title: Bubbles in DNA melting.
abstract: This paper presents a review of largely our own work on the DNA melting transition, and some new measurements of the elastic energy of sharp bends in single-stranded DNA and RNA. The purpose is to present the point of view that studying the transition of intermediate size oligomers leads to valuable tests of the models, in particular the ingredients most important for a reduced-degrees-of-freedom description, such as the different role of base pairing and base stacking. We make the case that, with intermediate size oligomers, one can actually measure the bubble length, which exhibits a more interesting behavior than the fraction of dissociated bases alone. Here is where more work seems necessary, both on the experimental and the modeling side, to understand the differences between theory and experiments. We summarize our previous results on the cooperativity parameters, which suggest that the transition is never exactly two-state no matter how short the molecule, or in other words the nucleation size for bubbles opening at the ends of the molecule is essentially 1 base pair. We briefly discuss our own modification of the nearest-neighbor model which treats pairing and stacking separately, as a way to fit the experimental melting profiles in this intermediate length regime. Finally we go on to present some new measurements on the stability of DNA and RNA hairpins with very short loops.
authors.affiliation: Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547, USA.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Gonzalez
authors.forename: Yan
authors.initials: Y
authors.lastname: Zeng
authors.forename: Vassili
authors.initials: V
authors.lastname: Ivanov
authors.forename: Giovanni
authors.initials: G
authors.lastname: Zocchi