H. M. Al-Hashimi

Direct Measurement of 8OG syn-anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics Using 1H CEST NMR

This paper measures 8OG syn-anti flips and Hoogsteen breathing dynamics in damaged DNA using 1H CEST NMR, revealing their impact on DNA conformation and repair.

RNA conformational propensities determine cellular activity

The paper alters and measures conformational propensities of HIV-1 TAR RNA to predict binding affinities and cellular activity.

Measuring thermodynamic preferences to form non-native conformations in nucleic acids using melting experiments reveals a rich sequence-specific DNA conformational landscape

This paper introduces delta-melt, a method using chemical modifications and melting experiments to measure thermodynamic preferences for non-native DNA conformations, revealing sequence-specific variations in conformational stability.

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

The paper shows m6A modification slows nucleic acid hybridization by altering conformational dynamics through isomerization pathways.

Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage

This study shows that Hoogsteen base pairs in dsDNA increase susceptibility to methylation damage, challenging the assumption that Watson-Crick faces are fully protected.

An RNA dynamic ensemble at atomic resolution

This study determines an atomic-resolution RNA ensemble for HIV-1 TAR using structure prediction and NMR refinement, revealing cooperative conformational changes.

Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

This study examines the non-specific binding of three drug-like compounds to HIV-1 stem-loop RNAs, showing they inhibit RNA function and exhibit off-target interactions.

Probing RNA conformational equilibria within the functional cellular context

The paper develops a method to assess RNA excited-state stability and abundance in cells using mutations and applies it to HIV-1 regulatory RNAs, showing ESs form with comparable abundance in vitro and in vivo.

DNA mismatches reveal widespread conformational penalties in protein-DNA recognition

The paper uses a novel assay to show that DNA mismatches can increase TF binding, revealing conformational penalties as a key factor in protein-DNA recognition.

Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev binding site

The paper identifies non-native conformations in HIV-1 RRE stem IIB that disrupt Rev binding and are potential targets for anti-HIV therapeutics.

High Performance Virtual Screening by Targeting a High-resolution RNA Dynamic Ensemble

The paper evaluates ensemble-based virtual screening for RNA targets using a high-resolution TAR RNA ensemble and shows improved accuracy over single-structure docking.