Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids

Area of Science:

• Biochemistry
• Computational Biology
• Molecular Biophysics

Background:

• Protonation states of nucleic acid bases are experimentally challenging to determine.
• Cytidine protonation in the third strand of DNA triplexes is essential for Hoogsteen hydrogen bond formation.
• Locked nucleic acid (LNA) modifications are frequently used in triplex-forming oligonucleotides for genomic targeting.

Purpose of the Study:

• To develop and validate CHARMM force field parameters for LNA within DNA triplexes.
• To computationally assess the protonation state of third-strand cytidine in various DNA triplex contexts.
• To predict the impact of LNA modifications and cytidine methylation on cytidine's pKa in triplexes.

Main Methods:

• Development and validation of LNA parameters for the CHARMM force field against experimental data.
• Application of lambda-dynamics and multiple pH regime computational methods.
• Calculation of pKa values for cytidine in different DNA triplex environments.

Main Results:

• Both computational methods predict a pKa for third-strand cytidine above physiological pH in DNA triplexes.
• Cytidine methylation causes an observed upshift in predicted pKa values.
• LNA sugar locking results in a slight downshift of the predicted pKa.

Conclusions:

• Computational predictions provide insights into cytidine protonation in DNA triplexes.
• Understanding these pKa shifts is vital for designing more effective oligonucleotide therapeutics.
• The developed LNA parameters enhance the accuracy of molecular simulations for triplex systems.