Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (144K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (100)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Rouillard, J.-M.
Right arrow Articles by Gulari, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rouillard, J.-M.
Right arrow Articles by Gulari, E.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 12 3057-3062
© 2003 Oxford University Press

OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach

Jean-Marie Rouillard, Michael Zuker1 and Erdogan Gulari

Department of Chemical Engineering, University of Michigan, H.H. Dow, Ann Arbor, MI 48109, USA and 1 Department of Mathematical Sciences, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA

*To whom correspondence should be addressed. Tel: +1 734 764 0111; Fax: +1 734 763 5418; Email: jmrouill{at}umich.edu

There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally specific to their respective targets to avoid any cross-hybridization and should not form stable secondary structures that may interfere with the labeled probes during hybridization. We have developed OligoArray 2.0, a program that designs specific oligonucleotides at the genomic scale. It uses a thermodynamic approach to predict secondary structures and to calculate the specificity of targets on chips for a unique probe in a mixture of labeled probes. Furthermore, OligoArray 2.0 can adjust the oligonucleotide length, according to user input, to fit a narrow Tm range compatible with hybridization requirements. Combined with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on cDNA or oligonucleotide libraries. OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
A. Spandidos, X. Wang, H. Wang, and B. Seed
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
Nucleic Acids Res., November 11, 2009; (2009) gkp1005v1.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
C. Payen, G. Fischer, C. Marck, C. Proux, D. J. Sherman, J.-Y. Coppee, M. Johnston, B. Dujon, and C. Neuveglise
Unusual composition of a yeast chromosome arm is associated with its delayed replication
Genome Res., October 1, 2009; 19(10): 1710 - 1721.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. Even, C. Charlier, S. Nouaille, N. L. Ben Zakour, M. Cretenet, F. J. Cousin, M. Gautier, M. Cocaign-Bousquet, P. Loubiere, and Y. Le Loir
Staphylococcus aureus Virulence Expression Is Impaired by Lactococcus lactis in Mixed Cultures
Appl. Envir. Microbiol., July 1, 2009; 75(13): 4459 - 4472.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
Y. J. Goh, M. A. Azcarate-Peril, S. O'Flaherty, E. Durmaz, F. Valence, J. Jardin, S. Lortal, and T. R. Klaenhammer
Development and Application of a upp-Based Counterselective Gene Replacement System for the Study of the S-Layer Protein SlpX of Lactobacillus acidophilus NCFM
Appl. Envir. Microbiol., May 15, 2009; 75(10): 3093 - 3105.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Duitama, D. M. Kumar, E. Hemphill, M. Khan, I. I. Mandoiu, and C. E. Nelson
PrimerHunter: a primer design tool for PCR-based virus subtype identification
Nucleic Acids Res., May 1, 2009; 37(8): 2483 - 2492.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Lemoine, F. Combes, and S. Le Crom
An evaluation of custom microarray applications: the oligonucleotide design challenge
Nucleic Acids Res., April 1, 2009; 37(6): 1726 - 1739.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Q. Xu, M. R. Schlabach, G. J. Hannon, and S. J. Elledge
Design of 240,000 orthogonal 25mer DNA barcode probes
PNAS, February 17, 2009; 106(7): 2289 - 2294.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. G. Leparc, T. Tuchler, G. Striedner, K. Bayer, P. Sykacek, I. L. Hofacker, and D. P. Kreil
Model-based probe set optimization for high-performance microarrays
Nucleic Acids Res., February 1, 2009; 37(3): e18 - e18.
[Abstract] [Full Text] [PDF]

