Related Experiment Video
Updated: Jun 11, 2025
09:26
DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
Published on: December 29, 2021
4.1K
Sequence Context in DNA i-Motifs Can Nurture Very Stable and Persistent Kinetic Traps
Alexander S Minasyan1, Merlin Peacey1, Te'Kara Allen1
1Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
Chembiochem : a European Journal of Chemical Biology
|October 6, 2024
Summary
Understanding DNA i-motifs is key for biology and engineering. This study shows how nearby double-stranded DNA can trap stable i-motif structures, offering control over their folding.
Area of Science:
- Molecular Biology
- Biomaterials Science
- Structural DNA Nanotechnology
Background:
- I-motifs are non-canonical DNA structures with significant biological roles.
- Their unique folding properties are valuable for material engineering applications.
- Controlling i-motif behavior is crucial for advancing these fields.
Purpose of the Study:
- To investigate the influence of adjacent double-stranded DNA on i-motif thermodynamic and kinetic properties.
- To understand how proximity to duplex DNA affects i-motif folding and stability.
- To explore methods for rational control over i-motif folding topology.
Main Methods:
- Systematic investigation of i-motif structures adjacent to double-stranded DNA.
- Analysis of thermodynamic and kinetic properties.
- Exploration of folding topology control pathways.
Main Results:
- Double-stranded stems within i-motif loops were found to promote kinetic trapping.
- Stable and persistent partially folded i-motif conformations were observed.
- Evidence for pathways enabling rational control over folding topology was demonstrated.
Conclusions:
- Proximity to double-stranded DNA significantly impacts i-motif folding dynamics.
- Kinetic trapping by duplex stems leads to stable, persistent i-motif conformations.
- This work provides insights for controlling i-motif structures in biological and material contexts.
Related Concept Videos
02:05DNA as a Genetic Template
21.8K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
21.8K
02:13Cooperative Binding of Transcription Regulators
6.4K
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...
6.4K
01:03Single-Strand DNA Binding Proteins
14.0K
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...
14.0K
02:02DNA Topoisomerases
31.1K
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
31.1K
01:49Conserved Binding Sites
4.2K
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...
4.2K
02:02Cis-regulatory Sequences
9.8K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.8K