A structural basis for S1 nuclease sensitivity of double-stranded DNA

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• DNA typically exists in a Watson-Crick base-paired double helix.
• Protonation of DNA bases can alter its structure and properties.
• Repeating DNA sequences can form non-canonical structures.

Purpose of the Study:

• To investigate the structural and chemical properties of a protonated DNA sequence, d(TC)n X d(GA)n.
• To determine the base-pairing interactions in the protonated form.
• To explore the implications of this structure for DNA recognition.

Main Methods:

• Detection of protonated DNA forms using biophysical techniques.
• Enzymatic assays with single-strand-specific endonucleases.
• Analysis of pH-dependent protection of guanine residues.
• Structural modeling to assess stereochemical feasibility.
• Interaction studies with specific antibodies.

Main Results:

• A protonated form of d(TC)n X d(GA)n DNA exists in equilibrium with the Watson-Crick form up to pH 7.
• This protonated form exhibits high sensitivity to single-strand-specific endonucleases.
• Protection of guanine N-7 suggests Hoogsteen or reverse Hoogsteen base pairing with protonated cytosine.
• A proposed structure involves alternating Watson-Crick dA:dT and Hoogsteen syndG:dCH+ pairs.
• The protonated DNA interacts with an anti-Z DNA antibody.

Conclusions:

• Protonated DNA can adopt non-canonical structures involving Hoogsteen base pairs at neutral pH.
• These structures exhibit distinct enzymatic sensitivities and antibody interactions.
• The findings expand our understanding of DNA structural polymorphism and recognition.