Conformation and dynamics of the Pribnow box region of the self-complementary d(C-G-A-T-T-A-T-A-A-T-C-G) duplex in solution

Publisher Website
Google Scholar
Abstract
NMR was used to monitor the conformation and dynamics of the d(C1-G2-A3-T4-T5-A6-T6-A5-A4-T3-C2-G1) self-complementary dodecanuclotide duplex (henceforth called Pribnow 12-mer), which contains a TATAAT Pribnow box and a central core of 8 dA.cntdot.dT base pairs. The exchangeable imino and nonexchangeable base protons were assigned from 1-dimensional intra and inter base pair nuclear Overhauser effect (NOE) measurements. Premelting conformational changes are observed at all the dA.cntdot.dT base pairs in the central octanucleotide core in the Pribnow 12-mer duplex with the duplex to strand transition occurring at 55.degree. C in 0.1 M phosphate solution. The magnitude of the NOE measurements between minor groove H-2 protons of adjacent adenosines demonstrates that the base pairs are propeller twisted with the same handedness as observed in the crystalline state. The thymidine imino proton hydrogen exchange at the dA.cntdot.dT base pairs was measured from saturation recovery measurements as a function of temperature. The exchange rates and activation barriers show small variations among the 4 different dA.cntdot.dT base pairs in the Pribnow 12-mer duplex. The thymidine imino proton exchange rates for the TATAAT Pribnow box in the d(C-G-A-T-T-A-T-A-A-T-C-G) duplex are of similar magnitude to those observed for the TATA box in the d(C-G-C-G-T-A-T-A-C-G-C-G) duplex at 30.degree. C but are a factor of .apprx. 3-5 faster than those observed for the AATT segment in the d(C-G-C-G-A-A-T-T-C-G-C-G) duplex at the same temperature. The thymidine imino proton exchange rates in the Pribnow 12-mer are sensitive to basic pH, which suggests that both rate-limiting helix opening and preequilibrium pathways contribute to the hydrogen exchange in the central dA.cntdot.dT octanucleotide core of the Pribnow 12-mer duplex in solution.