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Title: Crystal structure of an RNA/DNA strand exchange junction
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-5′/DNA-3′ 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.
Authors:
; ; ;
Editors:
Kursula, Petri
Award ID(s):
1817593
Publication Date:
NSF-PAR ID:
10343312
Journal Name:
PLOS ONE
Volume:
17
Issue:
4
Page Range or eLocation-ID:
e0263547
ISSN:
1932-6203
Sponsoring Org:
National Science Foundation
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