Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis

Electrophoresis

Volumn 33, Issue 3, 2012, Pages 483-491

  Desmarais, Samantha M ^a   Leitner, Thomas ^b   Barron, Annelise E ^a  

^a Stanford University   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

CE; Dimerization; DNA barcodes; Drag tag; Mobility shift assay

Indexed keywords

BAR CODES; CAPILLARY ELECTROPHORESIS; DIMERIZATION; DIMERS; DNA SEQUENCES; DRAG; ELECTROPHORETIC MOBILITY; OLIGONUCLEOTIDES;

BASE PAIRS; BIOPHYSICAL PARAMETERS; CE; DIMER FORMATION; DIMERIZATIONS; DNA BARCODE; DRAG-TAG; EXPERIMENTAL DETERMINATION; FREE SOLUTIONS; MOBILITY SHIFT ASSAYS;

DNA;

DIMER; DNA FRAGMENT; DOUBLE STRANDED DNA; POLY(N METHOXYETHYLGLYCINE); POLYMER; PRIMER DNA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; BIOPHYSICS; CAPILLARY ELECTROPHORESIS; CONJUGATION; CONTROLLED STUDY; DIMERIZATION; DNA BARCODING; ELECTROPHORESIS; ELECTROPHORETIC MOBILITY; FLUORESCENCE; QUANTITATIVE ANALYSIS; TEMPERATURE; THERMODYNAMICS;

EID: 84856388462     PISSN: 01730835     EISSN: 15222683     Source Type: Journal    
DOI: 10.1002/elps.201100452     Document Type: Article

References (36)

