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Thermodynamics of RNA-RNA binding

U. Muckstein, H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, I. L. Hofacker
2006 Bioinformatics  
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†

David P. Mascotti, Timothy M. Lohman
1997 Biochemistry  
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

N. Kulshina, T. E. Edwards, A. R. Ferre-D'Amare
2009 RNA: A publication of the RNA Society  
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  
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

Enver Cagri Izgu, Albert C. Fahrenbach, Na Zhang, Li Li, Wen Zhang, Aaron T. Larsen, J. Craig Blain, Jack W. Szostak
2015 Journal of the American Chemical Society  
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

Brighton Samatanga, Antoine Cléry, Pierre Barraud, Frédéric H-T Allain, Ilian Jelesarov
2017 Nucleic Acids Research  
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

David P. Mascotti, Timothy M. Lohman
1992 Biochemistry  
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†

Andrea Újvári, Craig T. Martin
1996 Biochemistry  
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

Sunita Patel, Joshua M. Blose, Joshua E. Sokoloski, Lois Pollack, Philip C. Bevilacqua
2012 Biochemistry  
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

Jason B. Da Costa, Aurelia I. Andreiev, Thorsten Dieckmann
2013 Biochemistry  
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

Jonghoon Kang, Albert M. Kang
2021 Journal of Biological Chemistry  
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

Jermaine L. Jenkins, Haihong Shen, Michael R. Green, Clara L. Kielkopf
2008 Journal of Biological Chemistry  
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†

Jason R. Thomas, Xianjun Liu, Paul J. Hergenrother
2006 Biochemistry  
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†

Jon R. Lorsch, Daniel Herschlag
1998 Biochemistry  
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

V. K. Misra, D. E. Draper
2001 Proceedings of the National Academy of Sciences of the United States of America  
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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