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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Comparing Copy Number Variations and SNPs02:26

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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
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The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform
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Padlock Probes to Detect Single Nucleotide Polymorphisms.

Tomasz Krzywkowski1, Mats Nilsson2

  • 1Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 171 21, Solna, Sweden.

Methods in Molecular Biology (Clifton, N.J.)
|November 14, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a novel in situ method for detecting messenger RNA (mRNA) and single nucleotide polymorphisms (SNPs) using padlock probes and rolling circle amplification. This technique preserves spatial tissue context for accurate genetic analysis in single cells.

Keywords:
In situPadlock probeSNPSingle moleculeSingle nucleotide polymorphismSingle-cellmRNA genotyping

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • High-throughput DNA analysis methods offer cost-effective genetic characterization but often lose crucial spatial tissue context.
  • Current methods require nucleic acid isolation from the native cellular environment, hindering in situ analysis.
  • There is a need for methods that can analyze genetic material within its native tissue environment.

Purpose of the Study:

  • To present a novel multiplexed, in situ detection protocol for mRNAs and single nucleotide polymorphisms (SNPs).
  • To demonstrate the application of this protocol for differentiating species and genotyping specific genes in human brain tissue.
  • To provide a method for automated characterization and quantitation of target mRNA in single cells or specific tissue areas.

Main Methods:

  • Utilized padlock probes and rolling circle amplification for multiplexed, in situ detection of mRNA and SNPs.
  • Leveraged a single nucleotide variant in ACTB mRNA to distinguish human and mouse cells in cocultures.
  • Applied the protocol to genotype protocadherin (PCDH) X and Y homologs in human brain tissue.

Main Results:

  • Successfully differentiated human and mouse cells using a specific mRNA polymorphism.
  • Demonstrated successful genotyping of PCDH X and Y homologs in human brain tissue.
  • Developed a method for automated quantification of target mRNA within single cells or selected tissue regions.

Conclusions:

  • The presented protocol enables simultaneous in situ detection and genotyping of mRNA and SNPs while preserving spatial information.
  • This method offers a powerful tool for analyzing genetic variations and gene expression within their native tissue context.
  • The automated characterization capability enhances the efficiency and accuracy of single-cell and tissue-based genetic analysis.