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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

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.
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In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
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Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.

Peter Z Qin1, Ian S Haworth, Qi Cai

  • 1Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA. pzq@usc.edu

Nature Protocols
|October 20, 2007
PubMed
Summary

This study introduces a method to measure nanometer distances in nucleic acids using nitroxide probes. This technique aids in understanding nucleic acid structures and conformational changes.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Accurate measurement of nanometer distances within nucleic acids is crucial for understanding their structure and function.
  • Existing methods may have limitations in probing global structures or conformational dynamics.

Purpose of the Study:

  • To describe a protocol for measuring nanometer distances in nucleic acids using chemically attached nitroxide probes.
  • To provide a method for studying global nucleic acid structures and conformational changes in nucleic acids and protein/nucleic acid complexes.

Main Methods:

  • Labeling DNA or RNA with two nitroxide probes attached to phosphorothioates at specific sites.
  • Measuring inter-nitroxide distances using a four-pulse double electron-electron resonance (DEER) technique.
  • Correlating measured distances to nucleic acid structures using a web-accessible computer program.

Main Results:

  • The protocol allows for the attachment of nitroxide probes to any nucleotide within a nucleic acid sequence.
  • The DEER technique successfully measures inter-nitroxide distances.
  • A computational tool is available to correlate these distances to the parent nucleic acid structures.

Conclusions:

  • This method provides a reliable way to probe global structures of nucleic acids.
  • The technique is valuable for studying dynamic conformational changes in nucleic acids and their complexes.
  • The protocol offers a new tool for structural biology research on nucleic acids.