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Thermodynamics of RNA-RNA binding
2006
Bioinformatics
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We can show that RNAi efficiency correlates well with the binding probabilities of siRNAs to their respective mRNA target. ...
Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. ...
The partition function is the gateway to the thermodynamics of RNA folding. ...
doi:10.1093/bioinformatics/btl024
pmid:16446276
fatcat:zli4d3ynqvdhbozbmqzaiek2uy
Thermodynamics of Oligoarginines Binding to RNA and DNA†
1997
Biochemistry
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We have examined the equilibrium binding of a series of synthetic oligoarginines (net charge z ) +2 to +6) containing tryptophan to poly(U), poly(A), poly(C), poly(I), and double-stranded (ds) DNA. ...
The origin of this difference is entirely enthalpic, with ∆H obs , determined from van't Hoff analysis, being more exothermic for oligoarginine binding. ...
Nearly all thermodynamic studies of charged peptides binding to DNA and RNA have used oligolysines, yet many proteins also contain arginine in their nucleic acid binding sites. ...
doi:10.1021/bi970272n
pmid:9188729
fatcat:3l5tp6rhzrgs3ndvnvzjgg26sq
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch
2009
RNA: A publication of the RNA Society
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The thermodynamic signatures of these mutations, namely decreased favorable enthalpy of binding and small effects on entropy of binding, are consistent with the P3-L5 association contributing allosterically ...
to TPP-induced compaction of the RNA. . ...
ACKNOWLEDGMENTS We thank the staff of ALS beamline 5.0.2 and J. Bolduc for assistance with synchrotron and home laboratory diffraction data collection, respectively, and N. Baird ...
doi:10.1261/rna.1847310
pmid:19948769
pmcid:PMC2802028
fatcat:c4cokqz3azcrnbegp57u3vzugq
Linkage between proton binding and folding in RNA: A thermodynamic framework and its experimental application for investigating pKa shifting
2005
RNA: A publication of the RNA Society
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The formalism developed here is similar to that of Draper and coworkers for Mg 2+ binding to RNA, except that the unfolded state is described explicitly owing to the presence of specific proton-binding ...
Key features that emerge from the treatment are a comprehensive description of all the actions of proton binding on RNA folding: acid and alkaline denaturation of the helix and pK a shifting in the folded ...
Herein we establish a thermodynamic framework for proton binding to RNA and DNA that involves linkage to folding. ...
doi:10.1261/rna.7177505
pmid:15659356
pmcid:PMC1370705
fatcat:frxtioi6tzhuvjyjvbbaepcgfu
Uncovering the Thermodynamics of Monomer Binding for RNA Replication
2015
Journal of the American Chemical Society
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We also find that the binding of rGMP is only about 2-fold weaker than the binding of rAMP to 5′-U, consistent with the poor fidelity observed in the nonenzymatic copying of U residues in RNA templates ...
We have now used 1 H NMR spectroscopy to directly measure the thermodynamic association constants, K a s, of the standard ribonucleotide monophosphates (rNMPs) to native RNA primer−template complexes. ...
as a result of mismatches that lead to stalling of primer extension. 6 Understanding the thermodynamics of the binding interactions between a ribonucleotide and an RNA primer−template complex is of ...
doi:10.1021/jacs.5b02707
pmid:25901790
pmcid:PMC4984997
fatcat:lkqwaeuzfrby5nyiva46aspphe
Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs
2017
Nucleic Acids Research
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Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode ...
Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. ...
RESULTS
Favorable enthalpy drives the association of different RNA binding modes with cognate RNAs To determine the thermodynamic signatures characteristic of ssRNA binding by the different binding modes ...
doi:10.1093/nar/gkx136
pmid:28334819
pmcid:PMC5449602
fatcat:wbqj6povwbdxhcbqcqf2i4axfy
Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan
1992
Biochemistry
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The equilibrium binding to the synthetic RNA poly(U) of a series of oligolysines containing one, two, or three tryptophans has been examined as a function of pH, monovalent salt concentration (MX), temperature ...
of the peptide tryptophan fluorescence upon binding poly(U) . ...
Lohman for help in preparing some of the figures. ...
doi:10.1021/bi00152a033
pmid:1382582
fatcat:h7bm3e3jznh5zo5byc44ovi6qa
Thermodynamic and Kinetic Measurements of Promoter Binding by T7 RNA Polymerase†
1996
Biochemistry
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Previous steady state kinetic studies of the initiation of transcription by T7 RNA polymerase have shown that melting of the DNA helix near the transcription start site is not rate limiting [Maslak, M. ...
Equilibrium titrations at 25 °C with label at position -2 provide a thermodynamic measure of the dissociation constant (K d ) 4.8 nM) for promoter binding, while stopped-flow kinetic assays measure the ...
