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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Comparing Copy Number Variations and SNPs

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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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Related Experiment Video

Updated: May 18, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

A mechanistic basis for amplification differences between samples and between genome regions.

Colin D Veal1, Peter J Freeman, Kevin Jacobs

  • 1Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.

BMC Genomics
|September 7, 2012
PubMed
Summary

High C+G content DNA regions can resist denaturation, forming Thermodynamically Ultra-Fastened (TUF) regions that reduce amplification efficiency. Fragmentation of DNA samples prior to amplification can overcome this variability.

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Last Updated: May 18, 2026

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • DNA amplification efficiency varies across genomes and samples.
  • High C+G content regions are often affected, but this doesn't fully explain variability.

Purpose of the Study:

  • To explain the mechanism behind variable DNA amplification efficiency.
  • To identify factors contributing to inter-sample variability in amplification.

Main Methods:

  • Investigated DNA denaturation under aggressive melting conditions.
  • Analyzed the impact of sequence elements on DNA strand annealing.

Main Results:

  • Identified 'Thermodynamically Ultra-Fastened' (TUF) regions with high C+G content that resist denaturation.
  • Demonstrated that incomplete denaturation in TUF regions reduces DNA amplification efficiency.

Conclusions:

  • Proposed a model explaining amplification difficulties in specific genome regions and inter-sample variability.
  • Showed that DNA sample quality (nicks/breaks) influences TUF region length and amplification suppression.
  • Recommended routine DNA fragmentation (sonication, enzyme digestion) to mitigate amplification variability.