Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.

ABSTRACT: Three-way multibranch loops (junctions) are common in RNA secondary structures. Computer algorithms such as RNAstructure and MFOLD do not consider the identity of unpaired nucleotides in multibranch loops when predicting secondary structure. There is limited experimental data, however, to parametrize this aspect of these algorithms. In this study, UV optical melting and a fluorescence competition assay are used to measure stabilities of multibranch loops containing up to five unpaired adenosines or uridines or a loop E motif. These results provide a test of our understanding of the factors affecting multibranch loop stability and provide revised parameters for predicting stability. The results should help to improve predictions of RNA secondary structure.

SUBMITTER: Liu B

PROVIDER: S-EPMC3032278 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.

Liu Biao B Diamond Joshua M JM Mathews David H DH Turner Douglas H DH

Biochemistry 20110114 5

Three-way multibranch loops (junctions) are common in RNA secondary structures. Computer algorithms such as RNAstructure and MFOLD do not consider the identity of unpaired nucleotides in multibranch loops when predicting secondary structure. There is limited experimental data, however, to parametrize this aspect of these algorithms. In this study, UV optical melting and a fluorescence competition assay are used to measure stabilities of multibranch loops containing up to five unpaired adenosines ...[more]

PMID: 21133351

Similar Datasets

Predicting helical coaxial stacking in RNA multibranch loops.

Project description:The hypothesis that RNA coaxial stacking can be predicted by free energy minimization using nearest-neighbor parameters is tested. The results show 58.2% positive predictive value (PPV) and 65.7% sensitivity for accuracy of the lowest free energy configuration compared with crystal structures. The probability of each stacking configuration can be predicted using a partition function calculation. Based on the dependence of accuracy on the calculated probability of the stacks, a probability threshold of 0.7 was chosen for predicting coaxial stacks. When scoring these likely stacks, the PPV was 66.7% at a sensitivity of 51.9%. It is observed that the coaxial stacks of helices that are not separated by unpaired nucleotides can be predicted with a significantly higher accuracy (74.0% PPV, 66.1% sensitivity) than the coaxial stacks mediated by noncanonical base pairs (55.9% PPV, 36.5% sensitivity). It is also shown that the prediction accuracy does not show any obvious trend with multibranch loop complexity as measured by three different parameters.

| S-EPMC1894924 | biostudies-literature

A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

Project description:Specific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the α-globin enhancers are distributed between multiple promoters in a mouse model in which the α-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non- membrane bound nuclear compartments.

2019-10-11 | GSE130308 | GEO

A revised model for promoter competition based on multi-way chromatin interactions at the ?-globin locus.

Project description:Specific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the ?-globin enhancers are distributed between multiple promoters in a mouse model in which the ?-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non-membrane bound nuclear compartments.

| S-EPMC6881440 | biostudies-literature

Thermodynamic origin of surface melting on ice crystals.

Project description:Since the pioneering prediction of surface melting by Michael Faraday, it has been widely accepted that thin water layers, called quasi-liquid layers (QLLs), homogeneously and completely wet ice surfaces. Contrary to this conventional wisdom, here we both theoretically and experimentally demonstrate that QLLs have more than two wetting states and that there is a first-order wetting transition between them. Furthermore, we find that QLLs are born not only under supersaturated conditions, as recently reported, but also at undersaturation, but QLLs are absent at equilibrium. This means that QLLs are a metastable transient state formed through vapor growth and sublimation of ice, casting a serious doubt on the conventional understanding presupposing the spontaneous formation of QLLs in ice-vapor equilibrium. We propose a simple but general physical model that consistently explains these aspects of surface melting and QLLs. Our model shows that a unique interfacial potential solely controls both the wetting and thermodynamic behavior of QLLs.

| S-EPMC5098609 | biostudies-literature

A revised model for promoter competition based on multi-way chromatin interactions

Project description:A revised model for promoter competition based on multi-way chromatin interactions

| PRJNA535476 | ENA

Revised AMBER parameters for bioorganic phosphates.

