Nucleic acid solvation: from outside to insight
Nucleic acids are polyanionic molecules that were historically considered to be solely
surrounded by a shell of water molecules and a neutralizing cloud of monovalent and …
surrounded by a shell of water molecules and a neutralizing cloud of monovalent and …
Recent advances in the study of nucleic acid flexibility by molecular dynamics
The recent use of molecular dynamics (MD) simulations to study flexibility of nucleic acids
has been reviewed from an analysis of the publications appearing in the past two years …
has been reviewed from an analysis of the publications appearing in the past two years …
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
It is well recognized that base sequence exerts a significant influence on the properties of
DNA and plays a significant role in protein–DNA interactions vital for cellular processes …
DNA and plays a significant role in protein–DNA interactions vital for cellular processes …
[HTML][HTML] Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d (GCACGAACGAACGAACGC)
Background The structure and dynamics of DNA are critically related to its function.
Molecular dynamics simulations augment experiment by providing detailed information …
Molecular dynamics simulations augment experiment by providing detailed information …
Sequence-dependent DNA deformability studied using molecular dynamics simulations
Proteins recognize specific DNA sequences not only through direct contact between amino
acids and bases, but also indirectly based on the sequence-dependent conformation and …
acids and bases, but also indirectly based on the sequence-dependent conformation and …
Structure, stiffness and substates of the Dickerson-Drew dodecamer
The Dickerson–Drew dodecamer (DD) d [CGCGAATTCGCG] 2 is a prototypic B-DNA
molecule whose sequence-specific structure and dynamics have been investigated by many …
molecule whose sequence-specific structure and dynamics have been investigated by many …
Intrinsic flexibility of B-DNA: the experimental TRX scale
ABSTRACT B-DNA flexibility, crucial for DNA–protein recognition, is sequence dependent.
Free DNA in solution would in principle be the best reference state to uncover the relation …
Free DNA in solution would in principle be the best reference state to uncover the relation …
Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for loo** and nucleosome positioning
T Dršata, N Špačková, P Jurečka… - Nucleic acids …, 2014 - academic.oup.com
A-tracts are functionally important DNA sequences which induce helix bending and have
peculiar structural properties. While A-tract structure has been qualitatively well …
peculiar structural properties. While A-tract structure has been qualitatively well …
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA
Abstract cgDNA is a package for the prediction of sequence-dependent configuration-space
free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any …
free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any …
The role of water H-bond imbalances in B-DNA substate transitions and peptide recognition revealed by time-resolved FTIR spectroscopy
The conformational substates BI and BII of the phosphodiester backbone in B-DNA are
thought to contribute to DNA flexibility and protein recognition. We have studied by rapid …
thought to contribute to DNA flexibility and protein recognition. We have studied by rapid …