Single nucleotide polymorphism genotyping by nanoparticle-enhanced SPR imaging measurements of surface ligation reactions

Yuan Li, A.W. Wark, Hye Jin Lee, R.M. Corn

Research output: Contribution to journalArticle

149 Citations (Scopus)

Abstract

A sensitive method for the analysis of single nucleotide polymorphisms (SNPs) in genomic DNA that utilizes nanoparticle-enhanced surface plasmon resonance imaging (SPRI) measurements of surface enzymatic ligation reactions on DNA microarrays is demonstrated. SNP identification was achieved by using sequence-specific surface reactions of the enzyme Taq DNA ligase, and the presence of ligation products on the DNA microarray elements was detected with SPRI through the hybridization adsorption of complementary oligonucleotides attached to gold nanoparticles. The use of gold nanoparticles increases the sensitivity of the SPRI so that single bases in oligonucleotides can be successfully identified at a concentration of 1 pM. This sensitivity is amply sufficient for performing multiplexed SNP genotyping by using multiple PCR amplicons, and should also allow for the direct detection and identification of SNP sequences from 1 pM unamplified genomic DNA samples with this array-based and label-free SPRI methodology. As a first example of SNP genotyping, three different human genomic DNA samples were screened for a possible point mutation in the BRCA1 gene that is associated with breast cancer.
Original languageEnglish
Pages (from-to)3158-3164
Number of pages7
JournalAnalytical Chemistry
Volume78
Issue number9
DOIs
Publication statusPublished - 8 Aug 2006

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Surface reactions
Polymorphism
Nanoparticles
Surface Plasmon Resonance
Single Nucleotide Polymorphism
Ligation
Surface plasmon resonance
Nucleotides
Imaging techniques
DNA
Microarrays
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Gold
BRCA1 Gene
DNA Ligases
Point Mutation
Adsorption
Labels
Genes

Keywords

  • single nucleotide polymorphism genotyping
  • surface ligation reactions
  • nanoparticle-enhanced SPR imaging measurements

Cite this

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abstract = "A sensitive method for the analysis of single nucleotide polymorphisms (SNPs) in genomic DNA that utilizes nanoparticle-enhanced surface plasmon resonance imaging (SPRI) measurements of surface enzymatic ligation reactions on DNA microarrays is demonstrated. SNP identification was achieved by using sequence-specific surface reactions of the enzyme Taq DNA ligase, and the presence of ligation products on the DNA microarray elements was detected with SPRI through the hybridization adsorption of complementary oligonucleotides attached to gold nanoparticles. The use of gold nanoparticles increases the sensitivity of the SPRI so that single bases in oligonucleotides can be successfully identified at a concentration of 1 pM. This sensitivity is amply sufficient for performing multiplexed SNP genotyping by using multiple PCR amplicons, and should also allow for the direct detection and identification of SNP sequences from 1 pM unamplified genomic DNA samples with this array-based and label-free SPRI methodology. As a first example of SNP genotyping, three different human genomic DNA samples were screened for a possible point mutation in the BRCA1 gene that is associated with breast cancer.",
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Single nucleotide polymorphism genotyping by nanoparticle-enhanced SPR imaging measurements of surface ligation reactions. / Li, Yuan; Wark, A.W.; Lee, Hye Jin; Corn, R.M.

In: Analytical Chemistry, Vol. 78, No. 9, 08.08.2006, p. 3158-3164.

Research output: Contribution to journalArticle

TY - JOUR

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AU - Li, Yuan

AU - Wark, A.W.

AU - Lee, Hye Jin

AU - Corn, R.M.

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AB - A sensitive method for the analysis of single nucleotide polymorphisms (SNPs) in genomic DNA that utilizes nanoparticle-enhanced surface plasmon resonance imaging (SPRI) measurements of surface enzymatic ligation reactions on DNA microarrays is demonstrated. SNP identification was achieved by using sequence-specific surface reactions of the enzyme Taq DNA ligase, and the presence of ligation products on the DNA microarray elements was detected with SPRI through the hybridization adsorption of complementary oligonucleotides attached to gold nanoparticles. The use of gold nanoparticles increases the sensitivity of the SPRI so that single bases in oligonucleotides can be successfully identified at a concentration of 1 pM. This sensitivity is amply sufficient for performing multiplexed SNP genotyping by using multiple PCR amplicons, and should also allow for the direct detection and identification of SNP sequences from 1 pM unamplified genomic DNA samples with this array-based and label-free SPRI methodology. As a first example of SNP genotyping, three different human genomic DNA samples were screened for a possible point mutation in the BRCA1 gene that is associated with breast cancer.

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