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Phosphodiester Linkages

Phosphodiester Linkages

Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...

Single-Strand DNA Binding Proteins

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

Nucleic Acid Structure

Nucleic Acid Structure

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.
DNA Structure
DNA has a double-helix structure. The...

Preparation and Reactions of Thiols

Preparation and Reactions of Thiols

Thiols are prepared using the hydrosulfide anion as a nucleophile in a nucleophilic substitution reaction with alkyl halides. For instance, bromobutane reacts with sodium hydrosulfide to give butanethiol.

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Related Experiment Video

Updated: Jul 9, 2026

Constructing Thioether/Vinyl Sulfide-tethered Helical Peptides Via Photo-induced Thiol-ene/yne Hydrothiolation

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Published on: August 1, 2018

Stabilization of multi-stranded nucleic acid structures using 3'-S-phosphorothiolate linkages.

Richard Cosstick¹, Joanne Buckingham, John Brazier

¹Department of Chemistry, University of Liverpool, Liverpool, United Kingdom. rcosstic@liv.ac.uk

Nucleosides, Nucleotides & Nucleic Acids

|December 11, 2007

Summary

Incorporating phosphorothiolate linkages into oligodeoxynucleotides stabilizes RNA duplexes but destabilizes DNA duplexes. This modification also enhances the stability of the four-stranded i-motif structure.

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Published on: August 1, 2018

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Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures

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Published on: June 26, 2020

Area of Science:

Oligonucleotide chemistry
Structural biology
Biochemistry

Background:

Oligodeoxynucleotides are short DNA sequences with diverse applications.
Chemical modifications can alter oligonucleotide properties.
Phosphorothiolate linkages are a known modification with potential therapeutic uses.

Purpose of the Study:

To investigate the effect of 3'-S-phosphorothiolate linkages on oligonucleotide duplex stability.
To determine the impact of this modification on DNA-RNA and DNA-DNA duplexes.
To assess the influence of phosphorothiolate linkages on the i-motif structure.

Main Methods:

Synthesis of oligodeoxynucleotides containing 3'-S-phosphorothiolate linkages.
Formation and analysis of DNA-RNA and DNA-DNA duplexes.
Structural analysis of the i-motif in the presence of the modification.

Main Results:

3'-S-phosphorothiolate linkages stabilized duplexes with complementary RNA strands.
These linkages destabilized duplexes with complementary DNA strands.
The four-stranded i-motif structure was stabilized by this modification.

Conclusions:

3'-S-phosphorothiolate modification offers sequence-dependent stability effects.
This modification shows potential for selective targeting of RNA or i-motif structures.
Further research is warranted to explore applications in nucleic acid therapeutics.