Frontiers in molecular dynamics simulations of DNA

A Pérez, FJ Luque, M Orozco - Accounts of chemical research, 2012 - ACS Publications
It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …

RNA folding: conformational statistics, folding kinetics, and ion electrostatics

SJ Chen - Annu. Rev. Biophys., 2008 - annualreviews.org
RNA folding is a remarkably complex problem that involves ion-mediated electrostatic
interaction, conformational entropy, base pairing and stacking, and noncanonical …

Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor

S Sorgenfrei, C Chiu, RL Gonzalez Jr, YJ Yu… - Nature …, 2011 - nature.com
Single-molecule measurements of biomolecules can provide information about the
molecular interactions and kinetics that are hidden in ensemble measurements. However …

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins

MT Woodside, WM Behnke-Parks… - Proceedings of the …, 2006 - National Acad Sciences
Nucleic acid hairpins provide a powerful model system for probing the formation of
secondary structure. We report a systematic study of the kinetics and thermodynamics of the …

Studies on the structure and dynamics of the human telomeric G quadruplex by single-molecule fluorescence resonance energy transfer

L Ying, JJ Green, H Li, D Klenerman… - Proceedings of the …, 2003 - National Acad Sciences
We have investigated the structure and unfolding kinetics of the human telomeric
intramolecular G quadruplex by using single-molecule fluorescence resonance energy …

[PDF][PDF] Remotely triggered release from magnetic nanoparticles

AM Derfus, G von Maltzahn, TJ Harris, T Duza… - Advanced …, 2007 - academia.edu
Multivalent nanoparticles have tremendous potential in the diagnosis and treatment of
human disease.[1] Their multivalency allows simultaneous conjugation of targeting ligands …

[HTML][HTML] Folding and unfolding pathways of the human telomeric G-quadruplex

RD Gray, JO Trent, JB Chaires - Journal of molecular biology, 2014 - Elsevier
Sequence analogs of human telomeric DNA such as d [AGGG (TTAGGG) 3](Tel22) fold into
monomeric quadruplex structures in the presence of a suitable cation. To investigate the …

Effects of temperature and molecular weight on dissolution of cellulose in NaOH/urea aqueous solution

H Qi, C Chang, L Zhang - Cellulose, 2008 - Springer
Dissolution of cellulose having different viscosity-average molecular weight (M η) in 7 wt%
NaOH/12 wt% urea aqueous solution at temperature from 60 to− 12.6° C was investigated …

Defining the sequence-recognition profile of DNA-binding molecules

CL Warren, NCS Kratochvil… - Proceedings of the …, 2006 - National Acad Sciences
Determining the sequence-recognition properties of DNA-binding proteins and small
molecules remains a major challenge. To address this need, we have developed a high …

Compact intermediates in RNA folding

SA Woodson - Annual review of biophysics, 2010 - annualreviews.org
Large noncoding RNAs fold into their biologically functional structures via compact yet
disordered intermediates, which couple the stable secondary structure of the RNA with the …