New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey

H Zhou, BJ Hintze, IJ Kimsey… - Nucleic acids …, 2015 - academic.oup.com
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson–Crick
(WC) bps and can play unique functional roles in duplex DNA. Here, we use structural …

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

HS Alvey, FL Gottardo, EN Nikolova… - Nature …, 2014 - nature.com
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 …

Revealing AT and GC Hoogsteen base pairs in stressed protein-bound duplex DNA

H Shi, IJ Kimsey, S Gu, HF Liu, U Pham… - Nucleic acids …, 2021 - academic.oup.com
Watson–Crick base pairs (bps) are the fundamental unit of genetic information and the
building blocks of the DNA double helix. However, AT and GC can also form alternative …

A historical account of hoogsteen base‐pairs in duplex DNA

EN Nikolova, H Zhou, FL Gottardo, HS Alvey… - …, 2013 - Wiley Online Library
In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6
on adenine was proposed to explain how poly (rU) strands can associate with poly (rA)‐poly …

Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution

EN Nikolova, FL Gottardo… - Journal of the American …, 2012 - ACS Publications
Nucleic acids transiently morph into alternative conformations that can be difficult to
characterize at the atomic level by conventional methods because they exist for too little time …

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

H Shi, MC Clay, A Rangadurai… - Journal of biomolecular …, 2018 - Springer
NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson–Crick
base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state …

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

C Yang, E Kim, Y Pak - Nucleic acids research, 2015 - academic.oup.com
Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small
ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair …

Transient Hoogsteen base pairs in canonical duplex DNA

EN Nikolova, E Kim, AA Wise, PJ O'Brien, I Andricioaei… - Nature, 2011 - nature.com
Sequence-directed variations in the canonical DNA double helix structure that retain Watson–
Crick base-pairing have important roles in DNA recognition, topology and nucleosome …

Sequence dependence of transient Hoogsteen base pairing in DNA

A Pérez de Alba Ortíz, J Vreede… - PLoS computational …, 2022 - journals.plos.org
Hoogsteen (HG) base pairing is characterized by a 180° rotation of the purine base with
respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both …

Characterizing the protonation state of cytosine in transient G· C Hoogsteen base pairs in duplex DNA

EN Nikolova, GB Goh, CL Brooks III… - Journal of the …, 2013 - ACS Publications
G· C Hoogsteen base pairs can form transiently in duplex DNA and play important roles in
DNA recognition, replication, and repair. G· C Hoogsteen base pairs are thought to be …