Physical principles and visual-OMP software for optimal PCR design

Methods in Molecular Biology

Volumn 402, Issue , 2007, Pages 3-33

  SantaLucia Jr , John ^a  

^a NONE

Author keywords

Multi state model; Nearest neighbor model; Oligonucleotide design; Secondary structure; Software; Thermodynamics; Visual OMP

Indexed keywords

PRIMER DNA;

CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; REVIEW;

DNA PRIMERS; MODELS, CHEMICAL; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 36049051885     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-528-8:3     Document Type: Article

References (31)

1. Royce, R. D., SantaLucia, J., Jr. & Hicks, D. A. (2003). Building an in silico laboratory for genomic assay design. Pharm. Visions 10-12.
2. SantaLucia, J., Jr. & Hicks, D. (2004). The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415-440.
3. Puglisi, J. & Tinoco, I., Jr. (1989). Absorbance melting curves of RNA. Methods Enzymol. 180, 304-325.
4. SantaLucia, J. J. (2000). The use of spectroscopic techniques in the study of DNA stability. In Spectrophotometry and Spectrofluorometry. A Practical Approach (Gore, M. G., ed.), pp. 329-356. Oxford University Press.
5. SantaLucia, J., Jr. & Turner, D. H. (1997). Measuring the thermodynamics of RNA secondary structure formation. Biopolymers 44, 309-319.
6. Press, W. H., Flannery, B. P., Teukolsky, S. A. & Vetterling, W. T. (1989). Numerical Recipes in C, Cambridge University Press, New York.
7. SantaLucia, J., Jr. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U. S. A. 95, 1460-1465.
8. Bommarito, S., Peyret, N. & SantaLucia, J., Jr. (2000). Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28, 1929-1934.
9. Peyret, N., Seneviratne, P. A., Allawi, H. T. & SantaLucia, J., Jr. (1999). Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry 38, 3468-3477.
10. Allawi, H. T. & SantaLucia, J., Jr. (1997). Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 36, 10581-10594.
11. Watkins, N. E., Jr. & SantaLucia, J., Jr. (2005). Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res. 33, 6258-6267.
12. Rychlik, W. & Rhoads, E. R. (1989). A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing, and in vitro amplification of DNA. Nucleic Acids Res. 17, 8543-8551.
13. Rozen, S. & Skaletsky, H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods MoI. Biol. 132, 365-386.
14. Li, P., Kupfer, K. C., Davies, C. J., Burbee, D., Evans, G. A. & Garner, H. R. (1997). PRJMO: a primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40, 476-485.
15. Haas, S., Vingron, M., Poustka, A. & Wiemann, S. (1998). Primer design for large scale sequencing. Nucleic Acids Res. 26, 3006-3012.
16. Hillier, L. & Green, P. (1991). OSP: a computer program for choosing PCR and DNA sequencing primers. PCR Methods Appl. 1, 124-128.
17. Proutski, V. & Holmes, E. C. (1996). PrimerMaster: a new program for the design and analysis of PCR primers. Comput. Appl. Biosci. 12, 253-255.
18. Hyndman, D., Cooper, A., Pruzinsky, S., Coad, D. & Mitsuhashi, M. (1996). Software to determine optimal oligonucleotide sequences based on hybridization simulation data. Biotechniques 20, 1090-1097.
19. Wallace, R. B., Shaffer, J., Murphy, R. F., Bonner, J., Hirose, T. & Itakura, K. (1979). Hybridization of synthetic oligodeoxynucleotides to fX174 DNA: the effect of single base pair mismatch. Nucleic Acids Res. 6, 3543-3557.
20. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). In Molecular Cloning: A Laboratory Manual, 2 edition, Vol. II, pp. 11.46-11.47. Cold Spring Harbor Laboratory Press, New York.
21. Bolton, E. T. & McCarthy, B. J. (1962). A general method for the isolation of RNA complementary to DNA. Proc. Natl. Acad. Sci. U. S. A. 48, 1390.
22. Frank-Kamenetskii, M. D. (1971). Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution. Biopolymers 10, 2623-2624.
23. Bonner, T. I., Brenner, D. J., Neufeld, B. R. & Britten, R. J. (1973). Reduction in the rate of DNA reassociation by sequence divergence. J. Mol. Biol. 81, 123.
24. Owczarzy, R., Vallone, P. M., Paner, T. M., Lane, M. J. & Benight, A. S. (1997). Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 217-239.
25. Breslauer, K. J., Frank, R., Blocker, H. & Marky, L. A. (1986). Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. U. S. A. 83, 3746-3750.
26. Dimitrov, R. A. & Zuker, M. (2004). Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J. 87, 215-226.
27. Mathews, D., Burkard, M., Freier, S., Wyatt, J. & Turner, D. (1999). Predicting oligonucleotide affinity to nucleic acid targets. RNA 5, 1458-1469.
28. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
29. Innis, M. & Gelfand, D. H. (1999). Optimization of PCR: conversations between Michael and David. In PCR Applications: Protocols for Functional Genomics (Innis, M., Gelfand, D. H. & Sninsky, J. J., eds), pp. 3-22. Academic Press, New York.
30. Henegariu, O., Heerema, N. A., Dlouhy, S. R., Vance, G. H. & Vogt, P. H. (1997). Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques 23, 504-511.
31. Ishii, K. & Fukui, M. (2001). Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl. Environ. Microbiol. 67, 3753-3755.