NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure
- 1 May 1990
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 29 (17), 4193-4204
- https://doi.org/10.1021/bi00469a024
Abstract
Until very recently interproton distances from NOESY experiments have been derived solely from the two-spin approximation method. Unfortunately, even at short mixing times, these distances. A complete relaxation matrix approach employing a matrix eigenvalue/eigenvector solution to the Block equations avoids the approximation of the two-spin method. We have calculated the structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d-(CGCAGAATTCGCG)2, by an iterative refinement approach using a hybrid relaxation matrix method combined with restrained molecular dynamics calculations. Distances from the 2D NOESY spectra have been calculated from the relaxation rate matrix which has been evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix derived distances have then been used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure is then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. Although the crystal structure of the tridecamer clearly shows the extrahelical adenosine looped out way from the duplex, the NOESY distance restrined hybrid matrix/molecular dynamics structural refinement establishes that the extrahelical adenosine stacks into the duplex.This publication has 15 references indexed in Scilit:
- Extrahelical adenosine stacks into right-handed DNA: solution conformation of the d(C-G-C-A-G-A-G-C-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectraBiochemistry, 1986
- Mechanism of oligonucleotide loop formation in solutionBiochemistry, 1986
- Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: Application to 5′ d(C-G-T-A-C-G)2Journal of Molecular Biology, 1986
- Phosphorus-31 and two-dimensional phosphorus-31/proton correlated NMR spectra of duplex d(Ap[17O]Gp[18O]Cp[16O]T) and assignment of phosphorus-31 signals in d(ApGpCpT)2-actinomycin D complexBiochemistry, 1984
- A two-dimensional NMR method for assignment of deoxyribose proton NMR signals in d(ApGpCpT)Biochemical and Biophysical Research Communications, 1984
- Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methodsJournal of Molecular Biology, 1983
- Unpaired cytosine in the deoxyoligonucleotide duplex dCA3CA3G.cntdot.dCT6G is outside of the helixBiochemistry, 1983
- Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteinsBiochemical and Biophysical Research Communications, 1983
- Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solutionBiochemistry, 1982
- THE ACCOMMODATION OF NONCOMPLEMENTARY BASES IN HELICAL POLYRIBONUCLEOTIDES AND DEOXYRIBONUCLEIC ACIDSProceedings of the National Academy of Sciences, 1960