

Theoretical Study of the Hoogsteen–Watson-Crick Junctions in DNA

Elena Cubero *, F. Javier Luque {dagger} and Modesto Orozco * {ddagger}

* Molecular Modelling & Bioinformatic Unit, Institut de Recerca Biomèdica-Parc Científic de Barcelona, Barcelona 08028, Spain; and {dagger} Departament de Fisicoquímica, Facultat de Farmacia, and {ddagger} Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Barcelona 08028, Spain

Correspondence: Address reprint requests to M. Orozco, E-mail: modesto{at}mmb.pcb.ub.es or F. J. Luque, E-mail: javier{at}far1.far.ub.es.

A series of d (AT)n oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation.






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Copyright © 2006 by the Biophysical Society.