Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand.

ABSTRACT: Recent studies suggest noncoding RNAs interact with genomic DNA, forming an RNA•DNA-DNA triple helix that regulates gene expression. However, base triplet composition of pyrimidine motif RNA•DNA-DNA triple helices is not well understood beyond the canonical U•A-T and C•G-C base triplets. Using native gel-shift assays, the relative stability of 16 different base triplets at a single position, Z•X-Y (where Z = C, U, A, G and X-Y = A-T, G-C, T-A, C-G), in an RNA•DNA-DNA triple helix was determined. The canonical U•A-T and C•G-C base triplets were the most stable, while three non-canonical base triplets completely disrupted triple-helix formation. We further show that our RNA•DNA-DNA triple helix can tolerate up to two consecutive non-canonical A•G-C base triplets. Additionally, the RNA third

SUBMITTER: Kunkler CN 

PROVIDER: S-EPMC6698731 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature