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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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C4'-Fluorinated Oligodeoxynucleotides: Synthesis, Stability, Structural Studies.

Yifei Zhou¹, Kuan Lu¹, Qiang Li¹

¹State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.

Chemistry (Weinheim an Der Bergstrasse, Germany)

|August 25, 2021

Summary

This summary is machine-generated.

Introducing 4'-F-deoxythymidine (4'-F T) into oligodeoxyribonucleotides (ODNs) offers stability under neutral conditions. This modification structurally resembles 2'-F-deoxyribonucleotides but causes less duplex perturbation.

Keywords:

DNA fluorinated oligonucleotides nucleic acids

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Area of Science:

Nucleic acid chemistry
Biophysical chemistry
Oligonucleotide synthesis

Background:

Fluorine substitution on the ribose moiety is a common strategy to alter nucleic acid structure and function.
2'-Fluoro-deoxyribonucleotides are widely used to modulate ribose conformation.

Purpose of the Study:

To synthesize 4 acronym{'-F}deoxythymidine (4 acronym{'-F} T) and incorporate it into oligodeoxyribonucleotides (ODNs).
To evaluate the stability, conformational properties, and structural impact of 4 acronym{'-F} T-modified ODNs.

Main Methods:

Chemical synthesis of 4 acronym{'-F} T and its incorporation into ODNs.
Nuclear Magnetic Resonance (NMR) spectroscopy to determine nucleoside and oligonucleotide conformation.
Circular dichroism (CD) spectroscopy, thermal denaturation, and RNase H1 footprinting to assess duplex stability and structure.

Main Results:

4 acronym{'-F} T-modified ODNs exhibit stability in neutral buffers but undergo some strand cleavage under alkaline conditions.
NMR studies reveal that 4 acronym{'-F} T predominantly adopts the North conformation in both nucleoside and ODN forms.
Duplex studies confirm the North conformation preference of 4 acronym{'-F} T is maintained, causing local structural perturbations.

Conclusions:

4 acronym{'-F} T is a viable modification for ODNs, offering stability and specific conformational properties.
Structurally, 4 acronym{'-F} T is similar to 2 acronym{'-F} deoxyribonucleotides.
4 acronym{'-F} T induces less structural perturbation in duplexes compared to 2 acronym{'-F} deoxyribonucleotides, presenting a potentially advantageous alternative.