Oligonucleotide melting temperatures under PCR conditions: Nearest-neighbor corrections for MG2+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas

Clinical Chemistry

Volumn 47, Issue 11, 2001, Pages 1956-1961

  Von Ahsen, N ^a   Wittwer, C T ^a   Schutz E ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEOSIDE TRIPHOSPHATE; DIMETHYL SULFOXIDE; MAGNESIUM ION; SODIUM ION;

ACCURACY; ARTICLE; CONCENTRATION (PARAMETERS); MATHEMATICAL MODEL; MELTING POINT; MOLECULAR BIOLOGY; MULTIPLE REGRESSION; POLYMERASE CHAIN REACTION; THERMODYNAMICS;

EID: 0034771194     PISSN: 00099147     EISSN: None     Source Type: Journal    
DOI: 10.1093/clinchem/47.11.1956     Document Type: Article

References (48)

1. DNA probes: Applications of the principles of nucleic acid hybridization
2. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature
3. Investigations into denaturation of DNA
4. Cation effects on the denaturation of DNA
5. Evolution of sea urchin non-repetitive DNA
6. Dependence of the melting temperature of DNA on salt concentration
7. Molecular hybridization of immobilized nucleic acids: Theoretical concepts and practical considerations
8. Analysis of repeating DNA sequences by reassociation
9. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
10. Parallel thermodynamic analysis of duplexes on oligodeoxyribo-nucleotide microchips
11. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA
12. Application of a thermodynamic nearest-neighbor model to estimate nucleic acid stability and optimize probe design: Prediction of melting points of different mutations of apolipoprotein B 3500 and factor V Leiden with a hybridization probe genotyping assay on the LightCycler
13. n polymorphism by real-time fluorescence PCR
14. Thermodynamic parameters for DNA sequences with dangling ends
15. Thermal transitions in mixtures of polydeoxyribodinucleotides
16. The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: Energetics of a DNA nick
17. Nucleic acid duplex stability: Influence of base composition on cation effects
18. Demystified . . . the polymerase chain reaction
19. Organic solvents as facilitators of polymerase chain reaction
20. Influence of dimethylsulfoxide on transcription by bacteriophage T3- induced RNA polymerase
21. Thermal denaturation of DNA from bromodeoxyuridine substituted cells
22. Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: Acceleration of the renaturation rate
23. m reduction: A method for analyzing the role of renaturation temperature in the polymerase chain reaction
24. Monitoring hybridization during polymerase chain reaction
25. The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction
26. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase
27. Optimization of the annealing temperature for DNA amplification in vitro
28. Fluorescein-labeled oligonucleotides for real-time PCR: Using the inherent quenching of deoxyguanosine nucleotides
29. Using the nearest neighbor model for the estimation of matched and mismatched hybridization probe melting points and selection of optimal probes on the LightCycler
30. Predicting sequence-dependent melting stability of short duplex DNA oligomers
31. Thermodynamics and NMR of internal G*T mismatches in DNA
32. Nearest-neighbor thermodynamics of internal A*C mismatches in DNA: Sequence dependence and pH effects
33. Thermodynamics of internal C*T mismatches in DNA
34. Nearest neighbor thermodynamic parameters for internal G*A mismatches in DNA
35. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A*A, C*C, G*G, and T*T mismatches
36. Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches
37. Nucleic acid hybrids, formation and structure of
38. Hybridization of nucleic acids immobilized on solid supports
39. Determination of DNA base compositions from melting profiles in dilute buffers
40. Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution
41. Denaturation of DNA
42. Thermal stability of DNA
43. Rapid F508del and F508C assay using fluorescent hybridization probes
44. A quantitative method for evaluating the stabilities of nucleic acids
45. Genotyping of eight thiopurine methyltransferase mutations: Three-color multiplexing, "Two-Color/Shared" anchor, and fluorescence-quenching hybridization probe assays based on thermodynamic nearest-neighbor probe design
46. Genotyping the most common thiopurine methyltransferase mutations with the LightCycler
47. A method for homogeneous color-compensated genotyping of factor V (G1691A) and methylenetetrahydrofolate reductase (C677T) mutations using real-time multiplex fluorescence PCR
48. Rapid cycle allele-specific amplification: Studies with the cystic fibrosis ΔF508 locus