Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays

Journal of Nanobiotechnology

Volumn 9, Issue , 2011, Pages

  Agbavwe, Christy ^a   Kim, Changhan ^b,d   Hong, DongGee ^b   Heinrich, Kurt ^b   Wang, Tao ^c   Somoza, Mark M ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b University of Wisconsin Madison   (United States)

^c University of Notre Dame   (United States)

^d INTEL CORPORATION   (United States)

Author keywords

Gene synthesis; Microarray; Nppoc; Phosphoramidite chemistry

Indexed keywords

AVERAGE YIELD; CHEMICAL EXPOSURE; DEPROTECTION; DIGITAL MICROMIRRORS; DNA MICRO-ARRAY; EXPERIMENTAL STRATEGY; GENE ASSEMBLY; GENE SYNTHESIS; GLASS SUBSTRATES; HIGH-DENSITY ARRAYS; IN-SITU SYNTHESIS; LABORATORY SCALE; LIMITING FACTORS; LOCAL FLARE; LONG OLIGONUCLEOTIDE; MASK LESS; MASKLESS ARRAY SYNTHESIS; NPPOC; OLIGONUCLEOTIDE SYNTHESIS; PHOSPHORAMIDITES; SOLID PHASE SYNTHESIS; SYNTHESIS KINETICS; VERSATILE METHODS;

BIOASSAY; BIOCHIPS; CHEMICAL MODIFICATION; DIFFRACTION; GENES; MICROARRAYS; OLIGONUCLEOTIDES; SUBSTRATES;

SYNTHESIS (CHEMICAL);

HELIUM; OLIGONUCLEOTIDE; PHOSPHORAMIDOUS ACID; GLASS;

ARTICLE; CAPPING PHENOMENON; CLINICAL EFFECTIVENESS; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC ERROR; DNA MICROARRAY; LIGHT EXPOSURE; LIGHT SCATTERING; MOLECULAR HYBRIDIZATION; NUCLEOTIDE METABOLISM; OXIDATIVE COUPLING; PROTEIN ANALYSIS; PROTEIN DETERMINATION; CHEMISTRY; KINETICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PHOTOCHEMISTRY; SOLID PHASE SYNTHESIS; SYNTHESIS;

BASE SEQUENCE; GLASS; KINETICS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; PHOTOCHEMISTRY; SOLID-PHASE SYNTHESIS TECHNIQUES;

EID: 82955217299     PISSN: None     EISSN: 14773155     Source Type: Journal    
DOI: 10.1186/1477-3155-9-57     Document Type: Article

References (50)

