Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system.
Single-nucleotide polymorphisms (SNPs) in double-stranded DNA (dsDNA) have been straightforwardly genotyped by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS). Peptide nucleic acid (PNA), a DNA analog, was used as a probe molecule. In its presence, genomic dsDNA was first treated with exonuclease III and then with nuclease S1. By these one-pot reactions, single-stranded DNA fragments including the SNP sites were formed in situ. These fragments were directly analyzed by MALDI-TOF MS, and the identity of the DNA base at the SNP site was determined in terms of mass number. By using two or more PNA probes simultaneously, multiplex analysis was also successful. Various genotypes of apolipoprotein E gene (epsilon2/epsilon2, epsilon3/epsilon3, epsilon4/epsilon4, epsilon2/epsilon3 and epsilon3/epsilon4) were identified from dsDNA obtained by PCR from corresponding patients.
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
Binzhi
B
Ren
Jing-Min
JM
Zhou
Makoto
M
Komiyama
D001057:Apolipoproteins E / Q000235:genetics; D020137:Base Pair Mismatch / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004252:DNA Mutational Analysis / Q000379:methods*; D004277:DNA, Single-Stranded / Q000235:genetics; D005090:Exodeoxyribonucleases / Q000378:metabolism*; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D020135:Peptide Nucleic Acids / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D001057:Apolipoproteins E; D004277:DNA, Single-Stranded; D020135:Peptide Nucleic Acids; D004247:DNA; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III; D015719:Single-Strand Specific DNA and RNA Endonucleases