Home page
 J Med MicrobiolHome page
Y. Li, B. Cao, B. Liu, D. Liu, Q. Gao, X. Peng, J. Wu, D. A. Bastin, L. Feng, and L. Wang
Molecular detection of all 34 distinct O-antigen forms of Shigella
J. Med. Microbiol., January 1, 2009; 58(1): 69 - 81.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J.-M. Rouillard and E. Gulari
OligoArrayDb: pangenomic oligonucleotide microarray probe sets database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D938 - D941.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
K. S. Auernik and R. M. Kelly
Identification of Components of Electron Transport Chains in the Extremely Thermoacidophilic Crenarchaeon Metallosphaera sedula through Iron and Sulfur Compound Oxidation Transcriptomes
Appl. Envir. Microbiol., December 15, 2008; 74(24): 7723 - 7732.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. J. G. van de Werken, M. R. A. Verhaart, A. L. VanFossen, K. Willquist, D. L. Lewis, J. D. Nichols, H. P. Goorissen, E. F. Mongodin, K. E. Nelson, E. W. J. van Niel, et al.
Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus
Appl. Envir. Microbiol., November 1, 2008; 74(21): 6720 - 6729.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
S. J. Szyjka, J. G. Aparicio, C. J. Viggiani, S. Knott, W. Xu, S. Tavare, and O. M. Aparicio
Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae
Genes & Dev., July 15, 2008; 22(14): 1906 - 1920.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Wu, H. Zhao, K. Baggerly, R. Carta, and L. Zhang
Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
Bioinformatics, October 1, 2007; 23(19): 2566 - 2572.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
C. J. Paredes, R. S. Senger, I. S. Spath, J. R. Borden, R. Sillers, and E. T. Papoutsakis
A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum
Appl. Envir. Microbiol., July 15, 2007; 73(14): 4631 - 4638.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
W. Han, B. Liu, B. Cao, L. Beutin, U. Kruger, H. Liu, Y. Li, Y. Liu, L. Feng, and L. Wang
DNA Microarray-Based Identification of Serogroups and Virulence Gene Patterns of Escherichia coli Isolates Associated with Porcine Postweaning Diarrhea and Edema Disease
Appl. Envir. Microbiol., June 15, 2007; 73(12): 4082 - 4088.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
O. Emanuelsson, U. Nagalakshmi, D. Zheng, J. S. Rozowsky, A. E. Urban, J. Du, Z. Lian, V. Stolc, S. Weissman, M. Snyder, et al.
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Genome Res., June 1, 2007; 17(6): 886 - 897.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Feng and E. R.M. Tillier
A fast and flexible approach to oligonucleotide probe design for genomes and gene families
Bioinformatics, May 15, 2007; 23(10): 1195 - 1202.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Lipson, Z. Yakhini, and Y. Aumann
Optimization of probe coverage for high-resolution oligonucleotide aCGH
Bioinformatics, January 15, 2007; 23(2): e77 - e83.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
R. D. Stedtfeld, L. M. Wick, S. W. Baushke, D. M. Tourlousse, A. B. Herzog, Y. Xia, J. M. Rouillard, J. A. Klappenbach, J. R. Cole, E. Gulari, et al.
Influence of Dangling Ends and Surface-Proximal Tails of Targets on Probe-Target Duplex Formation in 16S rRNA Gene-Based Diagnostic Arrays
Appl. Envir. Microbiol., January 1, 2007; 73(2): 380 - 389.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
M. Mehlmann, E. D. Dawson, M. B. Townsend, J. A. Smagala, C. L. Moore, C. B. Smith, N. J. Cox, R. D. Kuchta, and K. L. Rowlen
Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus.
J. Clin. Microbiol., August 1, 2006; 44(8): 2857 - 2862.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. L. Brigand, R. Russell, C. Moreilhon, J.-M. Rouillard, B. Jost, F. Amiot, V. Magnone, C. Bole-Feysot, P. Rostagno, V. Virolle, et al.
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
Nucleic Acids Res., July 19, 2006; 34(12): e87 - e87.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Yamada, H. Soma, and S. Morishita
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W665 - W669.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. Tachdjian and R. M. Kelly
Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic Archaeon Sulfolobus solfataricus.
J. Bacteriol., June 1, 2006; 188(12): 4553 - 4559.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. He, L. Cai, G. Skogerbo, W. Deng, T. Liu, X. Zhu, Y. Wang, D. Jia, Z. Zhang, Y. Tao, et al.
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray
Nucleic Acids Res., May 31, 2006; 34(10): 2976 - 2983.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
D. P. Chandler, O. Alferov, B. Chernov, D. S. Daly, J. Golova, A. Perov, M. Protic, R. Robison, M. Schipma, A. White, et al.
Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates
J. Clin. Microbiol., January 1, 2006; 44(1): 244 - 250.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W.-H. Chung, S.-K. Rhee, X.-F. Wan, J.-W. Bae, Z.-X. Quan, and Y.-H. Park
Design of long oligonucleotide probes for functional gene detection in a microbial community
Bioinformatics, November 15, 2005; 21(22): 4092 - 4100.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Li, Z. He, and J. Zhou
Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
Nucleic Acids Res., October 24, 2005; 33(19): 6114 - 6123.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Ning, K. P. Choi, H. W. Leong, and L. Zhang
A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays
Nucleic Acids Res., September 28, 2005; 33(17): e144 - e144.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. J. Kim, A. Boyd, B. D. Athey, and J. M. Patel
miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST
Nucleic Acids Res., August 1, 2005; 33(13): 4335 - 4344.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
Z. He, L. Wu, X. Li, M. W. Fields, and J. Zhou
Empirical Establishment of Oligonucleotide Probe Design Criteria
Appl. Envir. Microbiol., July 1, 2005; 71(7): 3753 - 3760.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Wernersson and H. B. Nielsen
OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W611 - W615.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. K. Nordberg
YODA: selecting signature oligonucleotides
Bioinformatics, April 15, 2005; 21(8): 1365 - 1370.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Rimour, D. Hill, C. Militon, and P. Peyret
GoArrays: highly dynamic and efficient microarray probe design
Bioinformatics, April 1, 2005; 21(7): 1094 - 1103.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. W. Karaman, S. Groshen, C.-C. Lee, B. L. Pike, and J. G. Hacia
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays
Nucleic Acids Res., February 18, 2005; 33(3): e33 - e33.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Tanaka, A. Kameda, M. Yamamoto, and A. Ohuchi
Design of nucleic acid sequences for DNA computing based on a thermodynamic approach
Nucleic Acids Res., February 8, 2005; 33(3): 903 - 911.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. D. Wassman, P. Y. Tam, R. H. Lathrop, and G. A. Weiss
Predicting oligonucleotide-directed mutagenesis failures in protein engineering
Nucleic Acids Res., December 7, 2004; 32(21): 6407 - 6413.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Pancoska, Z. Moravek, and U. M. Moll
Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs
Nucleic Acids Res., August 27, 2004; 32(15): 4630 - 4645.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. M. Roche, K. Hokamp, M. Acab, L. A. Babiuk, R. E. W. Hancock, and F. S. L. Brinkman
ProbeLynx: a tool for updating the association of microarray probes to genes
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W471 - W474.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nagpal, M. W. Karaman, M. M. Timmerman, V. V. Ho, B. L. Pike, and J. G. Hacia
Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks
Nucleic Acids Res., March 18, 2004; 32(5): e51 - e51.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.