H. M. Al-Hashimi

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

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.

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

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

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

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.

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.

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.

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

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.