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Literature DB >> 20946778

Optical melting measurements of nucleic acid thermodynamics.

Abstract

Optical melting experiments provide measurements of thermodynamic parameters for nucleic acids. These thermodynamic parameters are widely used in RNA structure prediction programs and DNA primer design software. This review briefly summarizes the theory and underlying assumptions of the method and provides practical details for instrument calibration, experimental design, and data interpretation.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
RNA

Year: 2009 PMID： 20946778 PMCID： PMC4070882 DOI： 10.1016/S0076-6879(09)68017-4

Source DB: PubMed Journal: Methods Enzymol ISSN： 0076-6879 Impact factor: 1.600

49 in total

1. Thermodynamics of single mismatches in RNA duplexes.

Authors: R Kierzek; M E Burkard; D H Turner
Journal: Biochemistry Date: 1999-10-26 Impact factor: 3.162

2. 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.

Authors: J A Holbrook; M W Capp; R M Saecker; M T Record
Journal: Biochemistry Date: 1999-06-29 Impact factor: 3.162

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

Authors: S J Schroeder; D H Turner
Journal: Biochemistry Date: 2000-08-08 Impact factor: 3.162

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

Authors: S J Schroeder; D H Turner
Journal: Biochemistry Date: 2001-09-25 Impact factor: 3.162

5. Thermodynamics of three-way multibranch loops in RNA.

Authors: J M Diamond; D H Turner; D H Mathews
Journal: Biochemistry Date: 2001-06-12 Impact factor: 3.162

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

Authors: D H Mathews; J Sabina; M Zuker; D H Turner
Journal: J Mol Biol Date: 1999-05-21 Impact factor: 5.469

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

Authors: James M Ogle; Frank V Murphy; Michael J Tarry; V Ramakrishnan
Journal: Cell Date: 2002-11-27 Impact factor: 41.582

8. Rfam: an RNA family database.

Authors: Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

9. Specificity of microRNA target selection in translational repression.

Authors: John G Doench; Phillip A Sharp
Journal: Genes Dev Date: 2004-03-10 Impact factor: 11.361

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

Authors: M E Burkard; D H Turner
Journal: Biochemistry Date: 2000-09-26 Impact factor: 3.162

33 in total

1. NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.

Authors: Yelena V Lerman; Scott D Kennedy; Neelaabh Shankar; Marc Parisien; Francois Major; Douglas H Turner
Journal: RNA Date: 2011-07-21 Impact factor: 4.942

Optical melting measurements of nucleic acid thermodynamics.

1. Thermodynamics of single mismatches in RNA duplexes.

2. 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.

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

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

5. Thermodynamics of three-way multibranch loops in RNA.

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

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

8. Rfam: an RNA family database.

9. Specificity of microRNA target selection in translational repression.

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

1. NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.

2. Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions.

3. A tunable assay for modulators of genome-destabilizing DNA structures.

4. Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments.

5. Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

6. Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

7. The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide.

8. Bridging the gap between in vitro and in vivo RNA folding.

9. Effect of sodium ions on RNA duplex stability.

Review 10. Modulation of DNA structure formation using small molecules.