Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays

Bioinformatics

Volumn 23, Issue 19, 2007, Pages 2566-2572

  Wu, Chunlei ^a,b,c   Zhao, Haitao ^b   Baggerly, Keith ^b,c   Carta, Roberto ^d   Zhang, Li ^b,c  

^a GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c UNIVERSITY OF TEXAS   (United States)

^d UNIVERSITY OF CENTRAL FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; OLIGONUCLEOTIDE;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; BINDING AFFINITY; BINDING KINETICS; COMPUTER MODEL; CONCENTRATION (PARAMETERS); DATA ANALYSIS; FEEDBACK SYSTEM; GENE EXPRESSION PROFILING; GENOMICS; GENOTYPE; HYBRIDIZATION; INTERNET; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; MOLECULAR PROBE; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIGNAL PROCESSING; TRANSCRIPTOMICS;

EID: 35748978818     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm271     Document Type: Article

References (31)

1. Auer,H. et al. (2003) Chipping away at the chip bias: RNA degradation in microarray analysis. Nat. Genet., 35, 292-293.
2. Bolstad,B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
3. Dai,M. et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res., 33, e175.
4. Dapic,V. et al. (2003) Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res., 31 2097-2107.
5. Forman,J.E. et al. (1998) Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. In Molecular Modeling of Nucleic Acids. American Chemical Society, Washington, DC, pp. 206-228.
6. Held,G.A. et al. (2006) Relationship between gene expression and observed intensities in DNA microarrays - a modeling study. Nucleic Acids Res., 34, e70.
7. Hubbell,E. et al. (2002) Robust estimators for expression analysis. Bioinformatics, 18, 1585-1592.
8. Trizarry,R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
9. Keniry,M.A. (2000) Quadruplex structures in nucleic acids. Biopolymers, 56, 123-146.
10. Kennedy,G.C. et al. (2003) Large-scale genotyping of complex DNA. Nat. Biotechnol., 21, 1233-1237.
11. Lander,E.S. (1999) Array of hope. Nat. Genet., 21, 3-4.
12. Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
13. Li,F. and Stormo,G.D. (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinfomatics, 17, 1067-10?6.
14. Liu,W.M. et al. (2003) Algorithms for large-scale genotyping microarrays. Bioinformatics, 19, 2397-2403.
15. Lockhart,D.J. and Winzeler,E.A. (2000) Genomics, gene expression and DNA arrays. Nature, 405, 827-836.
16. Lockhart,D.J. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14 1675-1680.
17. Matsuzaki,H. et al. (2004) Genotyping over 100 000 SNPs on a pair of oligonucleotide arrays. Nat. Methods, 1, 109-111.
18. Matveeva,O.V. et al. (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res. 31, 4211-4217.
19. Mei,R. et al. (2003) Probe selection for high-density oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 100, 11237-11242.
20. Mergny,J.L. et al. (2005) Kinetics of tetramolecular quadruplexes. Nucleic Acid. Res., 33, 81-94.
21. Mir,K.U. and Southern,E.M. (1999) Determining the influence of structure on hybridization using oligonucleotide arrays. Nat. Biotechnol., 17, 788-792.
22. Naef,F. et al. (2002) Characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol. 3.
23. Naef,F. et al. (2003) A study of accuracy and precision in oligonucleotide arrays: Extracting more signal at large concentrations. Bioinformatics, 19, 178-184.
24. Olson, J.A. Jr (2004) Application of microarray profiling to clinical trials in cancer. Surgery, 136, 519-523.
25. Rouillard,J.M., et al. (2003) OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res., 31, 3057-3062.
26. Shchepinov,M.S. et al. (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res., 25, 1155-1161.
27. Sliwerska,E. et al. (2006) SNPs on Chips: The hidden genetic code in expression arrays. Biol. Psychiatry.
28. Su,A.I. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101 6062-6067.
29. Wu,F.X. et al. (2005) Dynamic model-based clustering for time-course gene expression data. J. Bioinform. Comput. Biol., 3, 821-836.
30. Zhang,L. et al. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol., 21, 818-821.
31. Zhang,L. et al. (2007) Free energy of DNA duplex formation on short oligonucleotide microarrays. Nucleic Acids Res., 35, e18.