Probing nucleic acid structure with nickel- and cobalt-based reagents

Area of Science:

• Biochemistry
• Chemical Biology
• Molecular Biology

Background:

• Guanine residues in DNA and RNA are critical for nucleic acid structure and function.
• Understanding the solvent exposure of guanine is essential for characterizing its local environment.
• Existing methods may perturb nucleic acid structure or fail to provide detailed environmental information.

Purpose of the Study:

• To develop and present nickel and cobalt reagents for characterizing guanine solvent exposure in DNA and RNA.
• To establish a method for probing the steric and electronic environment of guanine residues.
• To couple guanine oxidation with subsequent fragmentation or primer extension termination for analysis.

Main Methods:

• Utilizing nickel and cobalt reagents to promote guanine oxidation in the presence of monopersulfate.
• Quantifying the extent of guanine oxidation to infer steric and electronic properties.
• Applying piperidine treatment for fragmentation of smaller polynucleotides.
• Employing primer extension termination for analysis of larger polynucleotides.

Main Results:

• Demonstrated the utility of nickel and cobalt reagents in mapping guanine solvent exposure.
• Showcased that the extent of oxidation correlates with the surrounding steric and electronic environment.
• Confirmed that the oxidation process does not induce structural perturbation or strand scission.
• Successfully coupled oxidation with fragmentation or primer extension termination for analysis.

Conclusions:

• Nickel and cobalt reagents provide a robust method for assessing guanine solvent exposure in nucleic acids.
• This technique offers insights into the local environment of guanine without compromising nucleic acid integrity.
• The coupled oxidation and fragmentation/termination strategy enables sensitive detection and mapping of guanine environments.