Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.

Journal Article (Journal Article)

Hoogsteen (HG) base pairing involves a 180° rotation of the purine base relative to Watson-Crick (WC) base pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction and replication. Here, using nuclear magnetic resonance R1ρ relaxation dispersion, we show that transient HG base pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in HG base pair energetic stabilities that are comparable with variations in WC base pair stability, with HG base pairs being more abundant for energetically less favourable WC base pairs. Our results suggest that the variations in HG stabilities and rates of formation are dominated by variations in WC base pair stability, suggesting a late transition state for the WC-to-HG conformational switch. The occurrence of sequence and position-dependent HG base pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions.

Full Text

Duke Authors

Cited Authors

  • Alvey, HS; Gottardo, FL; Nikolova, EN; Al-Hashimi, HM

Published Date

  • September 4, 2014

Published In

Volume / Issue

  • 5 /

Start / End Page

  • 4786 -

PubMed ID

  • 25185517

Pubmed Central ID

  • PMC4537320

Electronic International Standard Serial Number (EISSN)

  • 2041-1723

Digital Object Identifier (DOI)

  • 10.1038/ncomms5786


  • eng

Conference Location

  • England