Integrating experimental data with molecular simulations to investigate RNA structural dynamics

M Bernetti, G Bussi - Current Opinion in Structural Biology, 2023 - Elsevier
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as
nuclear magnetic resonance, cryo-electron microscopy, small-and wide-angle X-ray …

Roadmap for optical tweezers

G Volpe, OM Maragò… - Journal of Physics …, 2023 - iopscience.iop.org
Optical tweezers are tools made of light that enable contactless pushing, trapping, and
manipulation of objects, ranging from atoms to space light sails. Since the pioneering work …

The development of single molecule force spectroscopy: from polymer biophysics to molecular machines

C Bustamante, S Yan - Quarterly Reviews of Biophysics, 2022 - cambridge.org
The advent of single-molecule force spectroscopy represents the introduction of forces,
torques, and displacements as controlled variables in biochemistry. These methods afford …

Universal cold RNA phase transitions

P Rissone, A Severino, I Pastor, F Ritort - Proceedings of the National …, 2024 - pnas.org
RNA's diversity of structures and functions impacts all life forms since primordia. We use
calorimetric force spectroscopy to investigate RNA folding landscapes in previously …

Investigating fundamental principles of nonequilibrium assembly using temperature-sensitive copolymers

SS Chittari, AC Obermeyer… - Journal of the American …, 2023 - ACS Publications
Both natural biomaterials and synthetic materials benefit from complex energy landscapes
that provide the foundation for structure–function relationships and environmental sensitivity …

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

N Hori, D Thirumalai - Nucleic Acids Research, 2023 - academic.oup.com
Folding of ribozymes into well-defined tertiary structures usually requires divalent cations.
How Mg2+ ions direct the folding kinetics has been a long-standing unsolved problem …

Temperature-dependent elastic properties of DNA

M Rico-Pasto, F Ritort - Biophysical Reports, 2022 - cell.com
Abstract Knowledge of the elastic properties, eg, the persistence length or interphosphate
distance, of single-stranded (ss) and double-stranded (ds) DNA under different experimental …

Experimental test of Sinai's model in DNA unzipping

C Ter Burg, P Rissone, M Rico-Pasto, F Ritort… - Physical Review Letters, 2023 - APS
The experimental measurement of correlation functions and critical exponents in disordered
systems is key to testing renormalization group (RG) predictions. We mechanically unzip …

Stick-slip unfolding favors self-association of expanded HTT mRNA

BM O'Brien, R Moulick, G Jiménez-Avalos… - Nature …, 2024 - nature.com
Abstract In Huntington's Disease (HD) and related disorders, expansion of CAG trinucleotide
repeats produces a toxic gain of function in affected neurons. Expanded huntingtin (exp …

Stacking correlation length in single-stranded DNA

X Viader-Godoy, M Manosas, F Ritort - Nucleic Acids Research, 2024 - academic.oup.com
Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-
stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are …