Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system | Zendy

Bing Ren | Zendy

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Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system

Author(s) -

Bing Ren

Publication year - 2004

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gnh039

Subject(s) - biology , peptide nucleic acid , exonuclease , microbiology and biotechnology , dna , nuclease , exonuclease iii , molecular inversion probe , single nucleotide polymorphism , multiplex , oligonucleotide , genomic dna , snp genotyping , klenow fragment , nucleic acid , genetics , gene , genotype , escherichia coli , dna polymerase

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 (ε2/ε2, ε3/ε3, ε4/ε4, ε2/ε3 and ε3/ε4) were identified from dsDNA obtained by PCR from corresponding patients

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