jz9b02356_si_001.pdf (29.52 MB)
Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes
journal contribution
posted on 2019-10-18, 17:45 authored by Shiyan Xiao, Daniel J. Sharpe, Debayan Chakraborty, David J. WalesStrand
hybridization is not only a fundamental molecular mechanism
underlying the biological functions of nucleic acids but is also a
key step in the design of efficient nanodevices. Despite recent efforts,
the microscopic rules governing the hybridization mechanisms remain
largely unknown. In this study, we exploit the energy landscape framework
to assess how sequence-specificity modulates the hybridization mechanisms
in DNA. We find that GG-tracts hybridize much more rapidly compared
to GC-tracts, via either zippering or slithering pathways. For the
hybridization of GG-tracts, both zippering and slithering mechanisms
appear to be kinetically relevant. In contrast, for the GC-tracts,
the zippering mechanism is dominant. Our work reveals that even for
the relatively small systems considered, the energy landscapes feature
multiple metastable states and kinetic traps, which is at odds with
the conventional “all-or-nothing” model of DNA hybridization
formulated on the basis of thermodynamic arguments alone. Interestingly,
entropic effects are found to play an important role in determining
the thermal stability of competing conformational ensembles and in
determining the preferred hybridization pathways.