Measuring thermodynamic details of DNA hybridization using fluorescence

Biopolymers

Volumn 95, Issue 7, 2011, Pages 472-486

  You, Yong ^a   Tataurov, Andrey V ^a   Owczarzy, Richard ^a  

^a INTEGRATED DNA TECHNOLOGIES   (United States)

Author keywords

duplex stability; fluorophore; nucleic acid; oligonucleotide folding; quencher

Indexed keywords

BLACK HOLES; COMPLEMENTARY STRAND; DNA DUPLEXES; DNA HYBRIDIZATION; DUPLEX STABILITY; FLUORESCENCE INTENSITIES; FLUORESCENT DYES; HIGH-THROUGHPUT; MELTING PROCESS; MELTING TEMPERATURES; MELTING TRANSITIONS; NEW STRATEGY; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID STRUCTURE; OPTICAL EXPERIMENTS; OPTIMAL PERFORMANCE; PREDICTIVE MODELS; QUENCHER; RANDOM COIL; REAL-TIME PCR; TWO-STATE;

BIOMOLECULES; FLUOROPHORES; METAL MELTING; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PHASE TRANSITIONS; REAL TIME SYSTEMS; TEMPERATURE; THERMODYNAMICS;

POLYMERASE CHAIN REACTION;

DOUBLE STRANDED DNA; FLUORESCEIN; FLUORESCENT DYE; OLIGONUCLEOTIDE; TETRAMETHYLRHODAMINE;

ARTICLE; DNA DENATURATION; DNA DETERMINATION; DNA HYBRIDIZATION; FLUORESCENCE; MEASUREMENT; MELTING POINT; NUCLEIC ACID STRUCTURE; PH; TEMPERATURE; THERMODYNAMICS;

DNA; FLUORESCENCE; HYDROGEN-ION CONCENTRATION; NUCLEIC ACID HYBRIDIZATION; TEMPERATURE; THERMODYNAMICS;

EID: 79955444475     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21615     Document Type: Article

References (43)

