Dynamic DNA nanotechnology: toward functional nanoscale devices

M DeLuca, Z Shi, CE Castro, G Arya - Nanoscale Horizons, 2020 - pubs.rsc.org
Dynamic DNA nanotechnology involves the creation of nanoscale devices made of DNA
whose primary function arises from their ability to undergo controlled motion or …

[HTML][HTML] Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook

S Hussain, A Haji-Akbari - The Journal of Chemical Physics, 2020 - pubs.aip.org
Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike
what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of …

Toehold-mediated strand displacement in random sequence pools

T Mayer, L Oesinghaus, FC Simmel - Journal of the American …, 2022 - ACS Publications
Toehold-mediated strand displacement (TMSD) has been used extensively for molecular
sensing and computing in DNA-based molecular circuits. As these circuits grow in …

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

MY Angela, PM Gasper, L Cheng, LB Lai, S Kaur… - Molecular cell, 2021 - cell.com
The series of RNA folding events that occur during transcription can critically influence
cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a …

Programming cell-free biosensors with DNA strand displacement circuits

JK Jung, CM Archuleta, KK Alam, JB Lucks - Nature chemical biology, 2022 - nature.com
Cell-free biosensors are powerful platforms for monitoring human and environmental health.
Here, we expand their capabilities by interfacing them with toehold-mediated strand …

Unmodificated stepless regulation of CRISPR/Cas12a multi-performance

R Zhao, W Luo, Y Wu, L Zhang, X Liu, J Li… - Nucleic Acids …, 2023 - academic.oup.com
As CRISPR technology is promoted to more fine-divided molecular biology applications, its
inherent performance finds it increasingly difficult to cope with diverse needs in these …

Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors

C Cretu, P Gee, X Liu, A Agrawal, TV Nguyen… - Nature …, 2021 - nature.com
Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA
splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy …

Cotranscriptionally encoded RNA strand displacement circuits

SW Schaffter, EA Strychalski - Science Advances, 2022 - science.org
Engineered molecular circuits that process information in biological systems could address
emerging human health and biomanufacturing needs. However, such circuits can be difficult …

Exploration of the Kinetics of Toehold-Mediated Strand Displacement via Plasmon Rulers

MX Li, CH Xu, N Zhang, GS Qian, W Zhao, JJ Xu… - ACS …, 2018 - ACS Publications
DNA/RNA strand displacement is one of the most fundamental reactions in DNA and RNA
circuits and nanomachines. In this work, we reported an exploration of the dynamic process …

A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity

B Eslami-Mossallam, M Klein, CVD Smagt… - Nature …, 2022 - nature.com
Abstract The S. pyogenes (Sp) Cas9 endonuclease is an important gene-editing tool. Sp
Cas9 is directed to target sites based on complementarity to a complexed single-guide RNA …