124D

STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE PURE RNA

Summary for 124D

• Entry DOI: 10.2210/pdb124d/pdb
• Descriptor: DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*G)-3'), RNA (5'-R(*CP*AP*UP*GP*UP*GP*AP*C)-3') (2 entities in total)
• Functional Keywords: dna-rna complex, double helix, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 4953.18

Authors

Fedoroff, O.Y.,Salazar, M.,Reid, B.R. (deposition date: 1993-05-07, release date: 1993-10-31, Last modification date: 2024-05-22)

Primary citation

Fedoroff, O.Y.,Salazar, M.,Reid, B.R.
Structure of a DNA:RNA Hybrid Duplex. Why Rnase H Does not Cleave Pure RNA
J.Mol.Biol., 233:509-523, 1993

PubMed Abstract: The solution structure of the DNA:RNA hybrid duplex d(GTCACATG):r(caugugac) has been determined by means of two-dimensional nuclear Overhauser effect (2D-NOE) spectra, restrained molecular dynamics and full-relaxation matrix stimulation of the 2D-NOE spectra. The DNA:RNA hybrid duplex assumes neither an A-form nor a B-form structure in solution, but an intermediate heteromerous duplex structure. The sugars of the RNA strand have a normal N-type C3'-endo conformation, but the DNA strand sugars have neither N-type nor S-type conformations; instead, they have an unexpected intermediate O4'-endo conformation. The negative x-displacement, as well as the small rise and positive inclination of the base-pairs, resembles A-form morphology but the minor groove width is intermediate between that of A-form and B-form duplexes. Both the DNA and RNA strands show prominent sequence-dependent variations in their helical parameters. Combined analysis of NOE and J-coupling data indicates that the DNA sugars are not in a dynamical two-state equilibrium. The detailed three-dimensional structure of this DNA:RNA hybrid molecule leads to a proposed model for its interaction with RNase H. Several specific structural features of the enzyme complexed with the hybrid duplex appear to explain the mechanism whereby RNase H discriminates between DNA:RNA hybrid duplexes and pure RNA:RNA duplexes.

PubMed: 8411159
DOI: 10.1006/jmbi.1993.1528

Experimental method

SOLUTION NMR