How does RNase H recognize a DNA.RNA hybrid?
- 15 December 1991
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 88 (24), 11535-11539
- https://doi.org/10.1073/pnas.88.24.11535
Abstract
The mechanism of RNase H substrate recognition is proposed from a model of a chemically modified DNA.RNA hybrid Escherichia coli RNase H complex. Site-directed mutagenesis of the enzyme and substrate titration observed by heteronuclear two-dimensional NMR spectra have been carried out. A model complex has been built, based on free structures of the enzyme and the substrate independently determined by x-ray crystallography and NMR distance geometry, respectively. In addition to steric and electrostatic complementarities between the molecular surfaces of the enzyme and the minor groove of the hybrid in the model, putative hydrogen bonds between the polar groups in the enzyme and 2'-oxygens of the RNA strand of the hybrid fix the hybrid close to the active site of the enzyme. The enzymatic activities of the mutant proteins and the changes in NMR spectra during the course of substrate titration are consistent with the present model. Moreover, the specific cleavage of the RNA strand in DNA.RNA hybrids can be explained as well as cleavage modes in modified heteroduplexes. A mechanism of enzymatic action is proposed.Keywords
This publication has 25 references indexed in Scilit:
- Assignments of backbone proton, carbon-13, and nitrogen-15 resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopyBiochemistry, 1991
- High-resolution NMR study of a synthetic DNA-RNA hybrid dodecamer containing the consensus Pribnow promoter sequence: d(CGTTATAATGCG).cntdot.r(CGCAUUAUAACG)Biochemistry, 1989
- Renaturase and ribonuclease H: a novel mechanism that influences transcript displacement by RNA polymerase II in vitroBiochemistry, 1988
- A solution structure for poly(rA).cntdot.poly(dT) with different furanose pucker and backbone geometry in rA and dT strands and intrastrand hydrogen bonding of adenine 8CHBiochemistry, 1988
- Influence of probe structure on unique (regiospecific) cleavage of RNA by RNase HFEBS Letters, 1988
- Sequence‐dependent hydrolysis of RNA using modified oligonucleotide splints and RNase HFEBS Letters, 1987
- Structure of the represser–operator complex of bacteriophage 434Nature, 1987
- Structure of the DNA-Eco RI Endonuclease Recognition Complex at 3 Å ResolutionScience, 1986
- DNA-RNA hybrid secondary structuresJournal of Molecular Biology, 1986
- Secondary structure of the hybrid poly(rA) · poly(dT) in solution: Studies involving NOE at 500 MHz and stereochemical modelling within the constraints of NOE dataJournal of Molecular Biology, 1985