Single-nucleotide polymorphism detection using nanomolar nucleotides and single-molecule fluorescence

Analytical Biochemistry

Volumn 327, Issue 1, 2004, Pages 35-44

  Twist, Charles R ^a   Winson, Michael K ^a   Rowland, Jem J ^a   Kell, Douglas B ^a,b  

^a ABERYSTWYTH UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Assay; Detection; FCS; Miniaturization; Single molecule; SNP

Indexed keywords

ASSAYS; CHEMICAL REACTIONS; ERROR DETECTION; FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; MOLECULES; POLARIZATION; POLYMORPHISM; SPECTROSCOPIC ANALYSIS;

FLUORESCENCE INTENSITIES; MINIATURIZATION; POLARIZATION ANISOTROPY; SINGLE MOLECULE; SINGLE MOLECULE FLUORESCENCE; SINGLE MOLECULE FLUORESCENCE DETECTION; SINGLE NUCLEOTIDE POLYMORPHISM DETECTIONS; SINGLE NUCLEOTIDE POLYMORPHISMS;

NUCLEOTIDES;

BRCA1 PROTEIN; NANOPARTICLE; NUCLEOTIDE; TRANSMEMBRANE CONDUCTANCE REGULATOR;

ANISOTROPY; ARTICLE; FLUORESCENCE; FLUORESCENCE CORRELATION SPECTROSCOPY; MEASUREMENT; METHODOLOGY; POLARIZATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 1642339614     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ab.2003.12.023     Document Type: Article

References (93)

