High-speed DNA sequencing in ultrathin slab gels

Current Opinion in Biotechnology

Volumn 8, Issue 1, 1997, Pages 107-113

  Yager, Thomas D ^a,b,c   Dunn, James M ^a   Stevens, John K ^a  

^a Visible Genetics Inc   (Canada)

^b HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

ALGORITHM; DNA SEQUENCE; DNA TEMPLATE; GEL ELECTROPHORESIS; PRIORITY JOURNAL; REVIEW; THEORY; VELOCITY;

EID: 0031026705     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(97)80165-6     Document Type: Article

References (58)

1. 1. Nishikawa T, Kambara H: Analysis of limiting factors of DNA band separation by a DNA sequencer using fluorescence detection. Electrophoresis 1991, 12: 623-631.
2. 2. Lerman LS, Fritsch HL: Why does the electrophoretic mobility of DNA in gels vary with the length of the molecule? Biopolymers 1982, 21: 995-997.
3. 3. Zhang W, Bond JP, Anderson CF, Lohman TM, Record MT Jr: Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proc Natl Acad Sci USA 1996, 93:2511-2516. A demonstration that oligo(dT) displays the polyelectrolyte effect (a constant degree of neutralization of backbone phosphates by screening counterions), even at the moderately high salt concentrations used in gel electrophoresis. This finding allows the parameter β (net ionization per phosphate) to be fixed at a constant value in quantitative theories of DNA electrophoresis.
4. 4. Flory PJ: Principles of Polymer Chemistry. Ithaca, NY: Cornell University Press; 1953:626-629.
5. 5. Luckey JA, Morris TB, Smith LM: Analysis of resolution in DNA sequencing by capillary gel electrophoresis. J Phys Chem 1993, 97:3067-3075.
6. 6. Luckey JA, Smith LM: A model for the mobility of single-stranded DNA in capillary-gel electrophoresis. Electrophoresis 1993, 14:492-501.
7. 7. Zimm BH: Mechanism of gel electrophoresis of DNA: unexpected findings. Curr Opin Struct Biol 1993, 3:373-376.
8. 8. Zimm BH, Lumpkin O: Reptation of a polymer chain in an irregular matrix: diffusion and electrophoresis. Macromolecules 1993, 26:226-234.
9. 9. Smisek DL, Hoagland DA: Electrophoresis of flexible macromolecules: evidence for a new mode of transport in gels. Science 1990, 248:1221-1223.
10. 10. Calladine CR, Collis CM, Drew HR, Mott MR: A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J Mol Biol 1991, 221:981-1005.
11. 11. Niederweis M, Lederer T, Hillen W: Matrix effects suggest an important influence of DNA-polyacrylamide interactions on the electrophoretic mobility of DNA. J Biol Chem 1994, 269:10156-10162.
12. 12. Braithwaite DK, Ito J: Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res 1993, 21:787-802.
13. 13. Kim Y, Eom SH, Wang J, Lee D-S, Suh SW, Steitz TA: Crystal structure of Thermus aquaticus DNA polymerase. Nature 1995, 376:612-616. This and the independent paper of Korolev et al. [14••] provide the basis for the semirational design of Taq mutants for improved PCR sequencing.
14. 14. Korolev S, Nayal M, Barnes WM, De Cera E, Waksman G: Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 Å resolution: structural basis for thermostability. Proc Natl Acad Sci USA 1995, 92:9264-9268. This and the independent paper of Kim et al. [13••] provide the basis for the semirational design of Taq mutants for improved PCR sequencing.
15. 15. Tabor S, Richardson CC: A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy-and dideoxyribonucleotides. Proc Natl Acad Sci USA 1995, 92:6339-6343. A very good example of protein engineering as applied to DNA sequencing polymerases. Guided by the X-ray crystal structure, these scientists performed site-directed mutagenesis of a critical residue in the 'O' helix, which faces the dNTP-DNA binding cleft. The replacement of one amino acid residue causes the enzyme to lose its ability to discriminate between dNTPs and ddNTPs.
16. 16. Voss H, Wiemann S, Grothues D, Sensen C, Zimmermann J, Schwager C, Stegemann J, Erfle H, Rupp T, Ansorge W: Automated low-redundancy large-scale DNA sequencing by primer walking. Biotechniques 1993, 15:714-721.
17. 17. Innis MA, Myambo KB, Gelfand DH, Brow MA: DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc Natl Acad Sci USA 1988, 85:9436-9440.
18. 18. Olson M, Hood L, Cantor C, Botstein D. A common language for physical mapping of the human genome. Science 1989, 245:1434-1435.
19. 19. Venter JC, Smith HO, Hood L: A new strategy for genome sequencing. Nature 1996, 381:364-366. A coherent argument for the view that large-scale sequencing of the human genome can be achieved with existing technologies. This proposal is of special note because it presents a strategy to dispense with the current labor-intensive approach of subcloning the genome into successively smaller ordered fragments.
