PMID- 19891952
OWN - NLM
STAT- MEDLINE
DCOM- 20100408
LR  - 20100127
IS  - 1096-0309 (Electronic)
IS  - 0003-2697 (Linking)
VI  - 398
IP  - 1
DP  - 2010 Mar 1
TI  - A novel single nucleotide polymorphism detection of a double-stranded DNA target 
      by a ribonucleotide-carrying molecular beacon and thermostable RNase HII.
PG  - 83-92
LID - 10.1016/j.ab.2009.10.042 [doi]
AB  - Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic 
      variation. SNPs are important markers that link sequence variations to phenotypic 
      changes. Because of the importance of SNPs in the life and medical sciences, a 
      great deal of effort has been devoted to developing accurate, rapid, and 
      cost-effective technologies for SNP analysis. In this article, we describe a 
      novel method for SNP genotyping based on differential fluorescence emission due 
      to cleavage by Thermus thermophilus RNase HII (TthRNase HII) of DNA 
      heteroduplexes containing an SNP site-specific chimeric DNA-rN(1)-DNA molecular 
      beacon (cMB). We constructed a loop sequence for a cMB that contains a single 
      SNP-specific ribonucleotide at the central site. When the cMB probe is hybridized 
      to a target double-stranded DNA (dsDNA), a perfect match of the cMB/DNA duplex 
      permits efficient cleavage with TthRNase HII, whereas a mismatch in the duplex 
      due to an SNP greatly reduces efficiency. Cleavage efficiency is measured by the 
      incremental difference of fluorescence emission of the beacon. We show that the 
      genotypes of 10 individuals at 12 SNP sites across a series of human leukocyte 
      antigen (HLA) can be determined correctly with respect to conventional DNA 
      sequencing. This novel TthRNase HII-based method offers a platform for easy and 
      accurate SNP analysis.
CI  - Copyright 2009 Elsevier Inc. All rights reserved.
FAU - Liu, Xi-Peng
AU  - Liu XP
AD  - College of Life Science and Technology, Shanghai Jiao Tong University, Shanghai 
      200240, China.
FAU - Hou, Jing-Li
AU  - Hou JL
FAU - Liu, Jian-Hua
AU  - Liu JH
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20091103
PL  - United States
TA  - Anal Biochem
JT  - Analytical biochemistry
JID - 0370535
RN  - 0 (Fluorescent Dyes)
RN  - 0 (HLA Antigens)
RN  - 0 (Nucleic Acid Heteroduplexes)
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (Ribonucleotides)
RN  - EC 3.1.26.- (ribonuclease HII)
RN  - EC 3.1.26.4 (Ribonuclease H)
SB  - IM
MH  - Base Pair Mismatch
MH  - Base Sequence
MH  - DNA Cleavage
MH  - Fluorescent Dyes/chemistry
MH  - Genotype
MH  - HLA Antigens/genetics
MH  - Humans
MH  - Nucleic Acid Heteroduplexes/chemistry
MH  - Oligonucleotide Probes/*chemistry
MH  - *Polymorphism, Single Nucleotide
MH  - Ribonuclease H/*metabolism
MH  - Ribonucleotides/*chemistry
MH  - Sequence Analysis, DNA
MH  - *Spectrometry, Fluorescence
EDAT- 2009/11/07 06:00
MHDA- 2010/04/09 06:00
CRDT- 2009/11/07 06:00
PHST- 2009/08/04 00:00 [received]
PHST- 2009/10/26 00:00 [revised]
PHST- 2009/10/29 00:00 [accepted]
PHST- 2009/11/07 06:00 [entrez]
PHST- 2009/11/07 06:00 [pubmed]
PHST- 2010/04/09 06:00 [medline]
AID - S0003-2697(09)00754-4 [pii]
AID - 10.1016/j.ab.2009.10.042 [doi]
PST - ppublish
SO  - Anal Biochem. 2010 Mar 1;398(1):83-92. doi: 10.1016/j.ab.2009.10.042. Epub 2009 
      Nov 3.