rRNA binding sites and the molecular mechanism of action of the tetracyclines
CU Chukwudi - Antimicrobial agents and chemotherapy, 2016 - Am Soc Microbiol
The tetracycline antibiotics are known to be effective in the treatment of both infectious and
noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the …
noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the …
Continuum molecular electrostatics, salt effects, and counterion binding—a review of the Poisson–Boltzmann theory and its modifications
P Grochowski, J Trylska - Biopolymers: Original Research on …, 2008 - Wiley Online Library
This work is a review of the Poisson–Boltzmann (PB) continuum electrostatics theory and its
modifications, with a focus on salt effects and counterion binding. The PB model is one of the …
modifications, with a focus on salt effects and counterion binding. The PB model is one of the …
Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations
R Owczarzy, BG Moreira, Y You, MA Behlke… - Biochemistry, 2008 - ACS Publications
Accurate predictions of DNA stability in physiological and enzyme buffers are important for
the design of many biological and biochemical assays. We therefore investigated the effects …
the design of many biological and biochemical assays. We therefore investigated the effects …
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 …
interaction, conformational entropy, base pairing and stacking, and noncanonical …
Stem–loop formation drives RNA folding in mechanical unzipping experiments
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and
function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 …
function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 …
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
RNA polymerase pausing represents an important mechanism of transcriptional regulation.
In this study, we use a single-molecule transcription assay to investigate the effect of …
In this study, we use a single-molecule transcription assay to investigate the effect of …
Understanding the relative flexibility of RNA and DNA duplexes: stretching and twist-stretch coupling
L Bao, X Zhang, YZ Shi, YY Wu, ZJ Tan - Biophysical journal, 2017 - cell.com
The flexibility of double-stranded (ds) RNA and dsDNA is crucial for their biological
functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be …
functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be …
Non-specific binding of Na + and Mg 2+ to RNA determined by force spectroscopy methods
RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are
exposed to both monovalent and multivalent ions. Despite recent advances, we do not have …
exposed to both monovalent and multivalent ions. Despite recent advances, we do not have …
Salt contribution to RNA tertiary structure folding stability
ZJ Tan, SJ Chen - Biophysical journal, 2011 - cell.com
Accurate quantification of the ionic contribution to RNA folding stability could greatly
enhance our ability to understand and predict RNA functions. Recently, motivated by the …
enhance our ability to understand and predict RNA functions. Recently, motivated by the …
[HTML][HTML] Coarse-grained modeling of RNA 3D structure
WK Dawson, M Maciejczyk, EJ Jankowska, JM Bujnicki - Methods, 2016 - Elsevier
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their
tasks within the cell. Understanding how these molecules interact to carry out their biological …
tasks within the cell. Understanding how these molecules interact to carry out their biological …