Scientific and practical applications of molecular colonies

Molecular Biology

Volumn 41, Issue 2, 2007, Pages 250-261

  Chetverin, A B ^a   Chetverina, E V ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

Molecular cloning; Molecular colony technique; Molecular diagnostics; Origin of life; Polonies; RNA recombination; RNA world; Spontaneous RNA synthesis

Indexed keywords

EID: 34247539042     PISSN: 00268933     EISSN: 16083245     Source Type: Journal    
DOI: 10.1134/S0026893307020070     Document Type: Article

References (85)

1. Chetverin A.B. 1998. Bacteriophage Qβ as a subject of molecular biology. Usp. Biol. Khim. 38, 3-75.
2. Chetverin A.B., Spirin A.S. 1995. Replicable RNA vectors: Prospects for cell-free gene amplification, expression and cloning. Prog. Nucleic Acid Res. Mol. Biol. 51, 225-270.
3. Haruna I., Spiegelman S. 1965. Autocatalytic synthesis of a viral RNA in vitro. Science. 150, 884-886.
4. Carmichael G.G., Landers T.A., Weber K. 1976. Immunochemical analysis of the functions of the subunits of phage Qβ ribonucleic acid replicase. J. Biol. Chem. 251, 2744-2748.
5. Blumenthal T., Carmichael G. 1979. RNA replication: function and structure of Qβ replicase. Annu. Rev. Biochem. 48, 525-545.
6. Biebricher C.K., Eigen M., Gardiner W.C. 1983. Kinetics of RNA replication. Biochemistry. 22, 2544-2559.
7. Rensing U., August J.T. 1969. The 3'-terminus and the replication of phage RNA. Nature. 224, 853-856.
8. Weber H., Weissmann C. 1970. The 3'-termini of bacteriophage Qβ plus and minus Strands. J. Mol. Biol. 51, 215-224.
9. Weissmann C., Feix G., Slor H. 1968. In vitro synthesis of phage RNA: The nature of the intermediates. Cold Spring Harbor Symp. Quant. Biol. 33, 83-100.
10. Chetverin A.B., Kopein D.S., Chetverina H.V., Demidenko A.A., Ugarov V.I. 2005. Viral RNA-directed RNA polymerases use diverse mechanisms to promote recombination between RNA molecules. J. Biol. Chem. 280, 8748-8755.
11. Haruna I., Spiegelman S. 1965. Specific template requirements of RNA replicases. Proc. Natl. Acad. Sci. USA. 54, 579-587.
12. Sumper M., Luce R. 1975. Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qβ replicase. Proc. Natl. Acad. Sci. USA. 72, 162-166.
13. Biebricher C.K., Eigen M., Luce R. 1981. Product analysis of RNA generated de novo by Qβ replicase. J. Mol. Biol. 148, 369-390.
14. Biebricher C.K., Eigen M., Luce R. 1986. Template-free RNA synthesis by Qβ replicase. Nature. 321, 89-91.
15. Chetverin A.B., Chetverina H.V., Munishkin A.V. 1991. On the nature of spontaneous RNA synthesis by Qβ replicase. J. Mol. Biol. 222, 3-9.
16. Biebricher C.K., Eigen M., McCaskil J.S. 1993. Template-directed and template-free RNA synthesis by Qβ replicase. J. Mol. Biol. 231, 175-179.
17. Brown D., Gold L. 1995. Selection and characterization of RNAs replicated by Qβ replicase. Biochemistry. 34, 14775-14782.
18. Biebricher C.K., Luce R. 1993. Sequence analysis of RNA species synthesized by Qβ replicase without template. Biochemistry. 32, 4848-4854.
19. Pasteur L. 1860. Expériences relatives aux géné rations dites spontanées. C. R. Acad. Sci. 50, 303-307.
20. Koch R. 1881. Zür Untersuchung von pathogenen Organismen. Mittheilungen aus dem Kaiserlichen Gesundheitsamte, 1, 1-48.
21. Chetverina H.V., Chetverin A.B. 1993. Cloning of RNA molecules in vitro. Nucleic Acids Res. 21, 2349-2353.
22. Crick F.H. 1958. On protein synthesis. Symp. Soc. Exp. Biol. 12, 138-163.
23. McCaskill J.S., Bauer G.J. 1993. Images of evolution: Origin of spontaneous RNA replication waves. Proc. Natl. Acad. Sci. USA. 90, 4191-4195.
24. Hirst G.K. 1962. Genetic recombination with Newcastle disease virus, poliovirus and influenza virus. Cold Spring Harbor Symp. Quant. Biol. 27, 303-309.
25. Ledinko N. 1963. Genetic recombination with poliovirus type 1: Studies of crosses between a normal horse serum-resistant mutant and several guanidine-resistant mutants of the same strain. Virology. 180, 107-119.
26. Romanova L.I., Tolskaya E.A., Kolesnikova M.S., Agol V.I. 1980. Biochemical evidence for intertypic genetic recombination of polioviruses. FEBS Lett. 118, 109-112.
27. King A.M.Q., McCahon D., Slade W.R., Newman J.W.I. 1982. Recombination in RNA. Cell. 29, 921-928.
