Abstract:
:The ligase detection reaction (LDR) is a highly specific genotyping method for single nucleotide variations. Although LDR typically discriminates single nucleotide polymorphism (SNP) alleles at the 3' end of so-called LDR discriminating probes, we designed probes in which the position of nucleotide differences for discrimination was shifted to the second and third nucleotides from the 3' end. Using the 3'-modified probes, we targeted SNPs of the human ABO group and investigated the specificity and efficiency of ligation by a universal LDR assay. We demonstrated that one or two nucleotide shifts of differences in discriminating probes improve the allele balance in detecting both base substitutions and short deletions. In regard to short deletions, moreover, the shifts of nucleotide differences in discriminating probes form the perfect-machted or multiple-mismatched structures (the bulge structures) in the discriminating probe-target DNA duplex and may contribute to enhance ligation efficiency.
journal_name
Mol Cell Probesjournal_title
Molecular and cellular probesauthors
Asari M,Omura T,Maseda C,Shiono H,Tasaki Y,Matsubara K,Shimizu Kdoi
10.1016/j.mcp.2010.08.005subject
Has Abstractpub_date
2010-12-01 00:00:00pages
381-6issue
6eissn
0890-8508issn
1096-1194pii
S0890-8508(10)00062-9journal_volume
24pub_type
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