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Sequence dependence of cross-hybridization on short oligo microarrays

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 cross-hybridization on short oligo...

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Detalles Bibliográficos
Autores principales: Wu, Chunlei, Carta, Roberto, Zhang, Li
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1140085/
https://www.ncbi.nlm.nih.gov/pubmed/15914663
http://dx.doi.org/10.1093/nar/gni082
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author Wu, Chunlei
Carta, Roberto
Zhang, Li
author_facet Wu, Chunlei
Carta, Roberto
Zhang, Li
author_sort Wu, Chunlei
collection PubMed
description 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 cross-hybridization 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 cross-hybridization 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 5′ ends of the probes, and are rarely seen at the 3′ ends. These results are useful for microarray design and data analysis.
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spelling pubmed-11400852005-05-25 Sequence dependence of cross-hybridization on short oligo microarrays Wu, Chunlei Carta, Roberto Zhang, Li Nucleic Acids Res Methods Online 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 cross-hybridization 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 cross-hybridization 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 5′ ends of the probes, and are rarely seen at the 3′ ends. These results are useful for microarray design and data analysis. Oxford University Press 2005 2005-05-24 /pmc/articles/PMC1140085/ /pubmed/15914663 http://dx.doi.org/10.1093/nar/gni082 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Methods Online
Wu, Chunlei
Carta, Roberto
Zhang, Li
Sequence dependence of cross-hybridization on short oligo microarrays
title Sequence dependence of cross-hybridization on short oligo microarrays
title_full Sequence dependence of cross-hybridization on short oligo microarrays
title_fullStr Sequence dependence of cross-hybridization on short oligo microarrays
title_full_unstemmed Sequence dependence of cross-hybridization on short oligo microarrays
title_short Sequence dependence of cross-hybridization on short oligo microarrays
title_sort sequence dependence of cross-hybridization on short oligo microarrays
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1140085/
https://www.ncbi.nlm.nih.gov/pubmed/15914663
http://dx.doi.org/10.1093/nar/gni082
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AT zhangli sequencedependenceofcrosshybridizationonshortoligomicroarrays