Project description:We report AMBER force field parameters for biological simulations involving phosphorylation of serine, threonine or tyrosine. The initial parameters used RESP fitting for the atomic partial charges and standard values for all other parameters such as Lennard-Jones coefficients. These were refined with the aid of a thermodynamic cycle consisting of experimentally determined pKa values, solvation energies from molecular dynamics free energy simulations, and gas phase basicities from QM calculations. A polarization energy term was included to account for the charge density change between the gas-phase and solution, and solvation free energies were determined using thermodynamic integration. Parameter adjustment is required to obtain consistent thermodynamic results with better balanced electrostatic interactions between water and the phosphate oxygens. To achieve this we modified the phosphate oxygen radii. A thermodynamically consistent parameter set can be derived for monoanions and requires an increase of the van der Waals phosphate oxygen radii of approximately 0.09 Å. Larger, residue-specific radii appear to be needed for dianions. The revised parameters developed here should be of particular interest for environments where simulations of multiple protonation states may be of interest.

| S-EPMC3524595 | biostudies-literature

The Melting Diagram of Protein Solutions and Its Thermodynamic Interpretation.

Project description:Here we present a novel method for the characterization of the hydration of protein solutions based on measuring and evaluating two-component wide-line ¹H NMR signals. We also provide a description of key elements of the procedure conceived for the thermodynamic interpretation of such results. These interdependent experimental and theoretical treatments provide direct experimental insight into the potential energy surface of proteins. The utility of our approach is demonstrated through the examples of two proteins of distinct structural classes: the globular, structured ubiquitin; and the intrinsically disordered ERD10 (early response to dehydration 10). We provide a detailed analysis and interpretation of data recorded earlier by cooling and slowly warming the protein solutions through thermal equilibrium states. We introduce and use order parameters that can be thus derived to characterize the distribution of potential energy barriers inhibiting the movement of water molecules bound to the surface of the protein. Our results enable a quantitative description of the ratio of ordered and disordered parts of proteins, and of the energy relations of protein?water bonds in aqueous solutions of the proteins.

| S-EPMC6274677 | biostudies-literature

Theory for RNA folding, stretching, and melting including loops and salt.

Project description:Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop formation, and salt effects. Using an iterative expression for the partition function that neglects pseudoknots, we calculate folding free energies and minimum free energy configurations based on the experimentally derived basepairing free energies. The configurational entropy of loop formation is modeled by the asymptotic expression -clnm, where m is the length of the loop and c the loop exponent, which is an adjustable constant. Salt effects enter in two ways: first, we derive salt-induced modifications of the free energy parameters for describing basepairing, and second, we include the electrostatic free energy for loop formation. Both effects are modeled on the Debye-Hückel level including counterion condensation. We validate our theory for two different RNA sequences. For tRNA-phe, the resultant heat capacity curves for thermal denaturation at various salt concentrations accurately reproduce experimental results. For the P5ab RNA hairpin, we derive the global phase diagram in the three-dimensional space spanned by temperature, stretching force, and salt concentration and obtain good agreement with the experimentally determined critical unfolding force. We show that for a proper description of RNA melting and stretching, both salt and loop entropy effects are needed.

| S-EPMC3117159 | biostudies-literature

Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA.

Project description:The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions. A comparison of our data with free energies predicted by currently available RNA secondary structure prediction programs shows that these programs do not accurately predict multibranch loop stabilities. These results will expand the existing parameters used for RNA secondary structure prediction from sequence in order to better inform RNA structure-function hypotheses and guide the rational design of functional RNA supramolecular assemblies.

| S-EPMC5340915 | biostudies-literature

Thermodynamic parameters for DNA sequences with dangling ends.

Project description:The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide dangling ends on a Watson-Crick pair are reported. In most instances, dangling ends are stabilizing with free energy contributions ranging from +0.48 (GT(A)) to-0.96 kcal/mol (). In comparison, Watson-Crick nearest-neighbor increments range from -0. 58 (TA/AT) to -2.24 (GC/CG) kcal/mol. Hence, in some cases, a dangling end contributes as much to duplex stability as a Watson-Crick A-T base pair. The implications of these results for DNA probe design are discussed. Analysis of the sequence dependence of dangling-end stabilities show that the nature of the closing base pair largely determines the stabilization. For a given closing base pair, however, adenine dangling ends are always more or equally as stable as the other dangling nucleotides. Moreover, 5' dangling ends are more or equally as stabilizing as their 3' counterparts. Comparison of DNA with RNA dangling-end motifs shows that DNA motifs with 5' dangling ends contribute to stability equally or more than their RNA counterparts. Conversely, RNA 3' dangling ends contribute to stability equally or more than their DNA counterparts. This data set has been incorporated into a DNA secondary structure prediction algorithm (DNA MFOLD) (http://mfold2.wustl.edu/mfold/dna/for m1.cgi) as well as a DNA hybridization prediction algorithm (HYTHERtrade mark) (http://jsl1.chem.wayne.edu/Hyther/hythermenu .html).

| S-EPMC103285 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data