Target concentration dependence of DNA melting temperature on oligonucleotide microarrays

Biotechnology Progress

Volumn 28, Issue 2, 2012, Pages 556-566

  Ozel, Ayse Bilge ^a,b   Srivannavit, Onnop ^a,b   Rouillard, Jean Marie ^a,b   Gulari, Erdogan ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

DNA hybridization thermodynamics; DNA melting temperature; Oligonucleotide microarray; Target concentration

Indexed keywords

AUTOMATED SYSTEMS; BULK SOLUTIONS; CONCENTRATION DEPENDENCE; DNA DUPLEXES; DNA HYBRIDIZATION; DNA MELTING; HYBRIDIZATION CONDITIONS; LOW TEMPERATURES; MELTING PROFILES; OLIGONUCLEOTIDE MICROARRAY; PROBE STRAND; SPACER LENGTHS; SURFACE AREA;

AUTOMATION; MELTING POINT; MICROARRAYS; OLIGONUCLEOTIDES; PROBES; THERMODYNAMICS;

DNA;

OLIGONUCLEOTIDE;

ARTICLE; CHEMISTRY; DNA DENATURATION; DNA MICROARRAY; GENETICS; INSTRUMENTATION; NUCLEIC ACID HYBRIDIZATION; TEMPERATURE;

NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; TEMPERATURE;

EID: 84859643171     PISSN: 87567938     EISSN: 15206033     Source Type: Journal    
DOI: 10.1002/btpr.1505     Document Type: Article

References (57)

