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Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure
Tomoko Sunami1, Jiro Kondo, Ichiro Hirao
1Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
Acta Crystallographica. Section D, Biological Crystallography
|December 20, 2003
Summary
This study reveals a unique DNA duplex structure formed by an octamer fragment, featuring intercalated adenine bases. This base-stacked motif may represent a stable DNA conformation under physiological conditions.
Area of Science:
- Biochemistry
- Structural Biology
- Crystallography
Background:
- DNA fragments can adopt unusual structures beyond the canonical double helix.
- The DNA sequence d(GCGAAAGC) was previously suggested to form a stable mini-hairpin structure.
Purpose of the Study:
- To determine the three-dimensional structure of the DNA fragment d(GCGAAAGC) using X-ray crystallography.
- To investigate the structural stability and solution behavior of this DNA fragment.
Main Methods:
- X-ray crystallography was employed to analyze the DNA fragment.
- Electrophoresis was used to study the DNA fragment's behavior in solution under varying Mg(2+) concentrations.
Main Results:
- The X-ray analysis revealed a DNA duplex formed by two antiparallel octamers.
- A novel structural motif was observed with intercalated and stacked adenine bases, forming a column.
- The structure features Watson-Crick G.C pairs and sheared G.A pairs at the ends, with exposed adenine bases.
Conclusions:
- The base-intercalated duplex represents a stable conformation for this specific DNA sequence.
- The octamer exists in monomeric and dimeric states in solution, influenced by Mg(2+) concentration.
- The observed structure is stable under conditions relevant to physiological environments.