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Tertiary base pair interactions in slipped loop-DNA: an NMR and model building study
N B Ulyanov1, K D Bishop, V I Ivanov
1Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.
Nucleic Acids Research
|October 11, 1994
Summary
Short direct repeats in gene regulatory regions can form non-standard Slipped Loop Structures (SLS). NMR and modeling reveal these structures involve a tertiary miniduplex, crucial for understanding DNA structure and gene regulation.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- Short direct repeat sequences are prevalent in gene regulatory regions.
- These sequences can exhibit hypersensitivity to S1 nuclease cleavage in supercoiled plasmids.
- A Slipped Loop Structure (SLS) has been proposed to explain this cleavage data and may play a role in transcription regulation.
Purpose of the Study:
- To investigate the structural basis of Slipped Loop Structures (SLS) in DNA.
- To develop a stereochemically sound model for the proposed SLS.
Main Methods:
- One-dimensional 1H NMR spectroscopy was used to study a synthetic 55-nucleotide DNA sequence.
- Conformational calculations were employed to build an all-atom stereochemically sound model.
Main Results:
- NMR data identified AT base pairs, indicating the formation of an additional tertiary miniduplex within the SLS.
- Stereochemically sound modeling confirmed that this tertiary miniduplex can form in one plausible SLS isomer but not another.
Conclusions:
- The study provides the first detailed stereochemical model for the Slipped Loop Structure (SLS).
- The formation of a tertiary miniduplex is a key feature of the SLS, potentially influencing gene transcription.
- The findings offer insights into the structural diversity of DNA and its regulatory implications.