20. 20. Lagerkvist A, Stewart J, Lagerstrom-Fermer M, Landegren U: Manifold sequencing: efficient processing of large sets of sequencing reactions. Proc Natl Acad Sci USA 1994, 91:2245-2249.
21. 21. Rolfs A, Weber I: Fully-automated, nonradioactive solid-phase sequencing of genomic DNA obtained from PCR. Biotechniques 1994, 17:782-787.
22. 22. Esaka Y, Yamaguchi Y, Kano K, Goto M, Haraguchi H, Takahashi J-I: Separation of hydrogen-bonding donors in capillary electrophoresis using polyethers as matrix. Anal Chem 1994, 66:2441-2445.
23. 23. Fung EN, Yeung ES: High-speed DNA sequencing by using mixed poly(ethylene oxide) solutions in uncoated capillary columns. Anal Chem 1995, 67:1913-1919.
24. 24. Patten TE, Xia J, Abernathy T, Matyjaszewski K: Polymers with very low polydispersities from atom transfer radical polymerization. Science 1996, 272:866-868. This paper describes a free-radical polymerization reaction that occurs via a 'living polymerization' mechanism. This type of mechanism has the property that no dead-end states are produced (in contrast to a chain-reaction mechanism). Consequently, a living polymerization scheme will produce polymers of very high uniformity (low polydispersity). A gel that is made from a homogeneous polymer is predicted to have superior resolving properties.
25. 25. Volkmuth WD, Austin RH: DNA electrophoresis in microlithographic arrays. Nature 1992, 358:600-602.
26. 26. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SBH, Hood LE: Fluorescence detection in automated DNA sequence analysis. Nature 1986, 321:674-679.
27. 27. Ansorge W, Sproat B, Stegemann J, Schwager C, Zenke M: Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acids Res 1987, 15:4593-4602.
28. 28. Prober JM, Trainor GL, Dam RJ, Hobbs FW, Robertson CW, Zagursky RJ, Cocuzza AJ, Jensen MA, Baumeister K: A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 1987, 238:336-341.
29. 29. Middendorf LR, Bruce JC, Bruce RC, Eckles RD, Grone DL, Roemer SC, Sloniker GD, Steffens DL, Sutter SL, Brumbaugh JA, Patonay G: Continuous on-line DNA sequencing using a versatile infrared laser scanner/electrophoresis apparatus. Electrophoresis 1992, 13:487-494.
30. 30. Shealy DB, Lipowska M, Lipowski J, Narayanan N, Sutter S, Strekowski L, Patonay G: Synthesis, chromatographic separation, and characterization of near-infrared-labeled DNA oligomers for use in DNA sequencing. Anal Chem 1995, 67:247-251.
31. 31. Williams DC, Soper SA: Ultrasensitive near-IR fluorescence detection for capillary gel electrophoresis and DNA sequencing applications. Anal Chem 1995, 67:3427-3432.
32. 32. Fasol G: Room-temperature blue gallium nitride laser diode. Science 1996, 272:1751-1752. At long last, an efficient blue diode laser. This eventually may be used in construction of low-cost multiwavelength sequencing instruments.
33. 33. Eggers M, Hogan M, Reich RK, Lamture J, Erlich D, Hollis M, Kosicki B, Powdrill T, Beattie K, Smith S et al.: A microchip for quantitative detection of molecules utilizing luminescent and radioisotope reporter groups. Biotechniques 1994, 17:516-525.
34. 34. Peacock A, Verhoeve P, Rando N, Van Dordrecht A, Taylor BG, Erd C, Perryman MAC, Venn R, Howlett J, Goldie DJ et al.: Single optical photon detection with a super-conducting tunnel junction. Nature 1996, 381:135-137. A description of an efficient CCD photon detector with inherent wavelength discrimination. Someday this may be used in the construction of multiwavelength sequencing instruments.
35. 35. Chen DY, Harke HR, Dovichi NJ: 2-label peak-height encoded DNA sequencing by capillary gel electrophoresis - 3 examples. Nucleic Acids Res 1992, 20:4873-4880.
36. 36. Ruiz-Martinez MC, Berka J, Belenkii A, Foret F, Miller AW, Karger BL: DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. Anal Chem 1993, 65:2851-2858.
37. 37. Kambara H, Nagai M, Hayasaka S: Real time automated simultaneous double-stranded DNA sequencing using two-color fluorophore labelling. Bio-Technology 1991, 9:648-651.
38. 38. Wiemann S, Stegemann J, Grothues D, Bosch A, Estivill X, Schwager C, Zimmermann J, Voss H, Ansorge W: Simumtaneous on-line DNA sequencing on both strands with two fluorescent dyes. Anal Biochem 1995, 224:117-121.
39. 39. Wiemann S, Stegemann J, Zimmermann J, Voss H, Benes V, Ansorge W: "Doublex" fluorescent sequencing: two independent sequences obtained simultaneously in one reaction with internal labelling and unlabeled primers. Anal Biochem 1996, 234:166-174.
