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One left-handed strand in DNA-oligonucleotide complexes?
1Physical Chemistry Laboratory, Oxford, England.
FEBS Letters
|January 2, 1989
Summary
Oligonucleotides can bind to DNA, forming a three-stranded region. This interaction may be energetically driven by changes in DNA supercoiling, influencing strand conformation.
Area of Science:
- Molecular Biology
- Biophysics
- Computational Chemistry
Background:
- Single-stranded oligonucleotides can interact with double-stranded DNA.
- This interaction necessitates unwinding of the DNA double helix to form a triple-stranded region.
- The energetic driving force for this process, particularly its entropic challenge, is not fully understood.
Purpose of the Study:
- To investigate the conformational changes involved in oligonucleotide binding to supercoiled DNA.
- To elucidate the molecular mechanisms underlying the formation of DNA triple helices.
- To explore the energetic contributions, specifically supercoiling, to this binding event.
Main Methods:
- Utilizing computer graphics to visualize molecular structures.
- Performing molecular mechanics calculations to assess energetic properties.
- Analyzing the conformational possibilities of DNA strands during triple helix formation.
Main Results:
- The binding of an oligonucleotide to supercoiled DNA can lead to the formation of a three-stranded region.
- A significant energetic contribution may arise from alterations in the DNA's supercoiling.
- Computational modeling suggests strand 2 may adopt a left-handed conformation, while strands 1 and 3 form Watson-Crick pairs.
Conclusions:
- Oligonucleotide binding to supercoiled DNA is feasible and involves conformational rearrangements.
- DNA supercoiling plays a crucial role in the thermodynamics of triple helix formation.
- The proposed model provides insights into the structural basis of DNA triple helix formation.