1. Fodor S, Read J, Pirrung M, Stryer L, Lu A, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991, 251:767-773.
2. Singh-Gasson S, Green RD, Yue YJ, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology 1999, 17:974-978.
3. Lackey JG, Mitra D, Somoza MM, Cerrina F, Damha MJ. Acetal Levulinyl Ester (ALE) Groups for 2'-Hydroxyl Protection of Ribonucleosides in the Synthesis of Oligoribonucleotides on Glass and Microarrays. Journal of the American Chemical Society 2009, 131:8496-8502.
4. Lackey JG, Somoza MM, Mitra D, Cerrina F, Damha MJ. In-situ chemical synthesis of rU-DNA chimeras on chips and enzymatic recognition. Chim Oggi-Chem Today 2009, 27:30-33.
5. Pellois JP, Zhou X, Srivannavit O, Zhou T, Gulari E, Gao X. Individually addressable parallel peptide synthesis on microchips. 2002, 20:922-926.
6. Shin D-S, Lee K-N, Yoo B-W, Kim J, Kim M, Kim Y-K, Lee Y-S. Automated Maskless Photolithography System for Peptide Microarray Synthesis on a Chip. Journal of Combinatorial Chemistry 2010, 12:463-471.
7. Phillips MF, Lockett MR, Rodesch MJ, Shortreed MR, Cerrina F, Smith LM. In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication. Nucleic Acids Research 2008, 36:e7.
8. Lockett MR, Weibel SC, Phillips MF, Shortreed MR, Sun B, Corn RM, Hamers RJ, Cerrina F, Smith LM. Carbon-on-Metal Films for Surface Plasmon Resonance Detection of DNA Arrays. Journal of the American Chemical Society 2008, 130:8611-8613.
9. Negrete OD, Onses MS, Nealey PF, Cerrina F. In situ synthesis and direct immobilization of ssDNA on electron beam patterned hydrogen silsesquioxane. J Vac Sci Technol B 2009, 27:3082-3087.
10. Pon RT, Yu S. Tandem oligonucleotide synthesis using linker phosphoramidites. Nucleic Acids Research 2005, 33:1940-1948.
11. Wang T, Oehrlein S, Somoza MM, Perez JRS, Kershner R, Cerrina F. Optical tweezers directed one-bead one-sequence synthesis of oligonucleotides. Lab Chip 2011, 11:1629-1637.
12. Lemoine S, Combes F, Le Crom S. An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Research 2009, 37:1726-1739.
13. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Research 2002, 30:e51.
14. Chou C-C, Chen C-H, Lee T-T, Peck K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Research 2004, 32:e99.
15. Microarrays. Preparation, Microfluidics, Detection Methods, and Biological Applications. 2009, Springer, Dill K, Liu R, Grodzinsky P.
16. Carlson CD, Warren CL, Hauschild KE, Ozers MS, Qadir N, Bhimsaria D, Lee Y, Cerrina F, Ansari AZ. Specificity landscapes of DNA binding molecules elucidate biological function. Proceedings of the National Academy of Sciences 2010, 107:4544-4549.
17. Warren CL, Kratochvil NCS, Hauschild KE, Foister S, Brezinski ML, Dervan PB, Phillips GN, Ansari AZ. Defining the sequence-recognition profile of DNA-binding molecules. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:867-872.
18. Puckett JW, Muzikar KA, Tietjen J, Warren CL, Ansari AZ, Dervan PB. Quantitative Microarray Profiling of DNA-Binding Molecules. Journal of the American Chemical Society 2007, 129:12310-12319.
19. Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G. Accurate multiplex gene synthesis from programmable DNA microchips. 2004, 432:1050-1054.
20. Binkowski BF, Richmond KE, Kaysen J, Sussman MR, Belshaw PJ. Correcting errors in synthetic DNA through consensus shuffling. Nucleic Acids Research 2005, 33:e55.
21. Carr PA, Park JS, Lee Y-J, Yu T, Zhang S, Jacobson JM. Protein-mediated error correction for de novo DNA synthesis. Nucleic Acids Research 2004, 32:e162.
22. Smith HO, Hutchison CA, Pfannkoch C, Venter JC. Generating a synthetic genome by whole genome assembly:ΦX174 bacteriophage from synthetic oligonucleotides. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:15440-15445.
23. Septak M. Kinetic Studies on Depurination and Detritylation of CPG-Bound Intermediates During Oligonucleotide Synthesis. Nucleic Acids Research 1996, 24:3053-3058.
24. Garland PB, Serafinowski PJ. Effects of stray light on the fidelity of photodirected oligonucleotide array synthesis. Nucleic Acids Research 2002, 30:e99.
25. McGall GH, Barone AD, Diggelmann M, Fodor SPA, Gentalen E, Ngo N. The Efficiency of Light-Directed Synthesis of DNA Arrays on Glass Substrates. Journal of the American Chemical Society 1997, 119:5081-5090.
