Interactions with aromatic rings in chemical and biological recognition

EA Meyer, RK Castellano… - Angewandte Chemie …, 2003 - Wiley Online Library
Intermolecular interactions involving aromatic rings are key processes in both chemical and
biological recognition. Their understanding is essential for rational drug design and lead …

The thermodynamics of DNA structural motifs

J SantaLucia Jr, D Hicks - Annu. Rev. Biophys. Biomol. Struct., 2004 - annualreviews.org
▪ Abstract DNA secondary structure plays an important role in biology, genotyping
diagnostics, a variety of molecular biology techniques, in vitro–selected DNA catalysts …

Primer3—new capabilities and interfaces

A Untergasser, I Cutcutache, T Koressaar… - Nucleic acids …, 2012 - academic.oup.com
Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity
of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of …

On the biophysics and kinetics of toehold-mediated DNA strand displacement

N Srinivas, TE Ouldridge, P Šulc… - Nucleic acids …, 2013 - academic.oup.com
Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for
controlling reaction kinetics. Although the dependence of strand displacement kinetics on …

Control of DNA strand displacement kinetics using toehold exchange

DY Zhang, E Winfree - Journal of the American Chemical Society, 2009 - ACS Publications
DNA is increasingly being used as the engineering material of choice for the construction of
nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function …

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker - Nucleic acids research, 2003 - academic.oup.com
The abbreviated name,'mfold web server', describes a number of closely related software
applications available on the World Wide Web (WWW) for the prediction of the secondary …

RNAstructure: software for RNA secondary structure prediction and analysis

JS Reuter, DH Mathews - BMC bioinformatics, 2010 - Springer
Background To understand an RNA sequence's mechanism of action, the structure must be
known. Furthermore, target RNA structure is an important consideration in the design of …

An extended APOBEC3A mutation signature in cancer

A Langenbucher, D Bowen, R Sakhtemani… - Nature …, 2021 - nature.com
APOBEC mutagenesis, a major driver of cancer evolution, is known for targeting TpC sites in
DNA. Recently, we showed that APOBEC3A (A3A) targets DNA hairpin loops. Here, we …

Planar chiral [2.2] paracyclophanes: from synthetic curiosity to applications in asymmetric synthesis and materials

Z Hassan, E Spuling, DM Knoll, J Lahann… - Chemical Society …, 2018 - pubs.rsc.org
Planar chiral [2.2] paracyclophane-based ligands and employment of such enantiopure
representative ligands to facilitate selective transformation of prochiral or racemic …

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

P Yakovchuk, E Protozanova… - Nucleic acids …, 2006 - academic.oup.com
Two factors are mainly responsible for the stability of the DNA double helix: base pairing
between complementary strands and stacking between adjacent bases. By studying DNA …