Accurate guanine:cytosine discrimination in T4 DNA ligase-based single nucleotide polymorphism analysis using an oxanine-containing ligation fragment.
T4 DNA ligase-based mismatch detection methods have been proposed as useful strategies for single nucleotide polymorphism (SNP) analyses. However, there is a critical problem for cytosine/thymine (C/T) SNP analyses: guanine:thymine (G:T) mismatch is not distinguished from guanine:cytosine (G:C). Here we employed chemically modified nucleobases, such as oxanine and hypoxanthine, at the end of a ligation fragment and analyzed their influence on the ligation efficiency between G:C and G:T. Successful ligation for G:C and no ligation for G:T were observed when oxanine was employed adjacent to guanine in the ligation junction. This ligation method using an oxanine-containing fragment has strong potentials for the accurate analysis of C/T SNPs.
Pack
Seung Pil
SP
Department of Biotechnology and Bioinformatics, Korea University, Jochiwon, Chungnam, Republic of Korea. spack@korea.ac.kr
Doi
Akihiro
A
Choi
Yoo Seong
YS
Kim
Hyong Bai
HB
Makino
Keisuke
K
D020137:Base Pair Mismatch; D001483:Base Sequence; D003596:Cytosine; D011088:DNA Ligases / Q000737:chemistry* / Q000235:genetics*; D006147:Guanine; D020641:Polymorphism, Single Nucleotide; D011684:Purine Nucleosides / Q000737:chemistry*
D011684:Purine Nucleosides; C468766:oxanine; D006147:Guanine; D003596:Cytosine; D011088:DNA Ligases