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Nucleic Acids02:43

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...
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Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
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Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids.

Yossa Dwi Hartono1,2, You Xu1, Andrey Karshikoff1

  • 1Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden.

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Determining the protonation state of cytidine in DNA triplexes is crucial for Hoogsteen hydrogen bonding. This study predicts its pKa shifts in triplex environments, aiding oligonucleotide design.

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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.