Although Watson-Crick base pairing is the most well-known arrangement in DNA structures, other non-canonical pairings exist given rise to interesting biological implications. Here we concentrate on Hoogsteen base pairing, which is widespread at a high level of abundance in cells(∼1%). Structurally, hoogsteen base pairs involve a 180-degree rotation of the purine base pair, resulting in alternative hydrogen bonding patterns as well as different minor and major groove signatures. The work of Al-Hashimi’s group in using nuclear magnetic resonance relaxation dispersion spectroscopy has raised awareness of transient Hoogsteen base pairing structures in DNA. This alternative pairing is not easily identified in x-ray structures, leading to the need to revisit structures deposited in the Protein Data Bank. Here, we use computational tools based on molecular dynamics to characterize the energy landscape and kinetic models of the transition between Watson Crick and Hoogsteen base pairing for a variety of sequences.

Exploring the Watson-Crick to Hoogsteen base pair flipping process through simulations

ACS Spring Meeting 2021

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