Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion

A Rangadurai, ES Szymaski, IJ Kimsey, H Shi… - Progress in nuclear …, 2019 - Elsevier
This review describes off-resonance R 1ρ relaxation dispersion NMR methods for
characterizing microsecond-to-millisecond chemical exchange in uniformly 13 C/15 N …

DNA mismatches reveal conformational penalties in protein–DNA recognition

A Afek, H Shi, A Rangadurai, H Sahay, A Senitzki… - Nature, 2020 - nature.com
Transcription factors recognize specific genomic sequences to regulate complex gene-
expression programs. Although it is well-established that transcription factors bind to specific …

Structural insights into tautomeric dynamics in nucleic acids and in antiviral nucleoside analogs

BI Fedeles, D Li, V Singh - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
DNA (2′-deoxyribonucleic acid) and RNA (ribonucleic acid) play diverse functional roles in
biology and disease. Despite being comprised primarily of only four cognate nucleobases …

Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

H Shi, A Rangadurai, H Abou Assi, R Roy… - Nature …, 2020 - nature.com
Biomolecules form dynamic ensembles of many inter-converting conformations which are
key for understanding how they fold and function. However, determining ensembles is …

High-order quantum-mechanical analysis of hydrogen bonding in hachimoji and natural DNA base pairs

RL Kumawat, CD Sherrill - Journal of Chemical Information and …, 2023 - ACS Publications
High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase
pairs [adenine: thymine (A: T) and guanine: cytosine (G: C)] and non-natural Hachimoji …

A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions

B Liu, H Shi, A Rangadurai, F Nussbaumer… - Nature …, 2021 - nature.com
ABSTRACT N 6-methyladenosine (m6A) is a post-transcriptional modification that controls
gene expression by recruiting proteins to RNA sites. The modification also slows …

Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy

DW Conroy, Y Xu, H Shi… - Proceedings of the …, 2022 - National Acad Sciences
The majority of base pairs in double-stranded DNA exist in the canonical Watson-Crick
geometry. However, they can also adopt alternate Hoogsteen conformations in various …

1-Deazaguanosine-modified RNA: The missing piece for functional RNA atomic mutagenesis

R Bereiter, E Renard, K Breuker, C Kreutz… - Journal of the …, 2022 - ACS Publications
Atomic mutagenesis is the key to advance our understanding of RNA recognition and RNA
catalysis. To this end, deazanucleosides are utilized to evaluate the participation of specific …

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R relaxation dispersion

A Rangadurai, ES Szymanski, I Kimsey, H Shi… - Journal of Biomolecular …, 2020 - Springer
NMR off-resonance R 1ρ relaxation dispersion measurements on base carbon and nitrogen
nuclei have revealed that wobble G· T/U mismatches in DNA and RNA duplexes exist in …

Application of FTIR spectroscopy to analyze RNA structure

F Geinguenaud, V Militello, V Arluison - RNA Spectroscopy: Methods and …, 2020 - Springer
Fourier transform infrared (FTIR) spectroscopy has been widely used for the analysis of both
protein and nucleic acid secondary structure. This is one of the vibration spectroscopy …