1. Anguiano A, Nevins J, Potti A. Toward the individualization of lung cancer therapy. Cancer 2008; 113: 1760-1767.
2. Cogburn L, Wang X, Carre W, Rejto L, Aggrey S, Duclos M, Simon J, Porter T. Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways. Comp Funct Genomics 2004; 5: 253-261.
3. Conejero-Goldberg C, Wang E, Yi C, Goldberg T, Jones-Brando L, Marincola F, Webster M, Torrey E. Infectious pathogen detection arrays: viral detection in cell lines and postmortem brain tissue. Biotechniques 2005; 39: 741-751.
4. Hughes M, Deharo L, Pulivarthy S, Gu J, Hayes K, Panda S, Hogenesch J. High-resolution time course analysis of gene expression from pituitary. Cold Spring Harb Symp Quant Biol 2007; 72: 381-386.
5. Milano A, Pendergrass S, Sargent J, George L, McCalmont T, Connolly M, Whitfield M. Molecular subsets in the gene expression signatures of scleroderma skin. PLoS One 2008; 3: e2696.
6. Owczarzy R, You Y, Moreira B, Manthey J, Huang L, Behlke M, Walder J. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 2004; 43: 3537-3554.
7. SantaLucia J Jr, Allawi H, Seneviratne P. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996; 35: 3555-3562.
8. Forman J, Walton I, Stern D, Rava R, Trulson M. Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. In: Leontis NB, SantaLucia J Jr, editors. ACS Symposium Series - Molecular Modeling of Nucleic Acids. Washington, DC: American Chemical Society; 1998: 206-228.
9. Glazer M, Fidanza J, McGall G, Trulson M, Forman J, Suseno A, Frank C. Kinetics of oligonucleotide hybridization to photolithographically patterned DNA arrays. Anal Biochem 2006; 358: 225-238.
10. Halperin A, Buhot A, Zhulina E. Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines. Biophys J 2005; 89: 796-811.
11. Schmitt T, Knotts T IV. Thermodynamics of DNA hybridization on surfaces. J Chem Phys 2011; 134: 205105.
12. Shchepinov M, Case-Green S, Southern E. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res 1997; 25: 1155-1161.
13. Horne M, Fish D, Benight A. Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions. Biophys J 2006; 91: 4133-4153.
14. Sartor M, Schwanekamp J, Halbleib D, Mohamed I, Karyala S, Medvedovic M, Tomlinson C. Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques 2004; 36: 790-796.
15. Wang Y, Miao Z, Pommier Y, Kawasaki E, Player A. Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips. Bioinformatics 2007; 23: 2088-2095.
16. Bhanot G, Louzoun Y, Zhu J, DeLisi C. The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys J 2003; 84: 124-135.
17. Wick N, Bruck J, Gurnhofer E, Steiner C, Giovanoli P, Kerjaschki D, Thurner S. Nonuniform hybridization: a potential source of error in oligonucleotide-chip experiments with low amounts of starting material. Diagn Mol Pathol 2004; 13: 151-159.
18. Peplies J, Glockner F, Amann R. Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 2003; 69: 1397-1407.
19. Yatsenko S, Shaw C, Ou Z, Pursley A, Patel A, Bi W, Cheung S, Lupski J, Chinault A, Beaudet A. Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA. J Mol Diagn 2009; 11: 226-237.
20. Allen J, Schoch E, Stubbs J. Effect of surface binding on heterogeneous DNA melting equilibria: a Monte Carlo simulation study. J Phys Chem B 2011; 115: 1720-1726.
21. Ambia-Garrido J, Vainrub A, Montgomery Pettitt B. Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach. J Phys Condens Matter 2011; 23: 325101.
22. Binder H. Thermodynamics of competitive surface adsorption. J Phys Condens Matter 2006; 18: 491-532.
23. Fuchs J, Dell'Atti D, Buhot A, Calemczuk R, Mascini M, Livache T. Effects of formamide on the thermal stability of DNA duplexes on biochips. Anal Biochem 2010; 397: 132-134.
24. Fuchs J, Fiche J, Buhot A, Calemczuk R, Livache T. Salt concentration effects on equilibrium melting curves from DNA microarrays. Biophys J 2011; 99: 1886-1895.
25. Hooyberghs J, Van Hummelen P, Carlon E. The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters. Nucleic Acids Res 2009; 37: e53.
26. Irving D, Gong P, Levicky R. DNA surface hybridization: comparison of theory and experiment. J Phys Chem B 2010; 114: 7631-7640.
27. Naiser T, Kayser J, Mai T, Michel W, Ott A. Stability of a surface-bound oligonucleotide duplex inferred from molecular dynamics: a study of single nucleotide defects using DNA microarrays. Phys Rev Lett 2009; 102: 218301.
28. Peterson A, Heaton R, Georgiadis R. The effect of surface probe density on DNA hybridization. Nucleic Acids Res 2001; 29: 5163-5168.
29. Vainrub A, Pettitt B. Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. Biopolymers 2003; 68: 265-270.
30. Tan P, Downey T, Spitznagel E Jr, Xu P, Fu D, Dimitrov D, Lempicki R, Raaka B, Cam M. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003; 31: 5676-5684.
31. Jayaraman A, Hall C, Genzer J. Computer simulation study of probe-target hybridization in model DNA microarrays: effect of probe surface density and target concentration. J Chem Phys 2007; 127: 144912.
32. Moreira B, You Y, Behlke M, Owczarzy R. Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem Biophys Res Commun 2005; 327: 473-484.
33. Branham W, Melvin C, Han T, Desai V, Moland C, Scully A, Fuscoe J. Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnol 2007; 7: 8.
34. Mandal S, Rouillard J, Srivannavit O, Gulari E. Cytophobic surface modification of microfluidic arrays for in situ parallel peptide synthesis and cell adhesion assays. Biotechnol Prog 2007; 23: 972-978.
35. Gao X, LeProust E, Zhang H, Srivannavit O, Gulari E, Yu P, Nishiguchi C, Xiang Q, Zhou X. A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res 2001; 29: 4744-4750.
36. Wick L, Rouillard J, Whittam T, Gulari E, Tiedje J, Hashsham S. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res 2006; 34: e26.
37. Owczarzy R. Melting temperatures of nucleic acids: discrepancies in analysis. Biophys Chem 2005; 117: 207-215.
38. Mergny J, Lacroix L. Analysis of thermal melting curves. Oligonucleotides 2003; 13: 515-537.
39. Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet. 1999; 21: 5-9.
40. Watterson J, Piunno P, Wust C, Krull U. Effects of oligonucleotide immobilization density on selectivity of quantitative transduction of hybridization of immobilized DNA. Langmuir 2000; 16: 4984-4992.
41. Marky L, Breslauer K. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 1987; 26: 1601-1620.
42. Fotin A, Drobyshev A, Proudnikov D, Perov A, Mirzabekov A. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res 1998; 26: 1515-1521.
43. Zlatanova J, Mirzabekov A. Gel-immobilized microarrays of nucleic acids and proteins. Production and application for macromolecular research. Methods Mol Biol 2001; 170: 17-38.
44. Georgiadis R, Peterlinz K, Peterson A. Quantitative measurements and modeling of kinetics in nucleic acid monolayer films using SPR spectroscopy. J Am Chem Soc 2000; 122: 3166-3173.
45. Gong P, Levicky R. DNA surface hybridization regimes. Proc Natl Acad Sci U S A. 2008; 105: 5301-5306.
46. Tawa K, Knoll W. Mismatching base-pair dependence of the kinetics of DNA-DNA hybridization studied by surface plasmon fluorescence spectroscopy. Nucleic Acids Res 2004; 32: 2372-2377.
47. Wong I, Melosh N. An electrostatic model for DNA surface hybridization. Biophys J 2010; 98: 2954-2963.
48. Halperin A, Buhot A, Zhulina E. On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions. J Phys Condens Matter 2006; 18: 5463-5490.
49. Smith J, Van Ness H, Abbott M. Introduction to Chemical Engineering Thermodynamics, 5th ed. New York: McGraw Hill, Inc.; 1996.
50. Holbrook J, Capp M, Saecker R, Record M Jr. Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry 1999; 38: 8409-8422.
51. Mikulecky P, Feig A. Heat capacity changes associated with nucleic acid folding. Biopolymers 2006; 82: 38-58.
52. Wu L, Thompson D, Li G, Hurt R, Tiedje J, Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 2001; 67: 5780-5790.
53. Yin H, Cao L, Qiu G, Wang D, Kellogg L, Zhou J, Dai Z, Liu X. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems. J Microbiol Methods 2007; 70: 165-178.
54. Gundry C, Vandersteen J, Reed G, Pryor R, Chen J, Wittwer C. Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin Chem 2003; 49: 396-406.
55. Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C. Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 2004; 50: 1156-1164.
56. Chung Y, Lin Y, Shiu M, Chang W. Microfluidic chip for fast nucleic acid hybridization. Lab Chip 2003; 3: 228-233.
57. Peytavi R, Raymond F, Gagne D, Picard F, Jia G, Zoval J, Madou M, Boissinot K, Boissinot M, Bissonnette L, Ouellette M, Bergeron M. Microfluidic device for rapid (<15 min) automated microarray hybridization. Clin Chem 2005; 51: 1836-1844.