ACKNOWLEDGMENT We are grateful to Professor Lila Gierasch and her group for their generous help and for the use of fluorescence instruments. ...
doi:10.1021/bi961165g
pmid:8931555
fatcat:egzojacuzjc4xhbnh76yprd2su
Specificity of the Double-Stranded RNA-Binding Domain from the RNA-Activated Protein Kinase PKR for Double-Stranded RNA: Insights from Thermodynamics and Small-Angle X-ray Scattering
2012
Biochemistry
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termed "p20" for various RNAs and to detect any RNA conformational changes induced upon protein binding. ...
We monitor binding of p20 to chimeric duplexes containing terminal RNA-DNA hybrid segments and a central dsRNA segment, which was either unbulged ("perfect") or bulged. ...
This work was supported by National Institutes of Health grant no. ...
doi:10.1021/bi300935p
pmid:23140277
pmcid:PMC3542976
fatcat:6zskq3zbanc3jghbhwhu45fizq
Thermodynamics and Kinetics of Adaptive Binding in the Malachite Green RNA Aptamer
2013
Biochemistry
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Adaptive binding, the ability of molecules to fold themselves around the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers. ...
Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the adaptive nature of RNA-ligand interaction. ...
Using this alternate model allows for direct comparison of the thermodynamic values to the results of binding to free RNA which were determined with the same model. ...
doi:10.1021/bi400549s
pmid:23984874
fatcat:dhwkyzwwybg6vpenhf462erv4u
Statistical and thermodynamic analysis of the binding of trans-activation response–binding proteins to HIV-1 TAR RNA
2021
Journal of Biological Chemistry
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test (W = 0.933, p = 0.607):
Figure 1 . 1 Statistical and thermodynamic analysis of the binding of TBPs to HIV-1 TAR RNA. ...
Here, we show our analysis of the thermodynamic data of the binding that identifies three quantitative features of the binding, which may provide further insight into the interactions. (1) The binding ...
doi:10.1016/j.jbc.2020.100067
pmid:33410412
pmcid:PMC7948981
fatcat:e67aryp2abbrrjcc2ltzhlxfyu
Solution Conformation and Thermodynamic Characteristics of RNA Binding by the Splicing Factor U2AF65
2008
Journal of Biological Chemistry
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Thermodynamic comparison of polyuridine 20-mer RNA binding by U2AF 65 variants. A-C, representative isotherms for U 20 titration into wtU2AF 65 R123 (A), ptbU2AF 65 R123 (B), and dU2AF 65 R123 (C). ...
To further test this model, the shapes and RNA interactions of the wild-type U2AF 65 RNA binding domain were compared with those of U2AF 65 variants containing either Py tract-binding protein linker sequences ...
Thermodynamic Characteristics of RNA Binding are Comparable for Wt-, Ptb-, and dU2AF 65 R123 Variants-ITC characterization allowed the detailed thermodynamic similarities or differences to be compared ...
doi:10.1074/jbc.m806297200
pmid:18842594
pmcid:PMC2586248
fatcat:2m3x643xdfhujikvrseh3jtfoq
Biochemical and Thermodynamic Characterization of Compounds That Bind to RNA Hairpin Loops: Toward an Understanding of Selectivity†
2006
Biochemistry
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However, to date no other RNA binding compounds have undergone such rigorous evaluation, and in general the origins of small molecule-RNA binding remain a mystery. ...
Elucidation of the molecular forces governing small molecule-RNA binding is paramount to the progress of rational design strategies. ...
The prevalence of RNA hairpin loop size and sequence is likely related to its thermodynamic stability. ...
doi:10.1021/bi0607296
pmid:16953578
fatcat:vj34unm2kna6vokgl6qmn3emiy
The DEAD Box Protein eIF4A. 1. A Minimal Kinetic and Thermodynamic Framework Reveals Coupled Binding of RNA and Nucleotide†
1998
Biochemistry
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As a step toward understanding the mechanism of action of this class of enzymes, a minimal kinetic and thermodynamic framework for the RNA-activated ATPase function has been established for eIF4A. ...
The enzyme binds its substrates in a random manner; contrary to previous suggestions, neither ATP binding nor hydrolysis is required for binding of single-stranded RNA. ...
We thank Alan Sachs and members of our laboratory for comments on the manuscript. ...
doi:10.1021/bi972430g
pmid:9485364
fatcat:bqy2txkhjjehzgv32o6io4jdjy
A thermodynamic framework for Mg2+ binding to RNA
2001
Proceedings of the National Academy of Sciences of the United States of America
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In this model, RNA stabilization arises from two energetically distinct modes of Mg 2؉ binding: diffuse-and site-binding. ...
In contrast, the contribution of site-binding to RNA stability is often quite small because of the large desolvation penalty. ...
The purpose of this work is to present a proper thermodynamic model describing how these different classes of ions together bind and stabilize specific RNA structures. ...
doi:10.1073/pnas.221234598
pmid:11675490
pmcid:PMC60075
fatcat:sbiskrljdzasnfikyx5cvtvv6e
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