AVS 52nd International Symposium
    DNA Topical Conference Monday Sessions
       Session DN-MoP

Paper DN-MoP7
Secondary Structure Effects on DNA Hybridization in Solution and on Surfaces

Monday, October 31, 2005, 5:00 pm, Room Exhibit Hall C&D

Session: DNA Poster Session
Presenter: Y. Gao, Boston University
Authors: Y. Gao, Boston University
L.K. Wolf, Boston University
R.M. Georgiadis, Boston University
Correspondent: Click to Email
The hybridization process in which a DNA probe strand binds to its complementary target, is the basis of many biological assays. For short oligonucleotides in solution, secondary structure effects on duplex formation kinetics are well known. In contrast, these effects are less understood for surface interactions and some recent work concludes that hybridization at surfaces is not affected by secondary structure. In this work, the effect of secondary structure on DNA hybridization is studied systematically by UV-vis and surface plasmon resonance (SPR) in solution and on the surface, respectively. Hybridization kinetics were measured for thermodynamically equivalent sequences with varying degrees of single-stranded secondary structure. Our results indicate that duplex hybridization in solution is always one or two orders of magnitude faster than hybridization on the surface, depending on the extent of secondary structure. In addition, we find a direct relationship between the number of base pairs involved in secondary structure and the observed association kinetic rate constants in both environments. On the surface, secondary structure also affects hybridization efficiency. DNA sequences lacking secondary structure achieve equivalent hybridization efficiencies regardless of bulk solution ionic strength. However, as ionic strength is reduced, sequences with secondary structure achieve drastically reduced efficiencies. The binding equilibrium is affected because of the competition between duplex formation and single-strand unfolding.