Identification of two novel arginine binding DNAs

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• RNA tertiary structure is crucial for RNA-protein interactions and biological functions.
• Understanding DNA tertiary structure's role in protein binding is less explored.
• Arginine is a key amino acid involved in nucleic acid recognition.

Purpose of the Study:

• To investigate DNA tertiary structures that bind arginine.
• To compare DNA-arginine binding motifs with known RNA-arginine interactions.
• To establish DNA-arginine systems as models for nucleic acid tertiary structure studies.

Main Methods:

• In vitro selection experiments to identify arginine-binding single-stranded DNAs.
• Comparison with analogous RNA-arginine binding experiments.
• Chemical interference, mutagenesis, dimethylsulfate footprinting, and circular dichroism analyses.

Main Results:

• Two novel DNA motifs binding arginine were identified, distinct from RNA motifs like HIV TAR RNA.
• One DNA motif formed a hairpin with a conserved loop; the other was G-rich.
• Arginine binding induced conformational changes in DNA, mediated by the guanidinium group.
• Specific nucleotides and guanine residues were implicated in arginine binding and protection.

Conclusions:

• DNA tertiary structures can specifically bind arginine through novel motifs.
• Arginine binding to DNA involves conformational changes and specific nucleotide interactions.
• These DNA-arginine systems serve as valuable models for studying nucleic acid tertiary structures.