eISSN: 2221-6197 DOI: 10.31301/2221-6197

Chemistry of oligonucleotides immobilization during DNA microarrays production

Year: 2015

Pages: 45-53

Number: Volume 7, issue 1

Type: scientific article

Summary:

The methods of chemical immobilization of oligonucleotides on the surface of solid supports used in DNA microarrays production are reviewed. The main attention is paid for the schemes of oligonucleotides covalent grafting to the glass surface. The techniques for spatial ordering and dilution of oligonucleotide molecules on the surface are considered.

Keywords:

DNA microarrays, oligonucleotides, support, surface functionalization, single anchor immobilization, multiple anchor immobilization

References:

  1. http://dna.pynny.ru
  2. Гарафутдинов Р.Р., Шепелевич И.С., Чемерис А.В., Талипов Р.Ф. Химические аспекты создания ДНК-чипов // Вестн. Башк. ун-та. 2005. Т. №1. С. 49-54.
  3. Beaucage S.L. Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications // Curr. Med. Chem. V. 8. P. 1213-1244.
  4. Ramsay G. DNA chips: state-of-the art // Biotechnol.1998. V. 16. P. 40-44.
  5. Чечеткин В.Р., Прокопенко Д.В., Макаров А.А., Заседателев А.С. Биочипы для медицинской диагностики // Росс. нанотехнол. 2006. Т. 1. №1-2. С. 13-28.
  6. Mikhailovich V., Gryadunov D., Makarov A.A., Zasedatelev A., Kolchinsky A. DNA microarrays in the clinic: infectious diseases // Bioassays. 2008. V. 30.P. 673-682.
  7. Грядунов Д.А., Гетман И.А., Чижова С.И., Михайлович В.М., Заседателев А.С., Романов Г.А. Идентификация генно-модифицированных источников растительного происхождения в пищевых продуктах и сырье с использованием гидрогелевого олигонуклеотидного микрочипа // Мол. биол. 2011. Т. 45. № 6. С. 973-983.
  8. Gryadunov D., Mikhailovich V., Zasedatelev A., Nicot F., Dubois M., Izopet J. Hepatitis C virus genotyping using an oligonucleotide microarray based on the NS5B sequence // Clin. Microbiol. 2010. V. 48.  P. 3910-3917.
  9. Emelyanova M.A., Chudinov A.V., Surzhikov S.A., Nasedkina T.V., Amossenko F.A., Kazubskaya T.P., Lubchenko L.N. Detection of Kras mutations in tumor cells using biochips // Biol. 2011. V. 45. P. 797-803.
  10. Низамутдинов И.И., Андреева Т.В., Степанов В.А., Марусин А.В., Рогаев Е.И., Заседателев А.С., Наседкина Т.В. Биочип для выявления генетических маркеров риска развития спорадической формы болезни Альцгеймера у славянского населения России // Мол. биол. Т. 47. № 6. С. 949.
  11. Belosludtsev Y., Iverson B., Lemeshko S., Eggers R., Wiese R., Lee S., Powdrill T., Hogan M. DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions // Biochem.2001. V. 292. P. 250-256.
  12. Tjong V., Tang L., Zauscher S., Chilkoti A. "Smart" DNA interfaces // Chem. Soc. Rev. 2014. V. 43. P. 1612-1626.
  13. Wang L., Wang X., Chen X., Liu J., Liu Sh., Zhao C. Development of an electrochemical DNA biosensor with the DNA immobilization based on in situ generation of dithiocarbamate ligands // Bioelectrochem. 2012. V. 88. P. 30-35.
  14. Sakata T., Maruyama S., Ueda A., Otsuka H., Miyahara Y. Stable immobilization of an oligonucleotide probe on a gold substrate using tripodal thiol derivatives // Langmuir. 2007. V. 23. P. 2269-2272.
  15. Li Z., Jin R., Mirkin C.A., Letsinger R.L. Multiple thiol-anchor capped DNA-gold nanoparticle conjugates // Nucleic Acids Research. 2002. V. 30. N. 7. P. 1558-1562.
  16. Shchepinov M.S., Mir K.U., Elder J.K., Frank-Kamenetskii M.D., Southern E.M. Oligonucleotide dendrimers: stable nano-structures // Nucleic Acids Res. 1999. V. 27. P. 3035-3041.
  17. http://www.glenresearch.com
  18. Phaner-Goutorbe M., Dugas V., Chevolot Y., Souteyrand E. Silanization of silica and glass slides for DNA microarrays by impregnation and gas phase protocols: a comparative study // Mater. Sci. Eng.: C. 2011. V. 31. P. 384-390.
