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DNA stem-loop structures in oligopurine-oligopyrimidine triplexes.

S C Harvey1, J Luo, R Lavery

  • 1Department of Biochemistry, University of Alabama, Birmingham 35294.

Nucleic Acids Research
|December 23, 1988
PubMed
Summary
This summary is machine-generated.

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Polypurine-polypyrimidine sequences in DNA can form triple helical stem-loops. Computational models reveal a four-nucleotide loop with 3'-stacking is most stable, predicting specific sequences favor this DNA structure.

Area of Science:

  • Molecular Biology
  • Structural Bioinformatics
  • Biochemistry

Background:

  • Closed circular DNA with polypurine-polypyrimidine sequences can form unusual structures.
  • Supercoiling pressure can induce triple helical stem-loop formation in these DNA sequences.

Purpose of the Study:

  • To develop an automated procedure for modeling DNA stem-loop structures.
  • To investigate the polypyrimidine loop conformation within triple helical stem-loops.
  • To predict sequence-dependent stability of these DNA structures.

Main Methods:

  • Automated computational modeling of DNA loop structures.
  • Examination of all possible 3 eal-stacked and 5 eal-stacked conformations for loops of varying lengths (3-6 nucleotides).
  • Energy minimization calculations to determine the lowest energy conformation.

Related Experiment Videos

  • Experimental validation of computational predictions.

    • Main Results:

    • The most stable conformation identified is a four-membered loop with bases stacked on the 3 eal-terminal strand.
    • Sequences like (GA)n, (GGGA)n, and (GAAA)n are predicted to form stem-loops more readily than (GGA)n and (GAA)n.
    • Triple-stranded stem-loop formation is favored when an even number of base pairs undergo the transition from double-stranded DNA.

    Conclusions:

    • The study provides a computational framework for predicting DNA stem-loop formation.
    • Specific DNA sequence motifs and loop lengths significantly influence the stability of triple helical stem-loops.
    • Findings offer insights into DNA structural dynamics and sequence recognition.