1. Morrison, L. E.,;, Stols, L. M., Biochemistry 1993, 32, 3095-3104.
2. Cardullo, R. A.,;, Agrawal, S.,;, Flores, C.,;, Zamecnik, P. C.,;, Wolf, D. E., Proc Natl Acad Sci USA 1988, 85, 8790-8794.
3. Didenko, V. V., Biotechniques 2001, 31, 1106-1121.
4. Lee, L. G.,;, Connell, C. R.,;, Bloch, W., Nucleic Acids Res 1993, 21, 3761-3766.
5. Bonnet, G.,;, Tyagi, S.,;, Libchaber, A.,;, Kramer, F. R., Proc Natl Acad Sci USA 1999, 96, 6171-6176.
6. Tsourkas, A.,;, Behlke, M. A.,;, Rose, S. D.,;, Bao, G., Nucleic Acids Res 2003, 31, 1319-1330.
7. Rachwal, P. A.,;, Fox, K. R., Methods 2007, 43, 291-301.
8. De Cian, A.,;, Guittat, L.,;, Kaiser, M.,;, Saccà , B.,;, Amrane, S.,;, Bourdoncle, A.,;, Alberti, P.,;, Teulade-Fichou, M. P.,;, Lacroix, L.,;, Mergny, J. L., Methods 2007, 42, 183-195.
9. Guédin, A.,;, Lacroix, L.,;, Mergny, J. L., Methods Mol Biol 2010, 613, 25-35.
10. Darby, R. A. J.,;, Sollogoub, M.,;, McKeen, C.,;, Brown, L.,;, Risitano, A.,;, Brown, N.,;, Barton, C.,;, Brown, T.,;, Fox, K. R., Nucleic Acids Res 2002, 30, e39.
11. Saccà , B.,;, Meyer, R.,;, Niemeyer, C. M., Nat Protoc 2009, 4, 271-285.
12. Nangreave, J.,;, Yan, H.,;, Liu, Y., Biophys J 2009, 97, 563-571.
13. Marky, L. A.,;, Breslauer, K. J., Biopolymers 1987, 26, 1601-1620.
14. Petersheim, M.,;, Turner, D. H., Biochemistry 1983, 22, 256-263.
15. Mergny, J. L.,;, Lacroix, L., Oligonucleotides 2003, 13, 515-537.
16. Blose, J. M.,;, Manni, M. L.,;, Klapec, K. A.,;, Stranger-Jones, Y.,;, Zyra, A. C.,;, Sim, V.,;, Griffith, C. A.,;, Long, J. D.,;, Serra, M. J., Biochemistry 2007, 46, 15123-15135.
17. Xia, T.,;, SantaLucia, J., Jr.,;, Burkard, M. E.,;, Kierzek, R.,;, Schroeder, S. J.,;, Jiao, X.,;, Cox, C.,;, Turner, D. H., Biochemistry 1998, 37, 14719-14735.
18. McTigue, P. M.,;, Peterson, R. J.,;, Kahn, J. D., Biochemistry 2004, 43, 5388-5405.
19. Moreira, B. G.,;, You, Y.,;, Behlke, M. A.,;, Owczarzy, R., Biochem Biophys Res Commun 2005, 327, 473-484.
20. Owczarzy, R.,;, You, Y.,;, Moreira, B. G.,;, Manthey, J. A.,;, Huang, L.,;, Behlke, M. A.,;, Walder, J. A., Biochemistry 2004, 43, 3537-3554.
21. Fasman, G. D., Handbook of Biochemistry and Molecular Biology; CRC Press: Cleveland, OH, 1975; Vol. 1.
22. Owczarzy, R., Biophys Chem 2005, 117, 207-215.
23. Kaiser, J. F.,;, Reed, W. A., Rev Sci Instrum 1977, 48, 1447-1457.
24. Fare, T. L.,;, Coffey, E. M.,;, Dai, H.,;, He, Y. D.,;, Kessler, D. A.,;, Kilian, K. A.,;, Koch, J. E.,;, LeProust, E.,;, Marton, M. J.,;, Meyer, M. R.,;, Stoughton, R. B.,;, Tokiwa, G. Y.,;, Wang, Y., Anal Chem 2003, 75, 4672-4675.
25. Stühmeier, F.,;, Lilley, D. M. J.,;, Clegg, R. M., Biochemistry 1997, 36, 13539-13551.
26. Vámosi, G.,;, Clegg, R. M., Biochemistry 1998, 37, 14300-14316.
27. Seidel, C. A. M.,;, Schulz, A.,;, Sauer, M. H. M., J Phys Chem 1996, 100, 5541-5553.
28. Sjöback, R.,;, Nygren, J.,;, Kubista, M., Biopolymers 1998, 46, 445-453.
29. Unruh, J. R.,;, Gokulrangan, G.,;, Wilson, G. S.,;, Johnson, C. K., Photochem Photobiol 2005, 81, 682-690.
30. Johansson, M. K.,;, Fidder, H.,;, Dick, D.,;, Cook, R. M., J Am Chem Soc 2002, 124, 6950-6956.
31. Marras, S. A. E.,;, Kramer, F. R.,;, Tyagi, S., Nucleic Acids Res 2002, 30, e122.
32. Buschmann, V.,;, Weston, K. D.,;, Sauer, M., Bioconjug Chem 2003, 14, 195-204.
33. Nazarenko, I.,;, Pires, R.,;, Lowe, B.,;, Obaidy, M.,;, Rashtchian, A., Nucleic Acids Res 2002, 30, 2089-2195.
34. Torimura, M.,;, Kurata, S.,;, Yamada, K.,;, Yokomaku, T.,;, Kamagata, Y.,;, Kanagawa, T.,;, Kurane, R., Anal Sci 2001, 17, 155-160.
35. Unruh, J. R.,;, Gokulrangan, G.,;, Lushington, G. H.,;, Johnson, C. K.,;, Wilson, G. S., Biophys J 2005, 88, 3455-3465.
36. Chen, C.,;, Wang, W.,;, Wang, Z.,;, Wei, F.,;, Zhao, X. S., Nucleic Acids Res 2007, 35, 2875-2884.
37. Saccà , B.,;, Meyer, R.,;, Niemeyer, C. M., Chem Phys Chem 2009, 10, 3239-3248.
38. Schneider, U. V.,;, Severinsen, J. K.,;, Géci, I.,;, Okkels, L. M.,;, JÃ̧hnk, N.,;, Mikkelsen, N. D.,;, Klinge, T.,;, Pedersen, E. B.,;, Westh, H.,;, Lisby, G., BMC Biotechnol 2010, 10, 4.
39. Owczarzy, R.,;, Vallone, P. M.,;, Goldstein, R. F.,;, Benight, A. S., Biopolymers 1999, 52, 29-56.
40. Tomaso, H.,;, Jacob, D.,;, Eickhoff, M.,;, Scholz, H. C.,;, Al Dahouk, S.,;, Kattar, M. M.,;, Reischl, U.,;, Plicka, H.,;, Olsen, J. S.,;, Nikkari, S.,;, Matero, P.,;, Beuret, C.,;, Ciammaruconi, A.,;, Lista, F.,;, Gala, J. L.,;, Broll, H.,;, Appel, B.,;, Cano, R. E. S.,;, Ybarra de Villavicencio, M. C.,;, Broekhuijsen, M.,;, Indra, A.,;, Petersen, R.,;, Neubauer, H., Clin Chem Lab Med 2008, 46, 1239-1244.
41. Nellãker, C.,;, Wãllgren, U.,;, Karlsson, H., Clin Chem 2007, 53, 98-103.
42. Kim, Y. H.,;, Yang, I.,;, Bae, Y. S.,;, Park, S. R., Biotechniques 2008, 44, 495-505.
43. Herrmann, M. G.,;, Durtschi, J. D.,;, Bromley, L. K.,;, Wittwer, C. T.,;, Voelkerding, K. V., Clin Chem 2006, 52, 494-503.