Gel-based microchips: History and prospects

Molecular Biology

Volumn 38, Issue 1, 2004, Pages 4-13

  Kolchinsky, A M ^a   Gryadunov, D A ^b   Lysov, Yu P ^b   Mikhailovich, V M ^b   Nasedkina, T V ^b   Turygin, A Yu ^b   Rubina, A Yu ^b   Barsky, V E ^b   Zasedatelev, A S ^b  

^a Health Front Line Ltd   (United States)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

Biological microchips; Diagnostics; Genomics; Proteomics

Indexed keywords

AMIDE; DNA BINDING PROTEIN; DNA FRAGMENT; LIGAND; METHACRYLAMIDE; PROTEIN; UNCLASSIFIED DRUG;

BIOSENSOR; DEVICE; DIAGNOSTIC KIT; DNA BINDING MOTIF; DNA MICROARRAY; GEL; GENE TECHNOLOGY; GENOME; HISTORY; MICROCHIP; MOLECULE; NONHUMAN; ORTHOPOXVIRUS; PHOTOACTIVATION; POLYMERIZATION; PROTEIN DNA INTERACTION; PROTEOMICS; QUANTUM YIELD; REVIEW; RUSSIAN FEDERATION; SMALLPOX VIRUS; TUBERCULOSIS;

ANTHRAX; BACTERIA (MICROORGANISMS); ORTHOPOXVIRUS; VARIOLA VIRUS;

EID: 3442881597     PISSN: 00268933     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:MBIL.0000015134.67385.fd     Document Type: Review

References (43)

