Sequence-dependent structural variations of DNA revealed by DNase I.

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• DNA-protein interactions are crucial for biological processes.
• DNase I enzyme activity is influenced by DNA helix geometry, specifically minor groove width and DNA stiffness.
• Understanding these parameters is key to predicting DNA-protein binding.

Purpose of the Study:

• To investigate the relationship between DNA sequence and global helix parameters affecting DNase I interaction.
• To develop a sequence-dependent measure for protein-induced DNA flexure.
• To compare the activity of Mg2+ and Mn2+ dependent DNase I.

Main Methods:

• Calculation of locally averaged P-O3' bond cutting frequencies (InP) to reflect global helix parameters.
• Approximation of InP values based on dinucleotide steps.
• Calculation of collective contribution (sigma Dd) for ten different dinucleotide steps.
• Analysis of DNase I digestion in the presence of Mg2+ and Mn2+.

Main Results:

• Global helix parameters, as revealed by DNase I, can be predicted from DNA sequence at a first approximation.
• The calculated sigma Dd function serves as a sequence-dependent measure of protein-induced DNA flexure towards the major groove.
• No significant difference was observed between Mg2+ and Mn2+ dependent DNase I digestions.

Conclusions:

• DNA sequence information can predict global helix parameters relevant to DNase I interaction.
• The sigma Dd function provides a novel sequence-dependent metric for DNA flexure and minor groove widening.
• The study suggests that the potential Mn2(+)-dependent active site of DNase I has lower activity compared to the primary active site.