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X-ray structure of d(CGAA), parallel-stranded DNA duplex with homo base pairs
Tomonori Kobuna1, Tomoko Sunami, Jiro Kondo
1Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
Nucleic Acids Research. Supplement (2001)
|August 9, 2003
Summary
Parallel DNA duplexes can form right-handed helices without anti-parallel strands. This structure, observed in d(CGAA) crystals, involves hemi-protonated cytosine bases and specific base pairings, even at neutral pH.
Area of Science:
- Structural Biology
- Biochemistry
- Crystallography
Background:
- DNA can form various helical structures beyond the canonical anti-parallel double helix.
- Previous studies suggested parallel duplexes might require anti-parallel components.
Purpose of the Study:
- To investigate the structural possibility of parallel-stranded DNA duplexes.
- To determine the crystal structures of d(CGAA) at different pH levels to understand their formation.
Main Methods:
- X-ray crystallography was employed to determine the crystal structures of d(CGAA).
- Analysis of two independent duplexes within the crystallographic asymmetric unit.
Main Results:
- Parallel-stranded, right-handed DNA duplexes were observed in d(CGAA) crystals at pH 6.0 and 7.0.
- Homo base pairing (C1:C1, G2:G2, A3:A3, A4:A4) occurred through hemi-protonation of cytosine and at minor groove, major groove, and Watson-Crick sites.
- Structural features remained consistent across pH 7.0, indicating hemi-protonation of C1:C1 even under neutral conditions.
Conclusions:
- Parallel-stranded DNA right-handed duplexes can form independently of anti-parallel strands.
- The hemi-protonated C1:C1 pair is crucial for stabilizing these parallel structures, persisting even at neutral pH.