Cited by 170Gene expression and cancer classificationAdvanced biosensing and bioanalysis techniquesGenomics and Phylogenetic Studies

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Design of 240,000 orthogonal 25mer DNA barcode probes

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Xu, Qikai, Schlabach, Michael R., Hannon, Gregory J., Elledge, Stephen J.·2009·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.0812506106PMC PMC2631075

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Abstract

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.

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Authors: Xu, Q., Schlabach, M. R., Hannon, G. J., & Elledge, S. J.
Affiliations: Brigham and Women's Hospital (US)
Howard Hughes Medical Institute (US)
ORCID: Xu, Qikai
Schlabach, Michael R.
Hannon, Gregory J.
Elledge, Stephen J.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2009-02-17
Volume: 106
Issue: 7
Pages: 2289-2294
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.0812506106
PMC: PMC2631075
OpenAlex: W2091266578
Cited by: 170
References: 22
Citations by year: 2026: 13 · 2025: 16 · 2024: 13 · 2023: 13 · 2022: 13 · 2021: 22 · 2020: 12 · 2019: 11 · 2018: 6 · 2017: 10 · 2016: 8 · 2015: 5 · 2014: 3 · 2013: 5 · 2012: 6
FWCI: 2.68
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
Funders: Howard Hughes Medical Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: DNA barcodes, probe design, microarray hybridization, cross-hybridization, shRNA library
MeSH terms: Algorithms, Electronic Data Processing, DNA, Nucleic Acid Conformation, Nucleic Acid Hybridization, RNA, Software, Temperature, DNA Probes, Oligonucleotide Probes, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling

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Design of 240,000 orthogonal 25mer DNA barcode probes

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