PMID- 19109921
OWN - NLM
STAT- MEDLINE
DCOM- 20090406
LR  - 20191210
IS  - 1096-0309 (Electronic)
IS  - 0003-2697 (Linking)
VI  - 386
IP  - 2
DP  - 2009 Mar 15
TI  - Genotyping of single nucleotide polymorphisms using base-quenched probe: a method 
      does not invariably depend on the deoxyguanosine nucleotide.
PG  - 161-6
LID - 10.1016/j.ab.2008.11.032 [doi]
AB  - Most available methods for detecting single nucleotide polymorphisms (SNPs) are 
      based principally on the system that can produce an increased fluorescence signal 
      during hybridization. In the current study, we demonstrate a method of 
      base-quenched probe for polymerase chain reaction (PCR) genotyping that requires 
      only a pair of primers and one fluorescent probe and does not invariably depend 
      on the deoxyguanosine nucleotide. This method further exploits the phenomenon of 
      fluorescence quenching of fluorescent-labeled probe during hybridization to its 
      complementary target gene's sequence. 6-Carboxyfluorescein (FAM) can be directly 
      conjugated to a base of either adenine (A), thymine (T), cytosine (C), or guanine 
      (G), referred to as A-, T-, C-, or G-quenched probe, respectively, at either the 
      5' or 3' end. For describing the method in detail, we chose apolipoprotein M 
      (apoM) as a target gene in the current study. DNA sequencing analyses validated 
      that all four types of base-quenched probes could provide unbiased genotyping 
      results (K = 1, P = 0.000), although the maximum speed of fluorescence increase, 
      max(dF/dT), when using the G-quenched probe method, was approximately twofold 
      lower than the others (P < 0.0001). Moreover, we applied this method to detect 
      another seven SNPs in the genomes of phospholipase A2, monocyte chemoattractant 
      protein 1 (MCP1), and l-ficolin, further confirming our method. It is concluded 
      that this method is precise, simple, and economic as well as suitable for 
      large-scale genotyping studies.
FAU - Luo, Guanghua
AU  - Luo G
AD  - Comprehensive Laboratory, Third Affiliated Hospital, Suzhou University, Changzhou 
      213003, China.
FAU - Zheng, Lu
AU  - Zheng L
FAU - Zhang, Xiaoying
AU  - Zhang X
FAU - Zhang, Jun
AU  - Zhang J
FAU - Nilsson-Ehle, Peter
AU  - Nilsson-Ehle P
FAU - Xu, Ning
AU  - Xu N
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20081203
PL  - United States
TA  - Anal Biochem
JT  - Analytical biochemistry
JID - 0370535
RN  - 0 (DNA Primers)
RN  - G9481N71RO (Deoxyguanosine)
SB  - IM
MH  - DNA Primers/*chemistry
MH  - Deoxyguanosine/*chemistry
MH  - Fluorescence
MH  - *Genotype
MH  - Polymerase Chain Reaction/*methods
MH  - *Polymorphism, Single Nucleotide
MH  - Sequence Analysis, DNA/methods
EDAT- 2008/12/27 09:00
MHDA- 2009/04/07 09:00
CRDT- 2008/12/27 09:00
PHST- 2008/09/03 00:00 [received]
PHST- 2008/11/22 00:00 [revised]
PHST- 2008/11/24 00:00 [accepted]
PHST- 2008/12/27 09:00 [entrez]
PHST- 2008/12/27 09:00 [pubmed]
PHST- 2009/04/07 09:00 [medline]
AID - S0003-2697(08)00802-6 [pii]
AID - 10.1016/j.ab.2008.11.032 [doi]
PST - ppublish
SO  - Anal Biochem. 2009 Mar 15;386(2):161-6. doi: 10.1016/j.ab.2008.11.032. Epub 2008 
      Dec 3.