  19. Yadav A.R., Sriram R., Carter J.A., Miller B.L. Comparative study of solution-phase and vapor-phase deposition of aminosilanes on silicon dioxide surfaces // Sci. Eng.: C. 2014. V. 35. P. 283-290.
  20. Berthelot T., Garcia A., Le X.T., Morsli J.E., Jegou P., Palacin S., Viel P. “Versatile toolset” for DNA or protein immobilization: Toward a single-step chemistry // Appl. Surf. Sci. 2011. V. 257. P. 3538-3546.
  21. Solomun T., Mix R., Sturm H. Immobilization of silanized DNA on glass: influence of the silane tether on the DNA hybridization // ACS Appl. Mater. Interf. 2012. V. 2. P. 2171-2174.
  22. Li X., Wang M., Wang L., Shi X., Xu Y., Song B., Chen H. Block copolymer modified surfaces for conjugation of biomacromolecules with control of quantity and activity // Langmuir. 2013. V. 29. P. 1122-1128.
  23. Demirci S., Caykara T. RAFT-mediated synthesis of cationic poly[(arylvinylbenzyl)tri-methylammonium chloride] brushes for quantitative DNA immobilization // Mater. Sci. Eng.: C. 2013. V. 33. P. 111-120.
  24. Mahajan S., Kumar P., Gupta K.C. Oligonucleotide microarrays: immobilization of phosphorylated oligonucleotides on epoxylated surface // Bioconj. Chem. V. 17. P. 1184-1189.
  25. Sethi D., Kumar A., Gandhi R.P., Kumar P., Gupta K.C. New protocol for oligonucleotide microarray fabrication using SU-8-coated glass microslides // Bioconj. Chem. 2010. V. 21. P. 1703-1708.
  26. Oh S.J., Cho S.J., Kim Ch.O., Park J.W. Characteristics of DNA microarrays fabricated on various aminosilane layers // Langmuir. 2002. V. 18. P. 1764-1769.
  27. Metwalli E., Haines D., Becker O., Conzone S., Pantano C.G. Surface characterizations of mono-, di-, and tri-aminosilane treated // J. Coll. Interf. Sci. 2006. V. 298. P. 825-831.
  28. Zhu M., Lerum M.Z., Chen W. How to prepare reproducible, homogeneous, and hydrolytically stable aminosilane-derived layers on silica // Langmuir. 2012. V. 28. P. 416-423.
  29. Choithani J., Kumar P., Gupta K.C. N-(3-Triethoxysilylpropyl)-6-(N-maleimido)-hexanamide: An efficient heterobifunctional reagent for the construction of oligonucleotide microarrays // Anal. Biochem. 2006. V. 357. P. 240-248.
  30. Misra А. N-(3-Triethoxysilylpropyl)-4-(N’-maleimidylmethyl)-cyclohexanamide (TPMC): A heterobifunctional reagent for immobilization of oligonucleotides on glass surface // Bioorg. Med. Chem. Lett. 2007. V. 17. Р. 3749-3753.
  31. Misra A., Dwivedi P. Immobilization of oligonucleotides on glass surface using an efficient heterobifunctional reagent through maleimide-thiol combination chemistry // Anal. Biochem. 2007. V. 369. P. 248-255.
  32. Misra A., Shahid M. Immobilization of self-quenched DNA hairpin probe with a heterobifunctional reagent on a glass surface for sensitive detection of oligonucleotides // Bioorg. Med. Chem. 2009. V. 17. P. 5826-5833.
  33. Rostovtsev V.V., Green L.G., Fokin V.V., Sharpless K.B. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes // Ang. Chem. Int. Ed. Engl. 2002. V. 41. P. 2596-2599. 
  34. Prakash Sh., Long T.M., Selby J.C., Moore J.S., Shannon M.A. “Click” modification of silica surfaces and glass microfluidic channels // Anal. Chem. 2007. V. 79. P. 1661-1667.
  35. Bayraktar A., Saracoglu B., Golgelioglu C., Tuncel A. Click-chemistry for surface modification of monodisperse-macroporous particles // J. Coll. Interf. Sci. 2012. V. 365. P. 63-71.
  36. Lummerstorfer T., Hoffmann H. Click chemistry on surfaces: 1,3-dipolar cycloaddition reactions of azide-terminated monolayers on silica //  Phys. Chem. B. 2004. V. 108. P. 3963-3966.