1. Wu, X., Xiao, H., Sci. Chin. C. Life. Sci. 2009, 52, 560-567.
2. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y. J., Chen, Z. T., Dewell, S. B., Du, L., Fierro, J. M., Gomes, X. V., Godwin, B. C., He, W., Helgesen, S., Ho, C. H., Irzyk, G. P., Jando, S. C., Alenquer, M. L. I., Jarvie, T. P., Jirage, K. B., Kim, J. B., Knight, J. R., Lanza, J. R., Leamon, J. H., Lefkowitz, S. M., Lei, M., Li, J., Lohman, K. L., Lu, H., Makhijani, V. B., McDade, K. E., McKenna, M. P., Myers, E. W., Nickerson, E., Nobile, J. R., Plant, R., Puc, B. P., Ronan, M. T., Roth, G. T., Sarkis, G. J., Simons, J. F., Simpson, J. W., Srinivasan, M., Tartaro, K. R., Tomasz, A., Vogt, K. A., Volkmer, G. A., Wang, S. H., Wang, Y., Weiner, M. P., Yu, P. G., Begley, R. F., Rothberg, J. M., Nature 2005, 437, 376-380.
3. Hagan, K. A., Reedy, C. R., Bienvenue, J. M., Dewald, A. H., Landers, J. P., Analyst 2011, 136, 1928-1937.
4. Fox, S., Filichkin, S., Mockler, T. C., Methods Mol. Biol. 2009, 553, 79-108.
5. Fischer, W., Ganusov, V. V., Giorgi, E. E., Hraber, P. T., Keele, B. F., Leitner, T., Han, C. S., Gleasner, C. D., Green, L., Lo, C. C., Nag, A., Wallstrom, T. C., Wang, S., McMichael, A. J., Haynes, B. F., Hahn, B. H., Perelson, A. S., Borrow, P., Shaw, G. M., Bhattacharya, T., Korber, B. T., PLoS One 2010, 5, e12303.
6. Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., Albert, J., PLoS One 2010, 5, e11345.
7. Tsibris, A. M., Korber, B., Arnaout, R., Russ, C., Lo, C. C., Leitner, T., Gaschen, B., Theiler, J., Paredes, R., Su, Z., Hughes, M. D., Gulick, R. M., Greaves, W., Coakley, E., Flexner, C., Nusbaum, C., Kuritzkes, D. R., PLoS One 2009, 4, e5683.
8. Hoppman-Chaney, N., Peterson, L. M., Klee, E. W., Middha, S., Courteau, L. K., Ferber, M. J., Clin. Chem. 2010, 56, 1297-1306.
9. Atrazhev, A., Manage, D. P., Stickel, A. J., Crabtree, H. J., Pilarski, L. M., Acker, J. P., Anal. Chem. 2010, 82, 8079-8087.
10. Elnifro, E. M., Ashshi, A. M., Cooper, R. J., Klapper, P. E., Clin. Microbiol. Rev. 2000, 13, 559-570.
11. Nesterova, I. V., Erdem, S. S., Pakhomov, S., Hammer, R. P., Soper, S. A., J. Am. Chem. Soc. 2009, 131, 2432-2433.
12. Lewis, C. L., Choi, C. H., Lin, Y., Lee, C. S., Yi, H., Anal. Chem. 2010, 82, 5851-5858.
13. Cai, S., Lau, C., Lu, J., Anal. Chem. 2010, 82, 7178-7184.
14. Bau, S., Schracke, N., Kranzle, M., Wu, H., Stahler, P., Hoheisel, J., Beier, M., Summerer, D., Anal. Bioanal. Chem. 2009, 393, 171-175.
15. Venkatasubbarao, S., Trends Biotechnol. 2004, 22, 630-637.
16. Hestekin, C. N., Jakupciak, J. P., Chiesl, T. N., Kan, C. W., O'Connell, C. D., Barron, A. E., Electrophoresis 2006, 27, 3823-3835.
17. Kourkine, I. V., Hestekin, C. N., Barron, A. E., Electrophoresis 2002, 23, 1375-1385.
18. Kourkine, I. V., Hestekin, C. N., Buchholz, B. A., Barron, A. E., Anal. Chem. 2002, 74, 2565-2572.
19. Mergny, J. L., Lacroix, L., Oligonucleotides 2003, 13, 515-537.
20. Lerman, L. S., Frisch, H. L., Biopolymers 1982, 21, 995-997.
21. Haynes, R. D., Meagher, R. J., Won, J. I., Bogdan, F. M., Barron, A. E., Bioconj. Chem. 2005, 16, 929-938.
22. Meagher, R. J., McCormick, L. C., Haynes, R. D., Won, J. I., Lin, J. S, Slater, G. W., Barron, A. E., Electrophoresis 2006, 27, 1702-1712.
23. Albarghouthi, M. N., Buchholz, B. A., Huiberts, P. J., Stein, T. M., Barron, A. E., Electrophoresis 2002, 23, 1429-1440.
24. Kourkine, I. V., Hestekin, C. N., Magnusdottir, S. O., Barron, A. E., BioTechniques 2002, 33, 318-320, 322, 324-325.
25. Hestekin, C. N., Barron, A. E., Electrophoresis 2006, 27, 3805-3815.
26. Tian, H., Emrich, C. A., Scherer, J. R., Mathies, R. A., Andersen, P. S., Larsen, L. A., Christiansen, M., Electrophoresis 2005, 26, 1834-1842.
27. Vallone, P. M., Butler, J. M., BioTechniques 2004, 37, 226-231.
28. SantaLucia, J., Jr., Proc. Natl. Acad. Sci. USA 1998, 95, 1460-1465.
29. Nedelcu, S., Meagher, R. J., Barron, A. E., Slater, G. W., J. Chem. Phys. 2007, 126, 175104.
30. Hughesman, C. B., Turner, R. F. B., Haynes, C., Biochemistry (NY) 2011, 50, 2642-2649.
31. Breslauer, K. J., Frank, R., Blocker, H., Marky, L. A., Proc. Natl. Acad. Sci. USA 1986, 83, 3746-3750.
32. SantaLucia, J., Jr., Allawi, H. T., Seneviratne, P. A., Biochemistry 1996, 35, 3555-3562.
33. Shea, R. G., Ng, P., Bischofberger, N., Nucleic Acids Res. 1990, 18, 4859-4866.
34. Huber, D. E., Markel, M. L., Pennathur, S., Patel, K. D., Lab. Chip 2009, 9, 2933-2940.
35. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D., Lander, E., Nusbaum, C., Nat. Biotechnol. 2009, 27, 182-189.
36. Kramer, M. F., Coen, D. M., Curr. Protoc. Cytom. 2006, 37, A.3K.1-A.3K.15.