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Related Experiment Videos

Parallel self-associated structures formed by T,C-rich sequences at acidic pH.

F Geinguenaud1, J Liquier, M G Brevnov

  • 1Laboratoire de Spectroscopie Biomoléculaire, UPRES-A CNRS 7031, UFR de Médecine, Université Paris Nord, F-93017 Bobigny Cedex, France.

Biochemistry
|October 12, 2000
PubMed
Summary

Short DNA strands form parallel structures through C-C(+) base pairs at acidic pH. These parallel-stranded (ps) DNA structures are stable and do not favor i-motif formation, impacting endonuclease activity.

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Targeting of Pu.Py Duplexes by GA and GT Rich Oligonucleotides on Microchip and in Solution.

Journal of biomolecular structure & dynamics·2012

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Oligonucleotides can adopt various secondary structures beyond the canonical double helix.
  • Understanding DNA secondary structures is crucial for gene regulation and therapeutic applications.
  • Nonregular DNA sequences present unique challenges and opportunities for structural studies.

Purpose of the Study:

  • To investigate the self-association of specific nonregular heteropyrimidine oligonucleotides.
  • To characterize the formation and properties of parallel-stranded (ps) DNA structures.
  • To determine the factors influencing the stability and formation of these ps structures.

Main Methods:

  • UV melting transitions at neutral and acidic pH.
  • Fourier-transform infrared (FTIR) spectroscopy.

Related Experiment Videos

  • Fluorescence spectroscopy of pyrene-labeled oligonucleotides.
  • Chemical joining of 5'-phosphorylated oligonucleotides.
  • Gel electrophoresis.

    • Main Results:

    • Oligonucleotides formed self-associated parallel-stranded (ps) structures at pH 4-5.5.
    • Ps structures are stabilized by C-C(+) base pairs and exhibit N- and S-types of sugar puckering.
    • Homoduplex formation was observed at low DNA strand concentrations.
    • Guanine, thymine, and purine inserts disfavor tetraplex i-motif formation.
    • MvaI restriction endonuclease did not cleave the parallel pseudosubstrates.

    Conclusions:

    • Specific nonregular oligonucleotides can form stable parallel-stranded structures.
    • C-C(+) base pairing is key to the stability of these ps structures.
    • The formation of ps structures is sequence-dependent and influenced by base composition.
    • These findings have implications for understanding DNA structural diversity and enzyme recognition.