Structure-specific DNA cleavage on surfaces

Manchun Lu, Jeff G. Hall, Michael R. Shortreed, Liman Wang, W. Travis Berggren, Priscilla Wilkins Stevens, David M. Kelso, Victor Lyamichev, Bruce Neri, James L. Skinner, Lloyd M. Smith*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


The structure-specific invasive cleavage reaction is a useful means for sensitive and specific detection of single nucleotide polymorphisms, or SNPs, directly from genomic DNA without a need for prior target amplification. A new approach integrating this invasive cleavage assay and surface DNA array technology has been developed for potentially large-scale SNP scoring in a parallel format. Two surface invasive cleavage reaction strategies were designed and implemented for a model SNP system in codon 158 of the human ApoE gene. The upstream oligonucleotide, which is required for the invasive cleavage reaction, is either co-immobilized on the surface along with the probe oligonucleotide or alternatively added in solution. The ability of this approach to unambiguously discriminate a single base difference was demonstrated using PCR-amplified human genomic DNA. A theoretical model relating the surface fluorescence intensity to the progress of the invasive cleavage reaction was developed and agreed well with experimental results.

Original languageEnglish (US)
Pages (from-to)7924-7931
Number of pages8
JournalJournal of the American Chemical Society
Issue number27
StatePublished - Jul 10 2002

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry


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