Format

Send to

Choose Destination
Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2289-94. doi: 10.1073/pnas.0812506106. Epub 2009 Jan 26.

Design of 240,000 orthogonal 25mer DNA barcode probes.

Author information

1
Department of Genetics, Center for Genetics and Genomics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.

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.

PMID:
19171886
PMCID:
PMC2631075
DOI:
10.1073/pnas.0812506106
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center