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Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

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Published on: August 3, 2018

Statistically significant Raman detection of midsequence single nucleotide polymorphisms.

Benjamin Moody¹, Gregory McCarty

¹North Carolina State University, 2147 Burlington Laboratories, Raleigh, North Carolina 27695, USA.

Analytical Chemistry

|February 10, 2009

Summary

This summary is machine-generated.

This study demonstrates surface-enhanced Raman spectroscopy for statistically significant single nucleotide polymorphism detection. Gold nanoparticles and a gold surface enable sensitive DNA hybridization analysis, differentiating mismatches.

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Area of Science:

Biophysical Chemistry
Spectroscopy
Genomics

Background:

Accurate detection of single nucleotide polymorphisms (SNPs) is crucial for genetic analysis and disease diagnostics.
Traditional methods for SNP genotyping can be complex and time-consuming.
Developing sensitive and statistically robust detection methodologies is an ongoing challenge.

Purpose of the Study:

To present a novel methodology for statistically significant SNP detection using surface-enhanced Raman spectroscopy (SERS).
To investigate the feasibility of using SERS to differentiate between perfectly matched, completely mismatched, and single-nucleotide mismatched DNA duplexes.

Main Methods:

Utilized single-stranded oligonucleotides functionalized with 40 nm gold nanoparticles.
Hybridized these nanoparticles with oligonucleotides immobilized on a photolithographically defined gold surface.
Created a surface-enhanced Raman scattering (SERS) environment around the DNA duplex.
Collected and analyzed Raman spectra to identify differences in DNA hybridization states.

Main Results:

Statistically significant differences in Raman intensity were observed for characteristic peaks.
The SERS approach successfully distinguished between complementary, completely mismatched, and single-nucleotide mismatched DNA duplexes.
The methodology provides a robust platform for sensitive SNP analysis.

Conclusions:

Surface-enhanced Raman spectroscopy, combined with gold nanoparticles and a gold surface, enables statistically significant detection of single nucleotide polymorphisms.
This technique offers a sensitive and specific method for analyzing DNA hybridization and identifying sequence variations.
The developed methodology holds promise for applications in genetic diagnostics and molecular biology research.