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Updated: Jul 10, 2026
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In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines
Published on: May 12, 2023
Preferred binding sites for the bifunctional intercalator TANDEM determined using DNA fragments that contain every
Andrew J Hampshire1, Keith R Fox
1School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
Analytical Biochemistry
|November 6, 2007
Summary
Synthetic quinoxaline antibiotic TANDEM binds most TpA steps in DNA. Flanking sequences significantly affect binding affinity, with ATAT being optimal, while TTAA and GTAC sites show variable TANDEM binding.
Area of Science:
- Molecular Biology
- Medicinal Chemistry
- Genomics
Background:
- DNA footprinting is crucial for understanding drug-target interactions.
- Synthetic quinoxaline antibiotics show potential therapeutic applications.
- Sequence-specific DNA binding is a key mechanism for many drugs.
Purpose of the Study:
- To synthesize and characterize novel DNA footprinting substrates.
- To determine the DNA sequence binding preferences of the synthetic quinoxaline antibiotic TANDEM.
- To investigate the influence of flanking sequences on TANDEM-DNA binding affinity.
Main Methods:
- Preparation of DNA restriction fragments containing all 64 symmetrical hexanucleotide sequences.
- Cloning of fragments into the pUC19 polylinker site in both orientations.
- Assessment of TANDEM binding affinities to various DNA sequences using footprinting assays.
Main Results:
- TANDEM exhibits binding to most TpA steps, but affinity is modulated by flanking sequences.
- Optimal binding sites for TANDEM include the tetranucleotide ATAT (YATATR > RATATY).
- Poor binding was observed at TTAA sites (especially TTTAAA), and GTAC binding was highly context-dependent (e.g., GGTACC vs. CGTACG).
Conclusions:
- TANDEM displays sequence-specific DNA binding preferences.
- Flanking sequences play a critical role in determining the affinity of TANDEM for DNA.
- Understanding these binding preferences can inform the development of novel quinoxaline-based therapeutics.
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