Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA

Area of Science:

• Structural Biology
• Biochemistry
• Crystallography

Background:

• Hexanucleotides have previously been crystallized in Z-DNA and B-DNA forms.
• Crystallization of hexanucleotides in the A-DNA form has not been previously reported.

Purpose of the Study:

• To solve the single-crystal X-ray structures of two different hexanucleotides: d(Gm5CGm5CGC) and d(Gm5CCGGC).
• To characterize the A-DNA conformation adopted by these hexanucleotides.
• To investigate sequence-dependent structural variations and the effect of cytosine methylation on A-DNA crystallization.

Main Methods:

• Single-crystal X-ray crystallography was employed to determine the structures.
• High-resolution structural analysis was performed on the obtained crystals.

Main Results:

• Both hexanucleotides crystallized readily as A-DNA in the orthorhombic space group C222(1).
• The determined A-DNA structures exhibit features characteristic of canonical A-DNA and are highly similar to A-DNA fibers.
• Sequence-dependent correlations were observed, particularly in d(CG) base steps, affecting twist and rise values.
• Cytosine methylation was found to significantly influence the ability of these sequences to crystallize as A-DNA, despite minimal structural effects.

Conclusions:

• The study establishes a new class of A-DNA forming hexanucleotides.
• This work provides a novel crystallographic system for studying DNA structure at near-atomic resolution.
• The findings offer valuable insights into DNA structural polymorphism and sequence-specific recognition.