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Related Concept Videos

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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.
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Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
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Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer.

Bin Chen1, Qiuling Huang2,3, Zhibei Qu4

  • 1Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.

Angewandte Chemie (International Ed. in English)
|December 14, 2020
PubMed
Summary

This study introduces a novel label-free fluorescence method to track dynamic DNA conformation changes. The technique uses a K21 DNA intercalator to monitor DNA structures, aiding in understanding gene expression and drug interactions.

Keywords:
DNA nanostructuresDNA transient conformation changeexcimerslabel freeplasmid

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • DNA conformation variations are crucial for gene regulation and drug interactions.
  • Probing transient DNA structural changes is difficult due to their dynamic nature.

Purpose of the Study:

  • To develop a label-free fluorescence method for monitoring transient DNA conformation changes.
  • To analyze the stability and dynamics of various DNA structures, including i-motifs and G-quadruplexes.

Main Methods:

  • Utilized a DNA intercalator, K21, which forms transient excimers on DNA surfaces.
  • Employed confocal fluorescence microscopy to analyze ratiometric emission correlating to DNA conformation stability.
  • Studied conformation dynamics of plasmid DNA before and after enzyme digestion.

Main Results:

  • Demonstrated a correlation between K21 excimer emission and DNA transient conformation stability.
  • Successfully monitored conformational dynamics in diverse DNA structures (i-motifs, G-quadruplexes, single nucleotide mutations).
  • Visualized conformation changes in plasmid DNA following enzymatic treatment.

Conclusions:

  • The developed label-free fluorescence strategy effectively probes transient DNA conformation changes.
  • This method offers potential for investigating dynamic genomic processes within living cells.