1. McCarthy J.J., Hilfiker R. Nat. Biotechnol. 18:2000;505-508.
2. Hoh J., Wille A., Zee R., Cheng S., Reynolds R., Lindpaintner K., Ott J. Ann. Hum. Genet. 64:2000;413-417.
3. Campbell D.A., Valdes A., Spurr N. Drug Discov. Today. 5:2000;388-396.
4. Kruglyak L. Nat. Genet. 22:1999;139-144.
5. Lindblad-Toh K., Winchester E., Daly M.J., Wang D.G., Hirschhorn J.N., Laviolette J.P., Ardlie K., Reich D.E., Robinson E., Sklar P., Shah N., Thomas D., Fan J.B., Gingeras T., Warrington J., Patil N., Hudson T.J., Lander E.S. Nat. Genet. 24:2000;381-386.
6. Reich D.E., Cargill M., Bolk S., Ireland J., Sabeti P.C., Richter D.J., Lavery T., Kouyoumjian R., Farhadian S.F., Ward R., Lander E.S. Nature. 411:2001;199-204.
7. Stephens J.C., Schneider J.A., Tanguay D.A., Choi J., Acharya T., Stanley S.E., Jiang R.H., Messer C.J., Chew A., Han J.H., Duan J.C., Carr J.L., Lee M.S., Koshy B., Kumar A.M., Zhang G., Newell W.R., Windemuth A., Xu C.B., Kalbfleisch T.S., Shaner S.L., Arnold K., Schulz V., Drysdale C.M., Nandabalan K., Judson R.S., Ruano G., Vovis G.F. Science. 293:2001;489-493.
8. Syvänen A.-C. Nat. Rev. Genet. 2:2001;930-942.
9. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C. et al. Science. 291:2001;1304-1351.
10. Wang D.G., Fan J.B., Siao C.J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J., Kruglyak L., Stein L., Hsie L., Topaloglou T., Hubbell E., Robinson E., Mittmann M., Morris M.S., Shen N.P., Kilburn D., Rioux J., Nusbaum C., Rozen S., Hudson T.J., Lipshutz R., Chee M., Lander E.S. Science. 280:1998;1077-1082.
11. Schork N.J., Fallin D., Lanchbury J.S. Clin. Genet. 58:2000;250-264.
12. McLeod H.L., Evans W.E. Annu. Rev. Pharmacol. Toxicol. 41:2001;101-121.
13. Vignal A., Milan D., SanCristobal M., Eggen A. Genet. Sel. Evol. 34:2002;275-305.
14. Kwok P.Y., Gu Z.J. Mol. Med. Today. 5:1999;538-543.
15. Kwok P.Y. Annu. Rev. Genomics Hum. Genet. 2:2001;235-258.
16. Prince J.A., Feuk L., Howell W.M., Jobs M., Emahazion T., Blennow K., Brookes A.J. Genome Res. 11:2001;152-162.
17. Beaudet L., Bedard J., Breton B., Mercuri R.J., Budarf M.L. Genome Res. 11:2001;600-608.
18. Myakishev M.V., Khripin Y., Hu S., Hamer D.H. Genome Res. 11:2001;163-169.
19. Drmanac S., Kita D., Labat I., Hauser B., Schmidt C., Burczak J.D., Drmanac R. Nat. Biotechnol. 16:1998;54-58.
20. Goto S., Takahashi A., Kamisango K., Matsubara K. Anal. Biochem. 307:2002;25-32.
21. Ahmadian A., Gharizadeh B., Gustafsson A.C., Sterky F., Nyren P., Uhlen M., Lundeberg J. Anal. Biochem. 280:2000;103-110.
22. Ronaghi M., Elahi E. Comp. Funct. Genomics. 3:2002;51-56.
23. Fakhrai-Rad H., Pourmand N., Ronaghi M. Hum. Mutat. 19:2002;479-485.
24. Goldrick M.M. Hum. Mutat. 18:2001;190-204.
25. Pusch W., Wurmbach J.H., Thiele H., Kostrzewa M. Pharmacogenomics. 3:2002;537-548.
26. Di Giusto D., King G.C. Nucleic Acids Res. 31:2003;E7-7.
27. Syvänen A.-C. Clin. Chim. Acta. 226:1994;225-236.
28. Chen X., Levine L., Kwok P.Y. Genome Res. 9:1999;492-498.
29. T.M. Hsu, X. Chen, S. Duan, R.D. Miller, P.Y. Kwok, Biotechniques 31 (2001) 560, 562, 564-8, passim
30. Hsu T.M., Law S.M., Duan S., Neri B.P., Kwok P.Y. Clin. Chem. 47:2001;1373-1377.
31. Kwok P.Y. Hum. Mutat. 19:2002;315-323.
32. Freeman B.D., Buchman T.G., McGrath S., Tabrizi A.R., Zehnbauer B.A. J. Mol. Diagn. 4:2002;209-215.
33. Levene M.J., Korlach J., Turner S.W., Foquet M., Craighead H.G., Webb W.W. Science. 299:2003;682-686.
34. Mir K.U., Southern E.M. Annu. Rev. Genomics Hum. Genet. 1:2000;329-360.
35. Miller R.D., Kwok P.Y. Hum. Mol. Genet. 10:2001;2195-2198.
36. The International SNP Map Working Group, Nature 409 (2001) 928-933
37. Braaten Ø., Rodningen O.K., Nordal I., Leren T.P. Comput. Methods Programs Biomed. 61:2000;1-9.
38. Dipple K.M., McCabe E.R.B. Am. J. Hum. Genet. 66:2000;1729-1735.
39. Ott J., Hoh J. Am. J. Hum. Genet. 67:2000;289-294.
40. Kruglyak L., Daly M.J., Reeve-Daly M.P., Lander E.S. Am. J. Hum. Genet. 58:1996;1347-1363.
41. Kell D.B. Trends Genet. 18:2002;555-559.
42. Judson R., Stephens J.C., Windemuth A. Pharmacogenomics. 1:2000;15-26.
43. Bader J.S. Pharmacogenomics. 2:2001;11-24.
44. Kell D.B. Trends Biotechnol. 17:1999;89-91.
45. Kell D.B. Trends Biotechnol. 18:2000;186-187.
46. Rotman B. Proc. Natl. Acad. Sci. USA. 47:1961;1981-1991.
47. Ambrose P., Goodwin P., Jett J., Johnson M., Martin J., Marrone B., Schecker J., Wilderson W., Keller R. Phys. Chem. 97:1993;1535-1542.
