Simultaneous genotyping of indels and SNPs by mass spectroscopy.
Nucleotide insertion/deletion polymorphisms (indels) in ApoE gene were precisely genotyped using artificial ribonucleases and MALDI-TOF MS. The RNA fragments for MS analysis were prepared by treating RNA specimens with our artificial ribonucleases, which consist of LuCl(3) (molecular scissors) and oligonucleotides bearing two acridine groups (RNA-activator for site-selective scission). RNA scission by Lu(III) ion always occurred at the phosphodiester linkages in front of the two acridines, even when the RNA specimens involved consecutive cytidine sequences of different lengths. Thus, even complicated mixtures of these indel specimens were completely genotyped by using only one acridine-bearing oligonucleotide and by subjecting the reaction mixture to single MS measurement. Moreover, single nucleotide polymorphism (SNP) in the consecutive sequences could be genotyped simultaneously with the indels.
Sasayama
Takuro
T
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan.
Kato
Mayu
M
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan.
Aburatani
Hiroyuki
H
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan.
Kuzuya
Akinori
A
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan.
Komiyama
Makoto
M
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan. komiyama@mkomi.rcast.u-tokyo.ac.jp.
D053318:Apolipoprotein E3; D001057:Apolipoproteins E / Q000235:genetics; D001483:Base Sequence; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012313:RNA / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics*; D017384:Sequence Deletion / Q000235:genetics*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014158:Transcription, Genetic
D053318:Apolipoprotein E3; D001057:Apolipoproteins E; D012313:RNA