Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding

Ryan R. Davisy, Nadine M. Shaban, Fred W. Perrino, Thomas Hollis

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


RNA-DNA hybrids play essential roles in a variety of biological processes, including DNA replication, transcription, and viral integration. Ribonucleotides incorporated within DNA are hydrolyzed by RNase H enzymes in a removal process that is necessary for maintaining genomic stability. In order to understand the structural determinants involved in recognition of a hybrid substrate by RNase H we have determined the crystal structure of a dodecameric nonpolypurine/ polypyrimidine tract RNA-DNA duplex. A comparison to the same sequence bound to RNase H, reveals structural changes to the duplex that include widening of the major groove to 12.5 A from 4.2 Å and decreasing the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H. This structure allows a direct comparison to be made about the conformational changes induced in RNA-DNA hybrids upon binding to RNase H and may provide insight into how dysfunction in the endonuclease causes disease.

Original languageEnglish (US)
Pages (from-to)668-673
Number of pages6
JournalCell Cycle
Issue number4
StatePublished - Feb 15 2015

Bibliographical note

Funding Information:
This work was supported by funding from the NCI CCSG P30CA012197; the American Heart Association Grant 10GRNT3650033 (TH); and National Institutes of Health [Grant RO1 GM110734 (FWP) and RO1 GM108827 (TH)]. The funding sources had no role in the study design; in data collection; analysis and interpretation of the data; in writing the manuscript; or in the decision to submit for publication.


  • Conformational changes
  • Protein nucleic acid interaction
  • RNA-DNA hybrid
  • RNase H

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