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Structural polymorphism of oligo(dC) with mixed alpha,beta-anomeric backbone
E N Timofeev1, O F Borisova, A K Shchyolkina
1W.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow. edward@genome.eimb.relarn.ru
Journal of Biomolecular Structure & Dynamics
|March 4, 2000
Summary
Mixed alpha,beta-oligocytidilates form semiprotonated complexes with DNA at low temperatures, not triplexes. Despite self-association, these oligonucleotides can target AT-rich DNA duplexes, forming three-stranded complexes.
Area of Science:
- Biochemistry
- Molecular Biology
- Oligonucleotide Chemistry
Background:
- Oligonucleotides with mixed alpha,beta-anomeric backbones offer new possibilities for DNA sequence recognition.
- Previous work suggested their potential for novel triplex motifs.
Purpose of the Study:
- To investigate alpha- and beta- anomers of cytidine for recognizing AT and TA base pairs in double-stranded DNA.
- To characterize the binding properties of beta-oligo(dC) and mixed alpha,beta-oligocytidilates.
Main Methods:
- UV absorption spectroscopy
- Ethidium bromide (EtBr) fluorescence polarization
- Circular dichroism (CD)
- UV thermal denaturation
- Non-denaturing gel electrophoresis
Main Results:
- Semiprotonated oligocytidilic complexes form at low temperatures and neutral pH, rather than intramolecular triplex folding.
- A low-temperature transition was observed in denaturation profiles of oligonucleotides with beta- or mixed alpha,beta- cytidine stretches.
- Self-association of alpha,beta-oligo(dC) was confirmed by CD bands characteristic of CC+ base pairs.
- Mixed alpha,beta-oligocytidilates successfully targeted AT-containing DNA duplexes, forming three-stranded complexes.
Conclusions:
- Mixed alpha,beta-oligocytidilates primarily form semiprotonated complexes at low temperatures.
- Despite self-association tendencies, these modified oligonucleotides demonstrate utility in targeting specific DNA sequences.