THEORETICAL STUDY OF THE HOOGSTEEN <=> WATSON-CRICK JUNCTIONS IN DNA
Elena Cubero 1, F. Javier Luque 2 and Modesto Orozco 3*
1 IRBB-Parc Cientific de Barcelona
2 Facultat de Farmacia, Universitat de Barcelona
3 IRBB-PCB & Facultat de Química, Universitat de Barcelona
* To whom correspondence should be addressed. E-mail: modesto{at}mmb.pcb.ub.es.
Submitted on January 14, 2005
Revised on June 9, 2005
Accepted on 20 October 2005
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Abstract |
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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, since the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counter intuitively 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 which are specific of the antiparallel Hoogsteen conformation.
Key Words:
B/apH chimeric duplexes, Molecular Dynamic Simulation, Nucleic Acids, antiparallel Hoogsteen structures
