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Determining the influence of structure on hybridization using oligonucleotide arrays

An Erratum to this article was published on 01 November 2000

An Erratum to this article was published on 01 October 1999

Abstract

We have studied the effects of structure on nucleic acid heteroduplex formation by analyzing hybridization of tRNAphe to a complete set of complementary oligonucleotides, ranging from single nucleotides to dodecanucleotides. The analysis points to features in tRNA that determine heteroduplex yield. All heteroduplexes that give high yield include both double-stranded stems as well as single-stranded regions. Bases in the single-stranded regions are stacked onto the stems, and heteroduplexes terminate at potential interfaces for coaxial stacking. Heteroduplex formation is disfavored by sharp turns or a lack of helical order in single-stranded regions, competition from bases displaced from a stem, and stable tertiary interactions. The study is relevant to duplex formation on oligonucleotide microarrays and to antisense technologies.

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Figure 1: Hybridization of tRNAphe to arrays of complementary oligonucleotides.
Figure 2: Higher yields from short sequences at the 3´ acceptor end
Figure 3: The cloverleaf depiction of tRNAphe showing sites of high yield.
Figure 4: The tertiary structure of tRNA and helical regions that give high yield.

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Acknowledgements

We thank S.C. Case-Green for valuable help, E. Westhof for advice, and W. Brown for comments on the manuscript. The work was supported by the MRC HGMP.

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Correspondence to Kalim U. Mir.

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Mir, K., Southern, E. Determining the influence of structure on hybridization using oligonucleotide arrays. Nat Biotechnol 17, 788–792 (1999). https://doi.org/10.1038/11732

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