Authors

C. L. Wu; R. Carta;L. Zhang

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Abbreviated Journal Title

Nucleic Acids Res.

Keywords

DENSITY OLIGONUCLEOTIDE ARRAYS; MOLECULAR-INTERACTIONS; SINGLE; MISMATCHES; THERMODYNAMICS; NORMALIZATION; SELECTION; DUPLEXES; MODEL; Biochemistry & Molecular Biology

Abstract

One of the critical problems in the short oligo microarray technology is how to deal with cross-hybridization that produces spurious data. Little is known about the details of cross-hybridization effect at molecular level. Here, we report a free energy analysis of crosshybridization on short oligo microarrays using data from a spike-in study. Our analysis revealed that cross-hybridization on the arrays is mostly caused by oligo fragments with a run of 10 - 16 nt complementary to the probes. Mismatches were estimated to be energetically much more costly in crosshybridization than that in gene-specific hybridization, implying that the sources of cross-hybridization must be very different between a PM - MM probe pair. Consequently, it is unreliable to use MM probe signal to track cross-hybridizing signal on a corresponding PM probe. Our results also showed that the oligo fragments tend to bind to the 50 ends of the probes, and are rarely seen at the 30 ends. These results are useful for microarray design and data analysis.

Journal Title

Nucleic Acids Research

Volume

33

Issue/Number

9

Publication Date

1-1-2005

Document Type

Article

Language

English

First Page

7

WOS Identifier

WOS:000229544600005

ISSN

0305-1048

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