Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• DNA structure and supercoiling are critical for genomic functions.
• Specific DNA sequences, like alternating adenine-thymine (A.T) tracts, exhibit distinct conformational properties.
• The influence of intercalating agents on DNA topology is an area of active research.

Purpose of the Study:

• To investigate the reactivity of alternating adenine-thymine tracts in DNA.
• To determine the effect of actinomycin D and supercoiling on these DNA sequences.
• To explore the torsional deformability of (A.T)n sequences.

Main Methods:

• Utilized a relaxed closed circular plasmid containing an alternating adenine-thymine tract.
• Applied osmium tetroxide as a chemical probe for DNA reactivity.
• Introduced actinomycin D to induce supercoiling via intercalation.

Main Results:

• Alternating adenine-thymine tracts became highly reactive to osmium tetroxide when actinomycin D was present.
• This increased reactivity is attributed to local overwinding of the (A.T)n tract.
• Positive supercoiling, induced by actinomycin D at GpC sites, drives this overwinding.
• Previously, negative supercoiling was shown to cause underwinding in these tracts.

Conclusions:

• Alternating adenine-thymine sequences are highly sensitive to torsional stress, deforming in both directions (overwinding and underwinding).
• The DNA-binding drug actinomycin D can induce topological changes that significantly alter the local structure of (A.T)n tracts.
• These findings highlight the sequence-dependent mechanical properties of DNA and their modulation by small molecules.