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Crystal structure of intercalated four-stranded d(C3T) at 1.4 A resolution
C H Kang1, I Berger, C Lockshin
1Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.
Summary
The crystal structure of d(C3T) reveals a unique four-stranded DNA complex. This intercalated structure, stabilized by protonated cytosine bases, exhibits significant asymmetry and microheterogeneity.
Area of Science:
- Structural biology
- Biochemistry
- Molecular genetics
Background:
- DNA can form complex secondary structures beyond the canonical double helix.
- Understanding these structures is crucial for deciphering their biological roles and potential applications.
Purpose of the Study:
- To determine the high-resolution crystal structure of the d(C3T) oligonucleotide.
- To elucidate the molecular architecture and stabilizing interactions within this unusual DNA complex.
Main Methods:
- X-ray crystallography at 1.4 A resolution.
- Analysis of DNA secondary structure and base pairing.
Main Results:
- d(C3T) forms a four-stranded intercalated complex comprising two parallel duplexes with opposite strand orientation.
- Cytosine-protonated cytosine base pairs stabilize the structure.
- The complex exhibits a flat, lath-like shape with a right-handed twist.
- Significant asymmetry is observed, with phosphate groups rotated and stabilized by bridging water molecules.
- Microheterogeneity and cytosine hemiprotonation occur even at neutral pH.
Conclusions:
- The crystal structure reveals a novel DNA quadruplex architecture stabilized by specific base pairing and hydration.
- The observed asymmetry and microheterogeneity provide insights into DNA structural dynamics and stability.
- Cytosine hemiprotonation at neutral pH suggests potential implications for DNA recognition and function in biological systems.