28. Jarvis T.C., Kirkegaard K. 1992. Poliovirus RNA recombination: mechanistic studies in the absence of selection. EMBO J. 11, 3135-3145.
29. ChetverinA.B., Chetverina H.V., Demidenko A.A., Ugarov V.I. 1997. Nonhomologous RNA recombination in a cell-free system: Evidence for a transesterification mechanism guided by secondary structure. Cell. 88, 503-513.
30. Olsthoorn R.C.L., van Duin J. 1996. Random removal of inserts from an RNA genome: Selection against single-stranded RNA. J. Virol. 70, 729-736.
31. Chetverin A.B. 1999. A new look at recombination of RNA. Mol. Biol. 33, 985-996.
32. Chetverin A.B. 1999. The puzzle of RNA recombination. FEBS Lett. 460, 1-5.
33. Chetverina H.V., Demidenko A.A., Ugarov V.I., Chetverin A.B. 1999. Spontaneous rearrangements in RNA sequences. FEBS Lett. 450, 89-94.
34. Nam K., Hudson R.H.E., Chapman K.B., Ganeshan K., Damha M.J., Boeke, J.D. 1994. Yeast lariat debranching enzyme: Substrate and sequence specificity. J. Biol. Chem. 269, 20,613-20,621.
35. Chetverin A.B. 2004. Replicable and recombinogenic RNAs. FEBS Lett. 567, 35-41.
36. Spirin A.S. 2002. Omnipotent RNA. FEBS Lett. 530, 4-8.
37. Spirin A.S. 2005. RNA world and its evolution. Mol. Biol. 39, 550-556.
38. Spirin A.S. 2005. Origin, probable life forms, and size of primeval creatures. Paleontol. Zh. 39, no. 4, 25-32.
39. Chetverina H.V., Samatov T.R., Ugarov V.I., Chetverin A.B. 2002. Molecular colony diagnostics: Detection and quantitation of viral nucleic acids by in-gel PCR. Bio-Techniques. 33, 150-156.
40. Saiki R.K., Scharf S., Faloona F., Mullis K.B., Horn G.T., Erlich H.A., Arnheim N. 1985. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 230, 1350-1354.
41. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., Mullis K.B., Erlich H.A. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239, 487-491.
42. Chetverin A.B., Chetverina H.V. 1995. RF Patent no. 2048522.
43. Chetverin A.B., Chetverina H.V. 1997. US Patent no. 5616478.
44. Chetverin A.B., Chetverina H.V. 2002. Precise diagnosis with the aid of molecular colonies. Mol. Biol. 36, 320-327.
45. Mitra R.D., Church G.M. 1999. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27, e34.
46. Mitra R.D., Butty V.L., Shendure J., Williams B.R., Housman D.E., Church G.M. 2003. Digital genotyping and haplotyping with polymerase colonies. Proc. Natl. Acad. Sci. USA. 100, 5926-5931.
47. Chetverina H.V., Kravchenko A.V., Falaleeva M.V., Chetverin A.B. 2007. Express hybridization of molecu lar colonies with fluorescent probes. Bioorg. Khim. 33, no. 2.
48. Chetverin A.B., Samatov T.R., Chetverina H.V. 2006. Application for RF Patent no. 2006109271.
49. Samatov T.R., Chetverina H.V., Chetverin A.B. 2006. Real-time monitoring of DNA colonies growing in a polyacrylamide gel. Anal. Biochem. 356, 300-302.
50. Cardullo R.A., Agrawal S., Flores C., Zamecnik P.C., Wolf D.E. 1988. Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA. 85, 8790-8794.
51. Tyagi S., Kramer F.R. 1996. Molecular beacons: Probes that fluoresce upon hybridization. Nature Biotechnol. 14, 303-308.
52. Wittwer C.T., Herrmann M.G., Moss A.A., Rasmunssen R.P. 1997. Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques. 22, 130-138.
53. Chetverina H.V., Falaleeva M.V., Chetverin A.B. 2004. Simultaneous assay of DNA and RNA targets in the whole blood using novel isolation procedure and molecular colony amplification. Anal. Biochem. 334, 376-381.
54. LeDuc J.W., Damon I., Meegan J.M., Relman D.A., Huggins J., Jahrling P.B. 2002. Smallpox research activities: US interagency collaboration, 2001. Emerg. Infect. Dis. 8, 743-745.
55. Samatov T.R., Chetverina H.V., Chetverin A.B. 2005. Expressible molecular colonies. Nucleic Acids Res. 33, e145.
56. Sambrook J., Russell D.W. 2001. Molecular Cloning, 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Lab. Press.
57. Roberts R.W., Ja W.W. 1999. In vitro selection of nucleic acids and proteins: What are we learning? Curr. Opin. Struct. Biol. 9, 521-529.
58. Lukyanov K.A., Matz M.V., Bogdanova E.A., Gurskaya N.G., Lukyanov S.A. 1996. Molecule by molecule PCR amplification of complex DNA mixtures for direct sequencing: an approach to in vitro cloning. Nucleic Acids Res. 24, 2194-2195.
