Related Experiment Video
Updated: Sep 25, 2025
10:05
Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin
Published on: January 20, 2016
8.4K
Size matters: DNA binding site kinetics as a function of polyamide size
Jacquelyn Niederschulte1, Yang Song1, James K Bashkin1
1Department of Chemistry & Biochemistry, University of Missouri St. Louis, St. Louis, MO, 63121, USA.
Biochimie
|April 26, 2022
Summary
This study reveals how hairpin polyamide (PA) size impacts DNA binding kinetics. Larger PAs, like the antiviral PA20, exhibit longer DNA residence times, crucial for biological activity.
Area of Science:
- Molecular Biology
- Biochemistry
- Drug Discovery
Background:
- Hairpin polyamides (PAs) are DNA-binding molecules with therapeutic potential.
- Previous research focused on smaller PAs (6-8 rings), with limited understanding of larger PA (≥14 rings) kinetics.
- Structure-activity relationships concerning PA size and DNA binding remain unclear.
Purpose of the Study:
- To conduct the first comparative kinetic study of hairpin PA-DNA interactions across a range of PA sizes.
- To elucidate the complexities of PA-DNA binding kinetics and their relationship to PA size.
- To investigate the role of PA size in DNA residence times and biological activity.
Main Methods:
- Characterization of DNA binding kinetics for hairpin polyamides (PA6 and PA20) using fluorescence spectroscopy.
- Comparative analysis of kinetic data with existing data for 8 and 14-ring hairpin PAs.
- Assessment of PA-DNA dissociation in the presence of competitor DNA.
Main Results:
- PA6 (6-ring) exhibits 1:1 stoichiometry and complex biphasic association kinetics with varying decay constants.
- PA20 (20-ring) shows higher stoichiometry (2.5:1) and simpler association kinetics (1e6 M⁻¹s⁻¹).
- While affinities are similar for PAs ≥8 rings, DNA residence times significantly increase with PA size (20s to >2500s).
Conclusions:
- Hairpin PA size profoundly influences DNA binding kinetics and residence times.
- Increased PA size correlates with significantly longer DNA residence times.
- The antiviral PA20's minimal dissociation suggests high residence times are critical for its biological efficacy.
More Related Videos
Related Concept Videos
00:49Ligand Binding and Linkage
5.0K
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...
5.0K
01:49Conserved Binding Sites
4.5K
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...
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...
4.5K
02:13Cooperative Binding of Transcription Regulators
6.7K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.7K
02:40Ligand Binding Sites
13.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
13.7K
01:25Nucleic Acid Structure
7.3K
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...
DNA Structure
DNA...
7.3K