48. Soper S.A., Mattingly Q.L., Vegunta P. Anal. Chem. 65:1993;740-747.
49. Rich A. Proc. Natl. Acad. Sci. USA. 95:1998;13999-14000.
50. Stipe B.C., Rezaei M.A., Ho W. Science. 280:1998;1732-1735.
51. Schenter G.K., Lu H.P., Xie X.S. J. Phys. Chem. A. 103:1999;10477-10488.
52. Xie X.S., Lu H.P. J. Biol. Chem. 274:1999;15967-15970.
53. Weiss S. Science. 283:1999;1676-1683.
54. Moerner W.E., Orrit M. Science. 283:1999;1670-1676.
55. Chen X.N. Combinatorial Chem. High Throughput Screen. 6:2003;213-223.
56. Tabor S., Richardson C.C. Proc. Natl. Acad. Sci. USA. 84:1987;4767-4771.
57. Elson E.L., Madge D. Biopolymers. 13:1974;1-27.
58. Madge D., Elson E.L., Webb W.W. Biopolymers. 13:1974;29-61.
59. Auer M., Moore K.J., Meyer-Almes F.J., Günther R., Pope A.J., Stöckli K.A. Drug Discov. Today. 3:1998;457-465.
60. Widengren J., Rigler R. Cell. Mol. Biol. 44:1998;857-879.
61. Schürer H., Buchynskyy A., Korn K., Famulok M., Welzel P., Hahn U. Biol. Chem. 382:2001;479-481.
62. Edman L. J. Phys. Chem. A. 104:2000;6165-6170.
63. Moore K.J., Turconi S., Ashman S., Ruediger M., Haupts U., Emerick V., Pope A.J. J. Biomol. Screen. 4:1999;335-353.
64. Pope A.J., Haupts U.M., Moore K.J. Drug Discov. Today. 4:1999;350-362.
65. Kral T., Langner M., Benes M., Baczynska D., Ugorski M., Hof M. Biophys. Chem. 95:2002;135-144.
66. Xu H., Frank J., Trier U., Hammer S., Schroder W., Behlke J., Schafer-Korting M., Holzwarth J.F., Saenger W. Biochemistry. 40:2001;7211-7218.
67. Kinjo M. Biotechniques. 25:1998;706.
68. Bjorling S., Kinjo M., Foldes-Papp Z., Hagman E., Thyberg P., Rigler R. Biochemistry. 37:1998;12971-12978.
69. Kinjo M. Anal. Chim. Acta. 365:1998;43-48.
70. Oehlenschläger F., Schwille P., Eigen M. Proc. Natl. Acad. Sci. USA. 93:1996;12811-12816.
71. Walter N.G., Schwille P., Eigen M. Proc. Natl. Acad. Sci. USA. 93:1996;12805-12810.
72. Stephan J., Dorre K., Brakmann S., Winkler T., Wetzel T., Lapczyna M., Stuke M., Angerer B., Ankenbauer W., Foldes-Papp Z., Rigler R., Eigen M. J. Biotechnol. 86:2001;255-267.
73. Winkler T., Kettling U., Koltermann A., Eigen M. Proc. Natl. Acad. Sci. USA. 96:1999;1375-1378.
74. Chen Y., Muller J.D., So P.T.C., Gratton E. Biophys. J. 77:1999;553-567.
75. Kettling U., Koltermann A., Eigen M. Curr. Top. Microbiol. Immunol. 243:1999;173-186.
76. Kask P., Palo K., Ullmann D., Gall K. Proc. Natl. Acad. Sci. USA. 96:1999;13756-13761.
77. Kask P., Palo K., Fay N., Brand L., Mets U., Ullmann D., Jungmann J., Pschorr J., Gall K. Biophys. J. 78:2000;1703-1713.
78. Müller J.D., Chen Y., Gratton E. Biophys. J. 78:2000;474-486.
79. Palo K., Metz U., Jager S., Kask P., Gall K. Biophys. J. 79:2000;2858-2866.
80. Rüdiger M., Haupts U., Moore K.J., Pope A.J. J. Biomol. Screen. 6:2001;29-37.
81. Palo K., Brand L., Eggeling C., Jager S., Kask P., Gall K. Biophys. J. 83:2002;605-618.
82. Haupts U., Rüdiger M., Ashman S., Turconi S., Bingham R., Wharton C., Hutchinson J., Carey C., Moore K.J., Pope A.J. J. Biomol. Screen. 8:2003;19-33.
83. Crockett A.O., Wittwer C.T. Anal. Biochem. 290:2001;89-97.
84. D.H. Densham, in Patent application WO 99/05315 (1999)
85. Sauer M., Angerer B., Ankenbauer W., Foldes-Papp Z., Gobel F., Han K.T., Rigler R., Schulz A., Wolfrum J., Zander C. J. Biotechnol. 86:2001;181-201.
86. Foldes-Papp Z., Angerer B., Thyberg P., Hinz M., Wennmalm S., Ankenbauer W., Seliger H., Holmgren A., Rigler R. J. Biotechnol. 86:2001;203-224.
87. Goodwin P.M., Cai H., Jett J.H., IshaugRiley S.L., Machara N.P., Semin D.J., VanOrden A., Keller R.A. Nucleosides Nucleotides. 16:1997;543-550.
88. Davis L.M., Fairfield F.R., Harger C.A., Jett J.H., Keller R.A., Hahn J.H., Krakowski L.A., Marrone B.L., Martin J.C., Nutter H.L., Ratliff R.L., Shera E.B., Simpson D.J., Soper S.A. Genet. Anal. Tech. Applic. 8:1991;1-7.
89. Braslavsky I., Hebert B., Kartalov E., Quake S.R. Proc. Natl. Acad. Sci. USA. 100:2003;3960-3964.
90. Donoho D.L. IEEE Trans. IT. 41:1995;613-627.
91. Alsberg B.K., Woodward A.M., Kell D.B. Chemometr. Intell. Lab. Systems. 37:1997;215-239.
92. Alsberg B.K., Woodward A.M., Winson M.K., Rowland J., Kell D.B. Analyst. 122:1997;645-652.
93. Shaw A.D., Winson M.K., Woodward A.M., McGovern A., Davey H.M., Kaderbhai N., Broadhurst D.I., Gilbert R.J., Taylor J., Timmins É.M., Alsberg B.K., Rowland J.J., Goodacre R., Kell D.B. Adv. Biochem. Eng. 66:1999;83-113.