title: Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton.
abstract: Using nuclear magnetic resonance line broadening, longitudinal relaxation and magnetization transfer from water, we have measured the imino proton exchange times in the duplex form of the 10-mer d-CGCGATCGCG and in seven other deoxy-duplexes, as a function of the concentration of exchange catalysts, principally ammonia. All exchange times are catalyst dependent. Base-pair lifetimes are obtained by extrapolation to infinite concentration of ammonia. Lifetimes of internal base-pairs are in the range of milliseconds at 35 degrees C and ten times more at 0 degrees C. Lifetimes of neighboring pairs are different, hence base-pairs open one at a time. Lifetimes of d(G.C) are about three times longer than those of d(A.T). The nature of neighbors usually has little effect, but lifetime anomalies that may be related to sequence and/or structure have been observed. In contrast, there is no anomaly in the A.T base-pair lifetimes of d-CGCGA[TA]5TCGCG, a model duplex of poly[d(A-T)].poly[d(A-T)]. The d(A.T) lifetimes are comparable to those of r(A.U) that we reported previously. End effects on base-pair lifetimes are limited to two base-pairs. The low efficiency of exchange catalysts is ascribed to the small dissociation constant of the deoxy base-pairs, and helps to explain why exchange catalysis had been overlooked in the past. This resulted in a hundredfold overestimation of base-pair lifetimes. Cytosine amino proteins have been studied in the duplex of d-CGm5CGCG. Exchange from the closed base-pair is indicated. Hence, the use of an amino exchange rate to evaluate the base-pair dissociation constant would result in erroneous, overestimated values. Catalyzed imino proton exchange is at this time the safest and most powerful, if not the only probe of base-pair kinetics. We propose that the single base-pair opening event characterized here may be the only mode of base-pair disruption, at temperatures well below the melting transition.
authors.affiliation: Groupe de Biophysique, Ecole Polytechnique, Palaiseau, France.
authors.forename: J L
authors.initials: JL
authors.lastname: Leroy
authors.forename: M
authors.initials: M
authors.lastname: Kochoyan
authors.forename: T
authors.initials: T
authors.lastname: Huynh-Dinh
authors.forename: M
authors.initials: M
authors.lastname: Guéron
mesh_terms: D001482:Base Composition; D003854:Deoxyribonucleotides; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D011522:Protons; D013696:Temperature; D013816:Thermodynamics
chemical_list: D003854:Deoxyribonucleotides; D011522:Protons