Nucleic acid base pair open states by hydrogen exchange

Abstract

Nucleic acid base pair open states that are actively driven to expose normally hidden sequences and host reactions with processing proteins have been highly studied. However, the spontaneous natural base pair opening behavior of native duplexes is still not understood. Hydrogen exchange (HX) experiments can measure the kinetic and equilibrium parameters of base pair opening reactions, but different approaches have led to discrepant datasets and opposing views of nucleic acid structural dynamics. Here, I reexamine the data and resolve these long-standing contradictory views. The conclusion is that the seemingly contradictory datasets characterize two different modes of base pair opening reactions that, for identifiable reasons, are selectively accessed by the different methods and molecular models used. H-T exchange of DNA, duplex RNA, and long synthetic duplexes is dominated by large multi-base-pair openings with reclosing times of milliseconds (kcl ~20/sec) and surprisingly high population (Kop ~10 −2 ). H-H exchange measured by NMR relaxation is limited to the study of small rapidly tumbling oligonucleotides. Their HX is dominated by single base pair openings with reclosing times of microseconds and extremely low population (Kop ~10 −6 ). The different openings are seen selectively by the different methods because small oligonucleotides cannot host the extensive openings, while in large polynucleotides, the minimal population of single base pair openings makes no perceptible contribution to measured HX. The unexpected kinetics, equilibrium occupation, and size of DNA base pair openings are suggestive of rapidly migrating traveling loop wave packets known as solitons that dynamically scan and expose candidate recognition sites.