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Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

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Oligonucleotides with 1,4-dioxane-based nucleotide monomers.

Andreas S Madsen¹, Jesper Wengel

¹Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.

The Journal of Organic Chemistry

|March 24, 2012

Summary

This summary is machine-generated.

Researchers synthesized H-phosphonate epimers and incorporated them into DNA oligonucleotides. Monomer incorporation reduced thermal stability, suggesting backbone and base interaction changes impact duplex stability.

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Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

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Published on: April 3, 2014

Area of Science:

Organic Chemistry
Nucleic Acid Chemistry
Biophysical Chemistry

Background:

H-phosphonate chemistry is crucial for oligonucleotide synthesis.
Understanding modified nucleosides' impact on DNA duplex stability is essential for therapeutic applications.

Purpose of the Study:

To synthesize and characterize H-phosphonate epimers (5R and 5S).
To investigate the effect of incorporating these modified monomers into DNA oligonucleotides on their thermal stability.

Main Methods:

Multi-step synthesis of H-phosphonate epimers from secouridine.
Separation of epimers using reversed-phase high-performance liquid chromatography (RP-HPLC).
Incorporation of monomers into 9-mer oligonucleotides and thermal affinity (Tm) measurements.
Circular Dichroism (CD) spectroscopy and molecular modeling.

Main Results:

Successful synthesis and separation of H-phosphonate epimers 5R and 5S.
Single incorporation of either monomer X or Y into a DNA 9-mer significantly decreased thermal affinity towards DNA and RNA complements.
Monomer X incorporation resulted in a ΔTm of -3.5 °C for both DNA and RNA complements.
Monomer Y incorporation resulted in a ΔTm of -11.0 °C for DNA and -6.5 °C for RNA complements.

Conclusions:

The incorporation of modified H-phosphonate monomers into DNA duplexes leads to a reduction in their thermal stability.
CD measurements indicated no major structural rearrangements, but molecular modeling suggested localized changes in the sugar-phosphate backbone and base stacking interactions contribute to decreased stability.