26. Agbavwe C, Somoza MM. Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays. PLoS ONE 2011, 6:e22177.
27. Pon RT, Damha MJ, Ogilvie KK. Modification of guanine bases by nucleoside phosphoramidite reagents during the solid phase synthesis of oligonucleotides. Nucleic Acids Research 1985, 13:6447-6465.
28. Chen S, Phillips MF, Cerrina F, Smith LM. Controlling Oligonucleotide Surface Density in Light-Directed DNA Array Fabrication. Langmuir 2009, 25:6570-6575.
29. Beier M, Hoheisel JD. Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays. Nucleic Acids Research 2000, 28:e11.
30. Wöll D, Walbert S, Stengele K-P, Albert TJ, Richmond T, Norton J, Singer M, Green RD, Pfleiderer W, Steiner UE. Triplet-Sensitized Photodeprotection of Oligonucleotides in Solution and on Microarray Chips. Helv Chim Acta 2004, 87:28-45.
31. Kim C, Li M, Lowe A, Venkataramaiah N, Richmond K, Kaysen J, Cerrina F. DNA microarrays: An imaging study. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 2003, 21:2946-2950.
32. Rodney WS, Spindler RJ. Index of Refraction of Fused Quartz Glass for Ultraviolet, Visible, and Infrared Wavelengths. Journal of the Optical Society of America 1954, 44:677-678.
33. Pacak P. Polarizability and molecular radius of dimethyl-sulfoxide and dimethylformamide from refractive index data. Book Polarizability and molecular radius of dimethyl-sulfoxide and dimethylformamide from refractive index data 1987, 16:71-77. City: Springer Netherlands.
34. Walbert S, Pfleiderer W, Steiner UE. Photolabile Protecting Groups for Nucleosides: Mechanistic Studies of the 2-(2-Nitrophenyl)ethyl Group. Helv Chim Acta 2001, 84:1601-1611.
35. Gao Y, Wolf LK, Georgiadis RM. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Research 2006, 34:3370-3377.
36. Peterson AW, Heaton RJ, Georgiadis RM. The effect of surface probe density on DNA hybridization. Nucleic Acids Research 2001, 29:5163-5168.
37. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, et al. Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography. Genome Research 2002, 12:1749-1755.
38. Kim C, Li M, Rodesch M, Lowe A, Richmond K, Cerrina F. Biological lithography: Improvements in DNA synthesis methods. J Vac Sci Technol B 2004, 22:3163-3167.
39. Kim C, Kaysen J, Richmond K, Rodesch M, Binkowski B, Chu L, Li M, Heinrich K, Blair S, Belshaw P, et al. Progress in gene assembly from a MAS-driven DNA microarray. Microelectronic Engineering 2006, 83:1613-1616.
40. Offner A. Wavelength and coherence effects on the performance of real optical projection systems. Photogr Sci Eng 1979, 23:374.
41. Cheng Y-K, Chern J-L. Irradiance formations in hollow straight light pipes with square and circular shapes. Journal of the Optical Society of America A 2006, 23:427-434.
42. Suzuki A. Complete analysis of a two-mirror unit magnification system. Part 1. Applied Optics 1983, 22:3943-3949.
43. Offner A. New concepts in projection mask aligners. Optical Engineering 1975, 14:130-132.
44. Beier M, Matysiak S, Hoheisel J. Method for the light-controlled synthesis of biochips. Book Method for the light-controlled synthesis of biochips 2004, City: Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts.
45. Pirrung MC, Wang L, Montague-Smith MP. 3'-Nitrophenylpropyloxycarbonyl (NPPOC) Protecting Groups for High-Fidelity Automated 5' to' 3' Photochemical DNA Synthesis. Organic Letters 2001, 3:1105-1108.
46. Naiser T, Ehler O, Kayser J, Mai T, Michel W, Ott A. Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: Comparison of single base mismatches and base bulges. BMC Biotechnology 2008, 8:48.
47. McQuain MK, Seale K, Peek J, Fisher TS, Levy S, Stremler MA, Haselton FR. Chaotic mixer improves microarray hybridization. Analytical Biochemistry 2004, 325:215-226.
48. Richmond KE, Li M-H, Rodesch MJ, Patel M, Lowe AM, Kim C, Chu LL, Venkataramaian N, Flickinger SF, Kaysen J, et al. Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis. Nucleic Acids Research 2004, 32:5011-5018.
49. Rubinstein RY. Simulation and the Monte Carlo Method 1981, John Wiley & Sons.
50. Kim C. Gene Synthesis from Photolithographic DNA Microarrays. Ph.D. thesis 2007, University of Wisconsin, Electrical Engineering.