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Related Experiment Videos

Protonated pyrimidine-purine-purine triplex

V A Malkov1, O N Voloshin, A G Veselkov

  • 1Institute of Molecular Genetics, Russian Academy of Science, Moscow.

Nucleic Acids Research
|January 11, 1993
PubMed
Summary

This study reveals a novel protonated pyrimidine-purine-purine (Py-Pu-Pu) triplex structure. Unexpected dimethyl sulfate (DMS) protection was observed for guanines in both the duplex and third strand of Py-Pu-Pu triplexes.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • DNA triplexes are three-stranded nucleic acid structures with potential applications in gene regulation and therapeutics.
  • Protonated DNA structures can form under acidic conditions, altering DNA conformation and stability.
  • Pyrimidine-purine-purine (Py-Pu-Pu) triplexes involve specific base-pairing interactions.

Purpose of the Study:

  • To investigate the formation and structure of a protonated Py-Pu-Pu triplex formed between a d(C)nd(G)n duplex and a d(AG)m oligonucleotide.
  • To characterize the base triads, including the protonated CG*A+ triad, within this triplex structure.
  • To explore the structural implications of bivalent cations and acidic conditions on triplex formation.

Main Methods:

  • Oligonucleotide synthesis and annealing.

Related Experiment Videos

  • Plasmid cloning and maintenance of superhelical DNA.
  • Photofootprinting and chemical modification assays (diethyl pyrocarbonate, potassium permanganate, dimethyl sulfate).
  • Structural probing using dimethyl sulfate (DMS) to identify modified bases.

    • Main Results:

    • An intermolecular protonated Py-Pu-Pu triplex was observed between d(C)18d(G)18 and d(AG)5 oligonucleotides at pH 4.0, stabilized by Na+ and further by bivalent cations.
    • Proposed structures for isomorphous base triads TA*A, CG*G, and CG*A+ were presented.
    • Evidence for an H-DNA-like structure with CG*G and CG*A+ base triads was confirmed under acidic conditions.
    • Unexpected DMS protection was observed for guanines in both the duplex and the third strand's major groove in protonated and non-protonated Py-Pu-Pu triplexes.

    Conclusions:

    • Protonated Py-Pu-Pu triplexes can form under physiological relevant conditions (acidic pH, salt).
    • The study identified novel base triad structures and confirmed the formation of H-DNA-like structures.
    • The unexpected DMS protection highlights a new aspect of DNA triplex probing and structural characterization.