Design principles of DNA enzyme-based walkers: translocation kinetics and photoregulation

TG Cha, J Pan, H Chen, HN Robinson… - Journal of the …, 2015 - ACS Publications
Dynamic DNA enzyme-based walkers complete their stepwise movements along the
prescribed track through a series of reactions, including hybridization, enzymatic cleavage …

[HTML][HTML] Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model

BG Moreira, Y You, R Owczarzy - Biophysical chemistry, 2015 - Elsevier
Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive
and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to …

Effect of salt concentration on the stability of heterogeneous DNA

A Singh, N Singh - Physica A: Statistical Mechanics and its Applications, 2015 - Elsevier
We study the role of cations on the stability of double stranded DNA (dsDNA) molecules. It is
known that the two strands of double stranded DNA (dsDNA) have negative charge due to …

Evaluation of the Gibbs free energy changes and melting temperatures of DNA/DNA duplexes using hybridization enthalpy calculated by molecular dynamics …

AA Lomzov, YN Vorobjev… - The Journal of Physical …, 2015 - ACS Publications
A molecular dynamics simulation approach was applied for the prediction of the thermal
stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA …

Equilibrium gels of trivalent DNA-nanostars: Effect of the ionic strength on the dynamics

F Bomboi, S Biffi, R Cerbino, T Bellini, F Bordi… - The European Physical …, 2015 - Springer
Self-assembling DNA-nanostars are ideal candidates to explore equilibrium gelation in
systems composed of limited-valence particles. We present here a light scattering study of …

Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures

G Weber - Bioinformatics, 2015 - academic.oup.com
Motivation: Free energy nearest-neighbour (NN) thermodynamics is widely used in DNA
biochemistry, ranging from the calculation of melting temperatures to the prediction of …

Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids

F Silvia, B Joana, M Pedro, F Céu, W Jesper… - Applied microbiology …, 2015 - Springer
In the past few years, several researchers have focused their attention on nucleic acid
mimics due to the increasing necessity of developing a more robust recognition of DNA or …

DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration

I Ferreira, TD Amarante, G Weber - The Journal of Chemical Physics, 2015 - pubs.aip.org
DNA base pairs are known to open more easily at the helix terminal, a process usually
called end fraying, the details of which are still poorly understood. Here, we present a …

Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment

CB Markegard, IW Fu, KA Reddy… - The Journal of Physical …, 2015 - ACS Publications
A novel coarse-grained model is developed to elucidate thermodynamics and kinetic
mechanisms of DNA self-assembly. It accounts for sequence and solvent conditions to …

How do non-covalent complexes dissociate in droplets? A case study of the desolvation of dsDNA from a charged aqueous nanodrop

M Sharawy, S Consta - Physical Chemistry Chemical Physics, 2015 - pubs.rsc.org
We present the desolvation mechanism of a double-stranded oligodeoxynucleotide (dsDNA)
from an aqueous nanodrop studied by using atomistic molecular dynamics methods. The …