59. Vogelstein B., Kinzler K.W. 1999. Digital PCR. Proc. Natl. Acad. Sci. USA. 96, 9236-9241.
60. Brenner S., Williams S.R., Vermaas E.H., Storck T., Moon K., McCollum C., Mao J.I., Luo S., Kirchner J.J., Eletr S., DuBridge R.B., Burcham T., Albrecht G. 2000. In vitro cloning of complex mixtures of DNA on micro-beads: Physical separation of differentially expressed cDNAs. Proc. Natl. Acad. Sci. USA. 97, 1665-1670.
61. Sepp A., Tawfik D.S., Griffiths A.D. 2002. Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS Lett. 532, 455-458.
62. Dressman D., Yan H., Traverse G., Kinzler K.W., Vogelstein B. 2003. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl. Acad. Sci. USA. 100, 8817-8822.
63. Guatelli J.C., Whitfield K.M., Kwoh D.Y., Barringer K.J., Richman D.D., Gingeras T.R. 1990. Isothermal in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA. 87, 1874-1878.
64. Compton J. 1991. Nucleic acid sequence-based amplification. Nature. 350, 91-92.
65. Walker G.T., Little M.C., Nadeau J.G., Shank D.D. 1992. Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc. Natl. Acad. Sci. USA. 89, 392-396.
66. Lizardi P.M., Huang X., Zhu Z., Bray-Ward P., Thomas D.C., Ward D.C. 1998. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19, 225-232.
67. Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., Amino N., Hase T. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28, e63.
68. Boles T.C., Kron S.J., Adams C.P. 1999. US Patent no. 5932711.
69. Merritt J., DiTonno J.R., Mitra R.D., Church G.M., Edwards J.S. 2003. Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. Nucleic Acids Res. 31, e84.
70. Butz J., Wickstrom E., Edwards J. 2003. Characterization of mutations and loss of heterozygosity of p53 and K-ras2 in pancreatic cancer cell lines by immobilized polymerase chain reaction. BMC Biotechnol. 3, 11.
71. Mikkilineni V., Mitra R. D., Merritt J., DiTonno J.R., Church G.M., Ogunnaike B., Edwards J.S. 2004. Digital quantitative measurements of gene expression. Biotechnol. Bioeng. 86, 117-124.
72. Butz J.A., Roberts K.G., Edwards J.S. 2004. Detecting changes in the relative expression of KRAS2 splice variants using polymerase colonies. Biotechnol. Prog. 20, 1836-1839.
73. Butz J.A., Yan H., Mikkilineni V., Edwards J.S. 2004. Detection of allelic variations of human gene expression by polymerase colonies. BMC Genet. 5, 3.
74. Merritt J., Ogunnaike B.A., Edwards J.S. 2005. Parallel analysis of mutant human glucose 6-phosphate dehydro genase in yeast using PCR colonies. Biotechnol Bioeng. 92, 519-531.
75. Zhang K., Zhu J., Shendure J., Porreca G.J., Aach J.D., Mitra R.D., Church G.M. 2006. Long-range polony haplotyping of individual human chromosome molecules. Nature Genet. 38, 382-387.
76. Mitra R.D., Shendure J., Olejnik J., Olejnik E.K., Church G.M. 2003. Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem. 320, 55-65.
77. Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D., Church G.M. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 309, 1728-1732.
78. Zhu J., Shendure J., Mitra R.D., Church G.M. 2003. Single molecule profiling of alternative pre-mRNA splicing. Science. 301, 836-838.
79. Marx V. 2004. Helping SNPs to speak up louder than before. Genomics Proteomics. March issue.
80. Gilbert W. 1986. Origin of life: The RNA world. Nature. 319, 618.
81. Gilbert W., de Souza S.J. 1999. Introns and the RNA world. In: The RNA World, 2nd ed. Eds. Gesteland R.F., Cech T.R., Atkins J.F. Cold Spring Harbor, NY: Cold Spring Harbor Lab. Press, 221-231.
82. Szostak J.W. 1999. Constrains on the sizes of the earliest cells. Size Limits of Very Small Microorganisms. Proc. of a Workshop, Washington, DC: Natl. Acad. Press, 120-125.
83. Oparin A.I. 1941. Vozniknovenie zhizni na Zemle (The Origin of Life on the Earth), 2nd ed. Moscow: Akad, Nauk SSSR.
84. Jay D.G., Gilbert W. 1987. Basic protein enhances the incorporation of DNA into lipid vesicles: Model for the formation of primordial cells. Proc. Natl. Acad. Sci. USA. 84, 1978-1980.
85. Woese C.R. 1998. The universal ancestor. Proc. Natl. Acad. Sci. USA. 95, 6854-6859.