40. 40. Nelson M, Van Etten JL, Grabherr R: DNA sequencing of four bases using three lanes. Nucleic Acids Res 1992, 20:1345-1348.
41. 41. Nelson M, Zhang Y, Steffens DL, Grabherr R, Van Etten JL: Sequencing two DNA templates in five channels by digital compression. Proc Natl Acad Sci USA 1993: 90:1647-1651.
42. 42. Noolandi J, Forsyth , Shi A-C: Sequencing using pulsed field and image reconstruction. Proc Natl Acad Sci USA 1993, 90:10101-10104.
43. 43. Wu Y, Mislan D: Automated DNA sequencing: an image processing approach. Appl Theor Electrophor 1993, 3:223-228.
44. 44. Naeve CW, Buck GA, Niece RL, Pon RT, Robertson M, Smith AJ: Accuracy of automated DNA sequencing: a multi-laboratory comparison of sequencing results. Biotechniques 1995, 19:448-453. An empirical assessment of the performance of automated DNA sequencing. Multiple laboratories were asked to sequence the same preparation of DNA using the four dye/single lane approach.
45. 45. Koop BF, Rowan L, Chen W-Q, Deshpande P, Lee H, Hood L: Sequence length and error analysis of Sequenase and automated Taq cycle sequencing methods. Biotechniques 1993, 14:442-447.
46. 46. Voss H, Schwager C, Wiemann S, Zimmermann J, Stegemann J, Erfle H, Voie A-M, Drzonek H, Ansorge W: Efficient low redundancy large-scale DNA sequencing at EMBL. J Biotechnol 1995, 41:121-129. An empirical assessment of the performance of automated DNA seqencing using the single-dye/single lane approach. Large-scale operation in a single laboratory.
47. 47. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al.: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269:496-512. A milestone in history - the first complete sequence of the genome of a living cell, a eubacterium.
48. 48. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM et al.: The minimal gene complement of Mycoplasma genitalium. Science 1995, 270:397-403. The second complete sequence of the genome of a living cell, another eubacterium.
49. 49. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD et al.: Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996, 273:1058-1073. The first complete genome sequence of an archaeon. Remarkably, only 44% of its genes bear any homology to known genes from the other two domains of life (eubacteria and eukaryotes).
50. 50. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al.: Life with 6000 genes. Science 1996, 274:546-567. The complete sequence of Brewer's yeast, Saccharomyces cerevisiae.
51. 51. Morell V: Life's last domain. Science 1996, 273:1043-1045.
52. 52. Olson MV: A time to sequence. Science 1995, 270:394-396. An eloquent argument to begin sequencing the human genome now with existing slab-gel technology.
53. 53. Gibbs RA: Pressing ahead with human genome sequencing. Nat Genet 1995, 11:121-125. An eloquent argument to begin sequencing the human genome now with existing slab-gel technology.
54. 54. Smith MW, Holmsen AL, Wei YH, Peterson M, Evans GA: Genomic sequence sampling: a strategy for high resolution sequence-based physical mapping of complex genomes. Nat Genet 1994, 7:40-47.
55. 55. Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E et al.: A gene map of the human genome. Science 1996, 274:540-546. The placement of >16000 partial gene sequences (mostly ESTs) on the human genetic map, under the auspices of the 'UNIGENE' project.
56. 56. Banfi S, Borsani G, Rossi E, Bernard L, Guffanti A, Rubboli F, Marchitiello A, Giglio S, Coluccia E, Zollo M et al.: Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching. Nat Genet 1996, 13:167-174. The human EST database was scanned for sequences that had homology to genes that mutate to give visible phenotypes in Drosophila. This suggests a very inexpensive route to the preliminary identification of human disease genes.
57. 57. Chadwick RB, Conrad MP, McGinnis MD, Johnston-Dow L, Spurgeon SL, Kronick MN: Heterozygote and mutation detection by direct automated fluorescent DNA sequencing using a mutant Taq DNA polymerase. Biotechniques 1996, 20:676-683. Very high quality sequencing data was obtained from double-stranded PCR products. The key was to use a new mutant form of Taq that does not discriminate between dNTPs and ddNTPs.
58. 58. Woolley AT, Mathies RA: Ultra-high-speed DNA sequencing using capillary electrophoresis chips. Anal Chem 1995, 67:3676-3680. A very impressive demonstration that DNA sequencing ladders can be resolved in a polyacrylamide-filled channel etched into a silicon chip.