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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Chromosome Structure02:40

Chromosome Structure

A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA sequence that links sister chromatids. This is also where kinetochores, protein complexes to which spindle microtubules attach, are constructed after the chromosome is replicated. The kinetochores allow the spindle microtubules to move the chromosomes within the cell during cell division.
Telomeres consist of non-coding repetitive nucleotide...
DNA Helicases00:55

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
S-Cdk Initiates DNA Replication02:38

S-Cdk Initiates DNA Replication

The cell cycle is a series of events leading to DNA duplication followed by the division of cell content to form two daughter cells. The cell cycle progresses in four stages—the cell increases in size (gap 1 or G1-phase), duplicates its DNA (synthesis or S-phase), prepares to divide (gap 2 or G2-phase), and divides (mitosis or M-phase).
Two states at the origin of replication
In eukaryotes, the initiation of replication occurs at many sites on the chromosomes, called the origins of replication.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

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Related Experiment Video

Updated: Jun 9, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Searching for sequence features that control DNA cyclizability.

Margarita Gordiychuk1, Jonghan Park2, Aakash Basu3,4

  • 1Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA.

PNAS Nexus
|June 8, 2026
PubMed
Summary
This summary is machine-generated.

DNA mechanics are sequence-dependent at short lengths. We developed a statistical model to predict DNA cyclizability based on nucleotide sequences, advancing understanding for DNA nanotechnology.

Keywords:
DNA cyclizabilitysequence-dependent DNA mechanicsstatistical-mechanics modeling

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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

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Last Updated: Jun 9, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

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Published on: October 5, 2018

CD Spectroscopy to Study DNA-Protein Interactions
06:48

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Published on: February 10, 2022

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

Area of Science:

  • Molecular Biology
  • Biophysics
  • Polymer Physics

Background:

  • DNA mechanical properties are vital for biological functions like DNA packaging and transcription.
  • While long DNA follows polymer models, short DNA mechanics, relevant to DNA-protein interactions, are sequence-dependent.
  • DNA cyclizability, the tendency to bend and form loops, is a key mechanical property influenced by DNA sequence.

Purpose of the Study:

  • To develop a statistical-mechanics framework to systematically analyze sequence-dependent DNA cyclizability.
  • To identify the minimal sequence features governing DNA cyclizability.
  • To predict DNA sequences with high and low cyclizability.

Main Methods:

  • Developed a statistical-mechanics framework to analyze DNA cyclizability based on nucleotide sequences.
  • Applied the framework to analyze large datasets of random and biological DNA sequences.
  • Validated predictions using all-atom molecular dynamics simulations.

Main Results:

  • Identified a minimal pairwise model accurately describing sequence-dependent DNA cyclizability.
  • Extracted key sequence features that dictate DNA cyclizability.
  • Successfully predicted and validated sequences with extreme cyclizability properties.

Conclusions:

  • The study provides a robust framework for understanding sequence-dependent DNA mechanics.
  • Identified sequence features controlling DNA cyclizability have implications for DNA nanotechnology and biological processes.
  • Advances the understanding of DNA mechanics at the nanoscale, crucial for DNA packaging and protein interactions.