Crystal structure of an RNA/DNA strand exchange junction

Joshua C. Cofsky, Gavin J. Knott, Christine L. Gee, Jennifer A. Doudna

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)

Abstract

Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types-an RNA: DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-50/DNA-30 strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.

Original languageEnglish
Article numbere0263547
Number of pages15
JournalPLoS ONE
Volume17
Issue number4
DOIs
Publication statusPublished - Apr 2022

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