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Multiple Routes to Characterize the Folding of a Small DNA Hairpin

Authors

  • Guillem Portella,

    1. Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB), Josep Samitier 1-5, Barcelona 08028 (Spain)
    2. Barcelona Supercomputing Centre (BSC), Jordi Girona 29, Barcelona 08034 (Spain)
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  • Modesto Orozco

    1. Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB), Josep Samitier 1-5, Barcelona 08028 (Spain)
    2. Barcelona Supercomputing Centre (BSC), Jordi Girona 29, Barcelona 08034 (Spain)
    3. Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028 (Spain)
    4. National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1–5, Barcelona 08028 (Spain)
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  • We are indebted to the computer resources provided by the Barcelona Supercomputing Center. This work was supported by BIO2009-10964, Consolider E-science and COMBIOMED ISCIII projects, and the Fundación Marcelino Botin. The authors thank Profs. F. J. Luque and V. Muñoz for critical comments.

Abstract

original image

DNA perming: Folding of a small DNA hairpin from an extended conformation follows two main folding pathways: direct folding (green arrows) and de-trapping from non-native compact structures (red arrows). (Also shown: guanosine 5′G anti form.)

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