  37. Uszczynska B., Ratajczak T., Frydrych E., Maciejewski H., Figlerowicz M., Markiewicz W.T., Chmielewski M.K. Application of click chemistry to the production of DNA microarrays // Lab Chip. 2012. V. 12. P. 1151-1156.
  38. Shimomura A., Nishino T., Maruyama T. Display of amino groups on substrate surfaces by simple dip-coating of methacrylate-based polymers and its application to DNA immobilization // Langmuir. 2013. V. 29. P. 932-938.
  39. Li X., Wang M., Wang L., Shi X., Xu Y., Song B., Chen H. Block copolymer modified surfaces for conjugation of biomacromolecules with control of quantity and activity // Langmuir. 2013. V. 29. P. 1122-1128.
  40. Vigano M., Levi M., Turri S., Chiari M., Damin F. New copolymers of N,N-dimethylacrylamide with blocked isocyanates for oligonucleotide immobilization in DNA microarray technology // Polymer. 2007. V. 48. P. 4055-4062.
  41. Gong P., Harbers G.M., Grainger D.W. Multi-technique comparison of immobilized and hybridized oligonucleotide surface density on commercial amine-reactive microarray slides // Anal. Chem. 2006. V. 78. P. 2342-2351.
  42. Chen S., Phillips M.F., Cerrina F., Smith L.M. Controlling oligonucleotide surface density in light-directed DNA array fabrication // Langmuir. 2009. V. 25. P. 6570-6575.
  43. Шляпникова Е. А., Шляпников Ю. М., Афанасьев В. Н., Афанасьева Г. В., Гаврюшкин А. В., Белецкий И. П. Исследование качества аминированных подложек, используемых для гибридизационного анализа // Биоорг. химия. 2007. Т. 33. №2. С. 261-268.
  44. Moon J.H., Shin J.W., Kim S.Y., Park J.W. Formation of Uniform Aminosilane Thin Layers: An Imine Formation To Measure Relative Surface Density of the Amine Group // 1996. V. 12. P. 4621-4624.
  45. Moon J.H., Kim J.H., Kim K. et al. Absolute Surface Density of the Amine Group of the Aminosilylated Thin Layers: Ultraviolet-Visible Spectroscopy, Second Harmonic Generation, and Synchrotron-Radiation Photoelectron Spectroscopy Study // 1997. V. 13. P. 4305-4310.
  46. Туктамышева А.Х., Гарафутдинов Р.Р., Талипов Р.Ф. Сравнительный анализ различных вариантов химической модификации поверхности кремнезема // Вестн. Башк. ун-та. 2012. т. 17. № 3. С. 1247-1252.
  47. Гарафутдинов Р.Р., Сахабутдинова А.Р., Чемерис А.В. Повышение стабильности конъюгатов олигонуклеотидов с наночастицами золота // Биоорг. химия. Т. 41. №3. С. 327-335.
  48. Shchepinov M.S., Udalova I.A., Bridgman A.J., Southern E.M.. Oligonucleotide dendrimers: synthesis and use as polylabelled DNA probes // Nucleic Acids Res. 1997. V. 25. P. 4447-4454.
  49. Berre V.L., Trevisiol E., Dagkessamanskaia A., Sokol S., Caminade A.-M., Majoral J.P., Meunier B., Francois J. Dendrimeric coating of glass slides for sensitive DNA microarrays analysis // Nucleic Acids Res. 2003. V. 31. e88.
  50. Shchepinov M.S., Case-Green S.C., Southern E.M. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays // Nucleic Acids Res. 1997. V. 25. P. 1155-
  51. Hong B.J., Oh S.J., Youn T.O., Kwon S.H., Park J.W. Nanoscale-controlled spacing provides DNA microarrays with the SNP discrimination efficiency in solution phase // Langmuir. 2005. V. 21. P. 4257-4261.
  52. Hong B.J., Sunkara V., Park J.W. DNA microarrays on nanoscale-controlled surface // Nucleic Acids Res. 2005. V. 12. P. 1-8.
  53. Hong B.J., Shim J.Y., Oh S.J., Park J.W. Self-Assembly of a Dendron through Multiple Ionic Interaction to Give Mesospacing between Reactive Amine Groups on the Surface // Langmuir. 2003. V. 19. P. 2357-2365.
  54. Boateng J., Peek J., Zahorchak R., Chittur K. Dendron-modified surfaces provide an ideal environment for stem–loop DNA probes // Anal. Biochem. 2012. V. 430. P. 39-44.
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eISSN: 2221-6197 DOI: 10.31301/2221-6197