Structure-specific DNA cleavage on surfaces.
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.
Lu
Manchun
M
Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396, USA.
Hall
Jeff G
JG
Shortreed
Michael R
MR
Wang
Liman
L
Berggren
W Travis
WT
Stevens
Priscilla Wilkins
PW
Kelso
David M
DM
Lyamichev
Victor
V
Neri
Bruce
B
Skinner
James L
JL
Smith
Lloyd M
LM
D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D013379:Substrate Specificity; D013499:Surface Properties; D013696:Temperature
D004247:DNA