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Related Concept Videos

Phosphodiester Linkages01:01

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...
Nucleic Acid Structure01:25

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...

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Chemical Triphosphorylation of Oligonucleotides
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Chemical Triphosphorylation of Oligonucleotides

Published on: June 2, 2022

5'-Iodination of solid-phase-linked oligodeoxyribonucleotides.

Eric T Kool1, Gregory P Miller

  • 1Stanford University, Stanford, California, USA.

Current Protocols in Nucleic Acid Chemistry
|April 23, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a method to create modified DNA by replacing a backbone oxygen with sulfur, forming stable thioether conjugates. This technique allows for easy attachment of labels to DNA for various applications.

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Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
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Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

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Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
15:22

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

Published on: April 3, 2014

Area of Science:

  • Oligonucleotide Chemistry
  • Bioconjugation Chemistry
  • Molecular Biology

Background:

  • Natural DNA has a phosphodiester backbone.
  • Chemical modifications of DNA are crucial for various biological and diagnostic applications.
  • Introducing sulfur into the DNA backbone can alter its properties and enable new conjugation strategies.

Purpose of the Study:

  • To develop a method for synthesizing DNA conjugates with a phosphorothioate backbone.
  • To functionalize the 5'-terminus of oligodeoxyribonucleotides for subsequent labeling.
  • To present procedures for both manual and automated synthesis of these modified DNA constructs.

Main Methods:

  • Reaction of 5'-iodinated oligodeoxyribonucleotides with 3'-phosphorothioated DNA in the presence of a complementary template.
  • Conversion of the 5'-iodo group to various functional groups.
  • Coupling of thiol-containing labels to the 5'-modified DNA via thioether linkage.
  • Manual and automated synthesis protocols for CPG-bound oligodeoxyribonucleotides.

Main Results:

  • Successfully synthesized DNA conjugates with a phosphorothioate backbone, structurally similar to natural DNA.
  • Demonstrated the versatility of the 5'-iodo group for conversion into other functional groups.
  • Achieved stable thioether conjugates by reacting the 5'-iodo group with thiol-containing labels.
  • Established reliable procedures for the synthesis and purification of these modified oligonucleotides.

Conclusions:

  • The developed method provides a robust way to create modified DNA with a phosphorothioate backbone.
  • The 5'-iodination strategy offers a flexible platform for introducing diverse labels and functional groups onto DNA.
  • The presented manual and automated procedures facilitate the accessibility and application of these novel DNA conjugates in research and diagnostics.