1. Drmanac R., Crkvenjakov R. 1987. Yugoslav Patent Application YU0057087A. Process for obtaining genome by hybridization and oligonucleotidic tests. [original spelling] Priority date: April 1, 1987, date of publication: August 31, 1990.
2. Southern E. M. 1988. Method and apparatus for analysing polynucleotide sequences. UK Patent Application, Isis Innovation. Priority date: May 3, 1988.
3. Roberts L. 1988. Carving up the human genome. Science. 242, 1244-1245.
4. The human genome in Russia. Interview with L.L. Kisselev. Electronic journal Znanie-Sila, September 22, 2000: www.znanie-sila.ru.
5. Lysov Yu., Florentiev V., Khorlin A., Khrapko K., Shik V., Mirzabekov A. 1988. Determination of the DNA nucleotide sequence by hybridization with oligonucleotides. A new method. Dokl. Akad. Nauk SSSR. 303, 1508-1511.
6. Bains W., Smith G.C. 1988. A novel method for nucleic acid sequence determination. J. Theor. Biol. 135, 303-307.
7. Cantor C.R., Mirzabekov A., Southern E. 1992. Report on the sequencing by hybridization workshop. Genomics. 13, 1378-1383.
8. Academician Andrei Mirzabekov about new professions of biochips and management in science. Rossiiskaya Gazeta, January 8, 2003: www.rg.ru
9. S nami vse yasno (Everything is clear with us). Poisk, March 20, 2003.
10. Schiermeier Q. 2001. Joint venture on biochips ends in disarray. Nature. 412, 845.
11. Barsky V.E., Kolchinsky A.M., Lysov Yu.P., Mirzabekov A.D. 2002. Biological microchips with hydrogel-immobilized nucleic acids, proteins, and other compounds: properties and applications in genomics. Mol. Biol. 36, 563-584.
12. Mirzabekov A., Kolchinsky A. 2002. MAGIChip: Properties and applications in genomic studies. In Genomic Technologies: Present and Future. Eds. Galas D.J., McCormack S.J. Caister Academic Press, pp. 163-196.
13. Vasiliskov V., Timofeev E., Surzhikov S., Drobyshev A., Shick V., Mirzabekov A. 1999. Fabrication of microarray of gel-immobilized compounds on a chip by copolymerization. BioTechnique. 27, 592-606.
14. Rubina A.Yu., Pan'kov S.V., Dementieva E.I., Pen'kov D.N., Butygin A.V., Vasiliskov V.A., Chudinov A.V., Mikheikin A.L., Mikhailovich V.M., Mirzabekov A.D. 2003. Hydrogel drop microchips containing immobilized oligonucleotides and DNA: their properties and two new efficient methods for large-scale production. Analyt. Biochem. in press.
15. Rehman F.N., Audeh M., Abrams E.S., Hammond P.W., Kenney M., Boles T.C. 1999. Immobilization of acrylamide-modified oligonucleotides by co-polymerization. Nucleic Acids Res. 27, 649-655.
16. Rubina A.Y., Dementieva E.I., Stomakhin A.A., Darii E.L., Pan'kov S.V., Barsky V.E., Ivanov S.M., Konovalova E.V., Mirzabekov A.D. 2003. Hydrogel-based protein microchips: manufacturing, properties, and applications. Biotechniques. 34, 1008-1014, 1016-1020, 1022.
17. Sorokin N.V., Chechetkin V.R., Chechetkin M.A., Vasiliskov V.A., Turygin A.Y., Mirzabekov A.D. 2003. Kinetics of hybridization on the oligonucleotide microchips with gel pads. J. Biomol. Struct. Dyn. 21, 279-288.
18. Khomyakova E.B., Livshits M.A., Sharonov A.Yu., Prokopenko D.V., Mirzabekov A.D. 2003. Analysis of perfect and mismatched DNA duplexes with a generic hexanucleotide microchip. Mol. Biol. 37, 726-741.
19. Drobyshev A., Zasedatelev A., Yershov G., Mirzabekov A. 1999. Massive parallel analysis of DNA-Hoechst 33258 binding specificity with a generic oligodeoxyribonucleotide microchip. Nucleic Acids Res. 27, 4100-4105.
20. Krylov A., Zasedateleva O., Prokopenko D., Rouviere-Yaniv J., Mirzabekov A. 2001. Large-scale parallel analysis of the binding specificity of HU protein with ss and ds DNA on generic oligonucleotide microchips. Nucleic Acids Res. 29, 2654-2660.
21. Zasedateleva O.A., Krylov A.S., Prokopenko D.V., Skabkin M.A., Ovchinnikov L.P., Kolchinsky A.M., Mirzabekov A.D. 2002. Specificity of mammalian Y-box binding protein p50 in binding to ss and ds DNA analyzed with generic oligonucleotide microchip. J. Mol. Biol. 324, 73-87.
