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Single nucleotide polymorphism typing with a surface plasmon resonance-based sensor using hybridization enhancement
Shiro Okumura1, Rieko Kuroda, Kuniyo Inouye
1Biotechnology and Food Research Institute, Fukuoka Industrial Technology Centre, 1465-5 Aikawa, Kurume, Fukuoka, 839-0861, Japan, sokumura@fitc.pref.fukuoka.jp.
Applied Biochemistry and Biotechnology
|August 2, 2014
Summary
A novel surface plasmon resonance (SPR) method uses a DNA "blocker" to significantly enhance binding volume for single nucleotide polymorphism (SNP) detection. This technique accurately discriminates SNP alleles, improving genetic analysis.
Area of Science:
- Biotechnology
- Genetics
- Biosensing
Background:
- Single nucleotide polymorphisms (SNPs) are crucial genetic markers.
- Accurate SNP genotyping is essential for disease research and diagnostics.
- Existing SNP detection methods can be complex or lack sensitivity.
Purpose of the Study:
- To develop a simple and sensitive method for single nucleotide polymorphism (SNP) discrimination.
- To enhance the sensitivity of surface plasmon resonance (SPR)-based biosensors for SNP detection.
- To validate the method's effectiveness using a canine SNP associated with progressive rod-cone degeneration.
Main Methods:
- Utilized a surface plasmon resonance (SPR)-based sensor to measure binding volume (BV).
- Introduced a novel single-stranded DNA additive, termed 'blocker,' complementary to the target SNP allele.
- Investigated the effect of blocker concentration on target binding to complementary probes.
Main Results:
- The 'blocker' additive enhanced the binding volume (BV) to the full-match probe by over 10-fold.
- SNP alleles were readily discriminated due to the significant increase in BV.
- Optimal blocker concentration was determined to be 300-500 nM for maximum BV enhancement.
- Genotyping results using this method showed high agreement with direct sequencing.
Conclusions:
- The developed SPR-based method with a blocker additive provides a simple and highly sensitive approach for SNP discrimination.
- The blocker significantly improves the signal-to-noise ratio, enabling accurate allele detection.
- This method holds promise for efficient genetic analysis and diagnostics.
