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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Single-Strand DNA Binding Proteins01:03

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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
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...
Nucleic Acids and Nucleotides01:20

Nucleic Acids and Nucleotides

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and have instructions for its functioning. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Deoxyribonucleic Acid (DNA)
DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and the organelles such as chloroplasts and mitochondria. In...

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Related Experiment Video

Updated: Jun 3, 2026

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
15:22

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

Published on: April 3, 2014

Designed nucleotide binding motifs.

Christoph Kröner1, Manuel Röthlingshöfer, Clemens Richert

  • 1Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.

The Journal of Organic Chemistry
|March 19, 2011
PubMed
Summary

Oligonucleotide triplexes with specific base pairing can tightly bind nucleoside phosphates like ATP. These designed DNA and RNA motifs show high affinity, even for the second messenger cyclic adenosine monophosphate (cAMP).

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Nucleic Acid Chemistry

Background:

  • Gaps in oligonucleotide triplexes are key binding sites.
  • Nucleoside phosphates are essential biological molecules.
  • Understanding specific binding interactions is crucial for molecular design.

Purpose of the Study:

  • To design oligonucleotide triplex motifs with high affinity for nucleoside phosphates.
  • To investigate the binding capabilities of these motifs for molecules like ATP and cAMP.
  • To demonstrate the applicability of the design in both DNA and RNA.

Main Methods:

  • Utilizing Watson-Crick and Hoogsteen base pairing principles.
  • Designing oligonucleotide triplex structures with central strand gaps.

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Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
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  • Testing binding affinity for various nucleoside phosphates, including ATP and 3',5'-cAMP.

    • Main Results:

    • Designed motifs exhibit tight binding to nucleoside phosphates, particularly those with adenine (A) or guanine (G) bases.
    • High affinity, in the nanomolar range, was observed for the second messenger cyclic adenosine monophosphate (cAMP).
    • A single DNA motif was engineered to accommodate up to seven nucleotides simultaneously.

    Conclusions:

    • Oligonucleotide triplexes can be rationally designed for high-affinity nucleoside phosphate binding.
    • The design principle is effective for targeting biologically relevant molecules.
    • The strategy is versatile, applicable to both DNA and RNA constructs.