Biochemistry Publications

Title

Distortion of Quantitative Genomic and Expression Hybridization by Cot-1 DNA: Mitigation of This Effect

Document Type

Article

Publication Date

12-14-2005

Journal

Nucleic Acids Research

Volume

33

Issue

22

First Page

e191

Abstract

Cross-hybridization of repetitive sequences in genomic and expression arrays is reported to be suppressed with repeat-blocking nucleic acids (Cot-1 DNA). Contrary to expectation, we demonstrated that Cot-1 also enhanced non-specific hybridization between probes and genomic targets. When added to target DNA, Cot-1 enhanced hybridization (2.2- to 3-fold) to genomic probes containing conserved repetitive elements. In addition to repetitive sequences, Cot-1 was found to be enriched for linked single copy (sc) sequences. Adventitious association between these sequences and probes distort quantitative measurements of the probes hybridized to desired genomic targets. Quantitative microarray hybridization studies using Cot-1 DNA are also susceptible to these effects, especially for probes that map to genomic regions containing conserved repetitive sequences. Hybridization measurements with such probes are less reproducible in the presence of Cot-1 than for probes derived from sc regions or regions containing divergent repeat elements, a finding with significant ramifications for genomic and expression microarray studies. We mitigated the requirement for Cot-1 either by hybridizing with computationally defined sc probes lacking repeats or by substituting synthetic repetitive elements complementary to sequences in genomic probes.

Notes

Published in: Nucleic Acids Research 2005 33(22):e191; doi:10.1093/nar/gni190. Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.