PMID- 12951771
OWN - NLM
STAT- MEDLINE
DCOM- 20040414
LR  - 20180928
IS  - 0736-6205 (Print)
IS  - 0736-6205 (Linking)
VI  - 35
IP  - 2
DP  - 2003 Aug
TI  - Single nucleotide polymorphism discrimination assisted by improved base stacking 
      hybridization using oligonucleotide microarrays.
PG  - 300-2, 304, 306 passim
AB  - Efficiencies of mismatch discrimination using size-varied capture probes were 
      examined at various hybridization temperatures. The probes were 17, 15, 13, 11, 
      9, and 7 nucleotides long and contained single-base mismatches at their 3' ends. 
      The optimal signal intensity and efficiency of base stacking hybridization on 
      mismatch discrimination were observed for capture probes with a melting 
      temperature (Tm) value of 36 degrees C, in the detection of DNA sequence 
      variations at 40 degrees C. We employed asymmetric PCR to prepare single-stranded 
      target DNA labeled with a fluorescent dye, and the PCR product was hybridized on 
      the DNA microarray with no further purification. Our efforts have enhanced the 
      sensitivity and simplified the procedures of base stacking hybridization on 
      mismatch discrimination. As a model experiment, this improved technology was used 
      to identify plasmid templates of human leukocyte antigen (HLA)-A alleles 2601, 
      2902, and 0206 on oligonucleotide microarrays. It is now possible to apply this 
      simple, rapid, sensitive, and reliable base stacking hybridization technology to 
      detect DNA sequence variations on microarrays in clinical diagnosis and other 
      applications.
FAU - Wang, D
AU  - Wang D
AD  - Tsinghua University, National Engineering Research Center for Beijing Biochip 
      Technology, Beijing, P.R. China.
FAU - Gao, H
AU  - Gao H
FAU - Zhang, R
AU  - Zhang R
FAU - Ma, X
AU  - Ma X
FAU - Zhou, Y
AU  - Zhou Y
FAU - Cheng, J
AU  - Cheng J
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Biotechniques
JT  - BioTechniques
JID - 8306785
RN  - 0 (DNA Probes)
RN  - 0 (DNA, Single-Stranded)
RN  - 0 (HLA-A Antigens)
RN  - 0 (Nucleotides)
SB  - IM
MH  - Alleles
MH  - *Base Pair Mismatch
MH  - Base Sequence
MH  - DNA Probes
MH  - DNA, Single-Stranded/chemistry
MH  - Genetic Variation
MH  - HLA-A Antigens/chemistry/*genetics
MH  - Humans
MH  - Leukocytes/immunology
MH  - *Nucleic Acid Hybridization
MH  - Nucleotides
MH  - Oligonucleotide Array Sequence Analysis/methods
MH  - Plasmids
MH  - Polymerase Chain Reaction
MH  - Polymorphism, Single Nucleotide/*genetics
MH  - Sensitivity and Specificity
MH  - Sequence Analysis, DNA
MH  - Temperature
EDAT- 2003/09/04 05:00
MHDA- 2004/04/15 05:00
CRDT- 2003/09/04 05:00
PHST- 2003/09/04 05:00 [pubmed]
PHST- 2004/04/15 05:00 [medline]
PHST- 2003/09/04 05:00 [entrez]
AID - 10.2144/03352st02 [doi]
PST - ppublish
SO  - Biotechniques. 2003 Aug;35(2):300-2, 304, 306 passim. doi: 10.2144/03352st02.