RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion
This review describes off-resonance R 1ρ relaxation dispersion NMR methods for
characterizing microsecond-to-millisecond chemical exchange in uniformly 13 C/15 N …
characterizing microsecond-to-millisecond chemical exchange in uniformly 13 C/15 N …
Conformational plasticity of parallel G-quadruplex─ implications on duplex–Quadruplex motifs
RKR Sannapureddi, MK Mohanty… - Journal of the …, 2023 - ACS Publications
DNA G-quadruplexes are essential motifs in molecular biology performing a wide range of
functions enabled by their unique and diverse structures. In this study, we focus on the …
functions enabled by their unique and diverse structures. In this study, we focus on the …
m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
The B-DNA double helix can dynamically accommodate GC and AT base pairs in either
Watson–Crick or Hoogsteen configurations. Here, we show that G-C+ (in which+ indicates …
Watson–Crick or Hoogsteen configurations. Here, we show that G-C+ (in which+ indicates …
Kinetic resolution of the atomic 3D structures formed by ground and excited conformational states in an RNA dynamic ensemble
Knowing the 3D structures formed by the various conformations populating the RNA free-
energy landscape, their relative abundance, and kinetic interconversion rates is required to …
energy landscape, their relative abundance, and kinetic interconversion rates is required to …
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction
Biomolecules form dynamic ensembles of many inter-converting conformations which are
key for understanding how they fold and function. However, determining ensembles is …
key for understanding how they fold and function. However, determining ensembles is …
High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble
Dynamic ensembles hold great promise in advancing RNA-targeted drug discovery. Here
we subjected the transactivation response element (TAR) RNA from human …
we subjected the transactivation response element (TAR) RNA from human …
Integrating NMR and simulations reveals motions in the UUCG tetraloop
We provide an atomic-level description of the structure and dynamics of the UUCG RNA
stem–loop by combining molecular dynamics simulations with experimental data. The …
stem–loop by combining molecular dynamics simulations with experimental data. The …
Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation
Structured RNAs and RNA complexes underlie biological processes ranging from control of
gene expression to protein translation. Approximately 50% of nucleotides within known …
gene expression to protein translation. Approximately 50% of nucleotides within known …
Demonstration that small molecules can bind and stabilize low-abundance short-lived RNA excited conformational states
Many promising RNA drug targets have functions that require the formation of RNA-protein
complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules …
complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules …