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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences
G Manzini1, N Yathindra, L E Xodo
1Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy.
Nucleic Acids Research
|November 11, 1994
Summary
Repetitive cytosine DNA sequences, including those from the human telomere and c-ki-ras promoter, form an intramolecular i-motif structure. This pH-dependent DNA structure is stable and reversible, suggesting significant biological roles.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Repetitive DNA sequences are crucial for genomic stability and gene regulation.
- Cytosine-rich sequences are known to form non-canonical DNA structures.
Purpose of the Study:
- To investigate the structural behavior of specific repetitive cytosine oligodeoxynucleotides.
- To characterize the pH-induced structural transitions and stability of these DNA sequences.
Main Methods:
- Circular dichroism (CD) spectroscopy to monitor structural changes.
- Gel electrophoresis (PAGE) to assess molecular structure and homogeneity.
- UV absorbance studies and pH titrations to determine structural properties.
Main Results:
- All three tested sequences (HTC4, KRC6, KRM6) exhibited a pH-induced structural transition.
- An intense positive CD band at 285 nm indicated the formation of protonated cytosine base pairs.
- The DNA structures were stable, reversible, and intramolecular, with melting temperatures around 50°C at pH 5.5.
Conclusions:
- The studied oligodeoxynucleotides adopt an intramolecular i-motif structure.
- The i-motif formation is dependent on pH and protonation of cytosine bases.
- The presence of i-motif structures in telomeric and proto-oncogene sequences suggests functional relevance in DNA.
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