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Single Nucleotide Polymorphisms-SNPs01:05

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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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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene
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A new method to evaluate trinucleotide repeats length polymorphism.

Limin Ning1, Dawei Yang1, Tao Gao1

  • 1State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, Nanjing University, Nanjing 210093, PR China.

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|June 17, 2015
PubMed
Summary
This summary is machine-generated.

A new fluorescent method uses doxorubicin to detect trinucleotide repeat (TNR) lengths, a key indicator of disease severity. This simple, cost-effective technique offers promise for diagnosing triplet expansion disorders.

Keywords:
DoxorubicinFluorescenceLength polymorphismSecondary structureTrinucleotide repeats

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Trinucleotide repeats (TNRs) are DNA sequences implicated in numerous diseases, with repeat length often correlating with disease severity.
  • Accurate assessment of TNR length polymorphism is crucial for understanding disease mechanisms and progression.

Purpose of the Study:

  • To develop a novel, simple, and cost-effective fluorescent method for evaluating TNR length polymorphism.
  • To utilize the DNA secondary structure of TNRs and doxorubicin's fluorescence quenching properties for length assessment.

Main Methods:

  • A fluorescent assay employing doxorubicin (Dox) as a probe was developed.
  • The method leverages the G-C rich nature of TNRs, which form stable intramolecular structures that quench Dox fluorescence upon intercalation.
  • The assay was validated using CAG repeats, demonstrating a linear relationship between fluorescence intensity and repeat numbers (10-35 repeats).

Main Results:

  • A novel fluorescent method for TNR length polymorphism evaluation was successfully developed.
  • The method demonstrated a linear correlation between fluorescence intensity and CAG repeat numbers.
  • The assay was effective in analyzing TNR length polymorphism in PCR products without chemical modifications.

Conclusions:

  • This new doxorubicin-based fluorescent method provides a simple, cost-effective, and convenient approach for assessing TNR length polymorphism.
  • The technique avoids the need for chemical modifications, making it highly practical.
  • This method holds significant potential for the diagnosis of diseases associated with triplet repeat expansions.