22. Chechetkin V., Prokopenko D., Zasedateleva O., Gitelson G., Lomakin E., Livshits M., Malinina L., Turygin A., Krylov A., Mirzabekov A. 2003. Analysis of binding specificity of disulfide bonded dimeric λ-cro V55C protein with generic hexamer oligonucleotide microchip. J. Biomol. Struct. Dyn. in press.
23. Kolchinsky A., Mirzabekov A. 2002. Analysis of SNPs and other genomic variations using gel-based chips. Human Mut. 19, 343-360.
24. Ramakrishnan R., Dorris D., Lublinsky A., Nguyen A., Domanus M., Prokhorova A., Gieser L., Touma E., Lockner R., Tata M., Zhu X., Patterson M., Shippy R., Sendera T.J., Mazumder A. 2002. An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res. 30, 30.
25. Mikhailovich V., Lapa S., Gryadunov D., Sobolev A., Strizhkov B., Chernych N., Skotnikova O., Irtuganova O., Moroz A., Litvinov V., Vladimirskiy M., Perelman M., Chernousova L., Erokhin V., Zasedatelev A., Mirzabekov A. 2001. Identification of rifampin-resistant Mycobacterium tuberculosis strains by hybridization, PCR, and ligase detection reaction on oligonucleotide microchips. J. Clinical Microbiology. 39, 2531-2540.
26. Gryadunov D.A., Mikhailovich V.M., Lapa S.A., Rudinsky N.I., Barsky V.E., Chudinov A.V., Zasedatelev A.S., Mirzabekov A.D. 2003. Identification of strains of Mycobacterium tuberculosis with simultaneous detection of their drug resistance by hybridization on oligonucleotide microchips. Molekular. Genetika. 4, 24-27.
27. http://www.roche-diagnostics.com/barmd/rmdproductsmycobaterial4.html
28. Gryadunov D.A., Mikhailovich V.M., Noskov A.N., Lapa S.A., Sobolev A.Yu., Pan'kov S.V., Rubina A.Yu., Zasedatelev A.S., Mirzabekov A.D. 2001. Detection of Bacillus anthracis using multiplex PCR on the oligonucleotide biochip. Dokl. Biochem. Biophys. 381, 384-386.
29. http://www.asc2002.com/summaries/k/KP-19.pdf
30. http://www.darpa.mil/body/pdf/DARPA%20BIO%20Program.pdf
31. Enserink M., Stone R. 2002. Dead virus walking. Science. 295, 2001-2005.
32. Lapa S., Mikheev M., Shchelkunov S., Mikhailovich V., Sobolev A., Blinov V., Babkin I., Guskov A., Sokunova E., Zasedatelev A., Sandakhchiev L., Mirzabekov A. 2002. Species-level identification of orthopox-viruses with an oligonucleotide microchip. J. Clin. Microbiol. 40, 753-757.
33. Nasedkina T., Domer P., Zharinov V., Hoberg J., Lysov Yu., Mirzabekov A. 2002. Identification of chromosomal translocations in leukemias by hybridization with oligonucleotide microarrays. Haematologica. 87, 363-372.
34. Nasedkina T., Zharinov V., Isaeva E., Karachunskii A., Gartenhaus R., Mirzabekov A. 2003. Clinical screening of gene rearrangements in childhood leukemia by microarray-based approach. Clin. Cancer Res. in press.
35. Mirzabekov A., Kolchinsky A. 2002. Emerging array-based technologies in proteomics. Curr. Opin. Chem. Biol. 6, 70-75.
36. Arenkov P., Kukhtin A., Gemmell A., Chupeeva V., Voloschuk S., Mirzabekov A. 2000. Protein microchips: Use for immunoassay and enzymatic reactions. Anal. Biochem. 278, 123-131.
37. Klibanov A.M. 1979. Enzyme stabilization by immobilization. Analyt. Biochem. 93, 1-25.
38. Fesenko D.O., Nasedkina T.V., Prokopenko D.V., Mirzabekov A.D. 2003. Hydrogel cell microchip for monitoring cell populations and enviromental pollutants. In preparation.
39. Ractorguev S.M., Zavil'gel'skii G.B. 2001. Lux biosensors for detection of arsenic ions. Biotekhnologiya. 2, 77-82.
40. Quackenbush J. 2002. Microarray data normalization and transformation. Nat. Genet. 32. Suppl., 496-501.
41. Mikheikin A.L., Chudinov A.V., Yaroshchuk A.I., Rubina A.Yu., Pan'kov S.V., Krylov A.S., Zasedatelev A.S., Mirzabekov A.D. 2003. A fluorescent dye with low specificity to DNA nucleotide sequences: quantitative assessment of oligonucleotides immobilized in microchip gel pads. Mol. Biol. 37, in press.
42. Barsky V., Perov A., Tokalov S., Chudinov A., Kreindlin E., Sharonov A., Kotova E., Mirzabekov A. 2002. Fluorescence data analysis on gel-based biochips. J. Biomol. Screen. 7, 247-257.
43. Bavykin S.G., Akowski J.P., Zakhariev V.M., Barsky V.E., Mirzabekov A.D. 2001. Microbial identification: A portable system for sample preparation and oligonucleotide microarray hybridization. Appl. Environ. Microbiology. 67, 922-928.