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Related Concept Videos

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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...
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...
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
DNA Replication02:40

DNA Replication

DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied.  After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
Replication in Prokaryotes
DNA replication uses a large number of...

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Related Experiment Video

Updated: Jun 22, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

A partition function algorithm for interacting nucleic acid strands.

Hamidreza Chitsaz1, Raheleh Salari, S Cenk Sahinalp

  • 1Lab for Computational Biology, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.

Bioinformatics (Oxford, England)
|May 30, 2009
PubMed
Summary
This summary is machine-generated.

Predicting nucleic acid strand interactions is crucial for RNA regulation. Our new algorithm accurately computes thermodynamic properties for interacting RNA, outperforming existing methods for target prediction.

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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

Published on: May 2, 2025

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Non-coding RNAs (ncRNAs) regulate gene expression by binding to target mRNAs.
  • Accurate prediction of ncRNA-mRNA interactions is vital due to limitations in high-throughput target detection methods.
  • Thermodynamic stability of base pairing dictates specificity in these molecular interactions.

Purpose of the Study:

  • To develop a computational model for analyzing the thermodynamics of two interacting nucleic acid strands.
  • To create an efficient algorithm for predicting base-pairing probabilities and related thermodynamic quantities.
  • To provide a tool for precise computational target prediction in RNA regulation.

Main Methods:

  • A dynamic programming algorithm was developed to compute the interaction partition function.
  • The algorithm considers a general type of interactions between two nucleic acid strands.
  • The computational complexity of the algorithm is O(n(6)).

Main Results:

  • The algorithm accurately predicts melting temperatures for interacting RNA pairs.
  • It also accurately calculates equilibrium concentrations for RNA complexes, such as the OxyS-fhlA complex.
  • The developed method demonstrates high accuracy and surpasses existing computational approaches.

Conclusions:

  • The presented model and algorithm offer a powerful tool for analyzing nucleic acid interactions.
  • This work addresses the need for high-throughput computational target prediction in RNA biology.
  • The findings have implications for understanding gene regulation by ncRNAs.