Optical melting measurements of nucleic acid thermodynamics (Q37800199)

23 August 2017

Optical melting measurements of nucleic acid thermodynamics (English)

1 reference

23 August 2017

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2

Douglas H Turner

1 reference

23 August 2017

Susan J Schroeder

1

1 reference

PMCID

4070882

23 August 2017

language of work or name

English

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publication date

17 November 2009

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23 August 2017

Methods in Enzymology

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23 August 2017

468

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23 August 2017

371-387

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Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Molecular basis for target RNA recognition and cleavage by human RISC.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

CONTRAfold: RNA secondary structure prediction without physics-based models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Heat capacity changes associated with nucleic acid folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Thermal difference spectra: a specific signature for nucleic acid structures.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Stability of 3' double nucleotide overhangs that model the 3' ends of siRNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Fast and reliable prediction of noncoding RNAs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Rfam: annotating non-coding RNAs in complete genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Specificity of microRNA target selection in translational repression

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Rfam: an RNA family database

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Selection of tRNA by the ribosome requires a transition from an open to a closed form

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Inhibition of human cytomegalovirus immediate-early gene expression by an antisense oligonucleotide complementary to immediate-early RNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Analysis of oligonucleotide structure using hyperchromism measurements at long wavelengths

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Predicting DNA duplex stability from the base sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

On finding all suboptimal foldings of an RNA molecule

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2' OH groups

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

3' terminal nucleotides determine thermodynamic stabilities of mismatches at the ends of RNA helices

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Thermodynamic stabilities of internal loops with GU closing pairs in RNA.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070882

Holmium Oxide Glass Wavelength Standards.

1 September 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Possible origin of differences between van't Hoff and calorimetric enthalpy estimates

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Thermodynamics of three-way multibranch loops in RNA

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Thermal methods for the analysis of RNA folding pathways

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Thermodynamics of single mismatches in RNA duplexes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Measuring the thermodynamics of RNA secondary structure formation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

The stability and structure of tandem GA mismatches in RNA depend on closing base pairs

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2809%2968017-4

7 January 2021

10.1016/S0076-6879(09)68017-4

Identifiers

DOI

1 reference

23 August 2017

1 reference

23 August 2017

1 reference

PMCID

4070882