Mass spectrometry of nucleic acid noncovalent complexes

E Largy, A Konig, A Ghosh, D Ghosh… - Chemical …, 2021 - ACS Publications
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the
unveiling of new biological roles in regulation of gene expression, specific DNA and RNA …

Origins of specificity in protein-DNA recognition

R Rohs, X Jin, SM West, R Joshi… - Annual review of …, 2010 - annualreviews.org
Specific interactions between proteins and DNA are fundamental to many biological
processes. In this review, we provide a revised view of protein-DNA interactions that …

B-DNA twisting correlates with base-pair morphology

AA Gorin, VB Zhurkin, K Wilma - Journal of molecular biology, 1995 - Elsevier
The observed sequence dependence of the mean twist angles in 38B-DNA crystal structures
can be understood in terms of simple geometrical features of the constituent base-pairs …

The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix: possible …

J Bednar, P Furrer, A Stasiak, J Dubochet… - Journal of molecular …, 1994 - Elsevier
A cryo-electron microscopy study of supercoiled DNA molecules freely suspended in cryo-
vitrified buffer was combined with Monte Carlo simulations and gel electrophoretic analysis …

Protein-DNA recognition patterns and predictions

A Sarai, H Kono - Annu. Rev. Biophys. Biomol. Struct., 2005 - annualreviews.org
▪ Abstract Structural data on protein-DNA complexes provide clues for understanding the
mechanism of protein-DNA recognition. Although the structures of a large number of protein …

The papillomavirus E2 proteins: structure, function, and biology

RS Hegde - Annual review of biophysics and biomolecular …, 2002 - annualreviews.org
▪ Abstract Nearly twenty years after the first high-resolution crystal structures of specific
protein-DNA complexes were determined, the stereo-chemical basis for protein-DNA …

Structure of the LexA–DNA complex and implications for SOS box measurement

APP Zhang, YZ Pigli, PA Rice - Nature, 2010 - nature.com
The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its
activation can contribute to antibiotic resistance,,. Under normal conditions, LexA represses …

Bending of DNA by transcription factors

PC van der Vliet, CP Verrijzer - Bioessays, 1993 - Wiley Online Library
An increasing number of transcription factors both from prokaryotic and eukaryotic sources
are found to bend the DNA upon binding to their recognition site. Bending can easily be …

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

JS Mitchell, CA Laughton, SA Harris - Nucleic acids research, 2011 - academic.oup.com
Although DNA is frequently bent and supercoiled in the cell, much of the available
information on DNA structure at the atomistic level is restricted to short linear sequences. We …

The structure of an RNA “kissing” hairpin complex of the HIV TAR hairpin loop and its complement

KY Chang, I Tinoco Jr - Journal of molecular biology, 1997 - Elsevier
We have used nuclear magnetic resonance (NMR) to obtain the structure of an RNA
“kissing” hairpin complex formed between the HIV-2 TAR hairpin loop and a hairpin with a …