Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA as a Genetic Template02:05

DNA as a Genetic Template

22.1K
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...
22.1K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.2K
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...
6.2K
DNA Base Pairing02:27

DNA Base Pairing

27.6K
Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
27.6K
The DNA Helix01:07

The DNA Helix

20.9K
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
20.9K
Proofreading01:31

Proofreading

6.4K
Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...
6.4K
Mismatch Repair01:20

Mismatch Repair

4.9K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
4.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.

Bioinformatics (Oxford, England)·2026
Same author

<b>Two new species of the genus <i>Tiwaripotamon</i> Bott, 1970 (Crustacea, Decapoda, Brachyura, Potamidae) from Guangxi, China</b>.

Zootaxa·2026
Same author

Natural variation in the COT1 promoter improves rice seedling cold tolerance by OsCBF3-dependent transcriptional activation.

Plant communications·2026
Same author

Recognition of non-standard base pairs by triplex-forming oligonucleotides containing an expanded genetic alphabet.

Nature communications·2026
Same author

Computational Resources for Molecular Biology 2026.

Journal of molecular biology·2026
Same author

Reparameterization of the Amber RNA Force Field Non-Bonded Terms.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jul 26, 2025

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

11.7K

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch

Tuan M Pham1, Terrel Miffin2, Hongying Sun3

  • 1Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY.

Biorxiv : the Preprint Server for Biology
|June 19, 2023
PubMed
Summary
This summary is machine-generated.

Expanding the DNA base pairing alphabet with novel P-Z pairs significantly improves in silico DNA secondary structure design. This advancement enhances prediction accuracy and reduces off-target folding, accelerating the design process.

More Related Videos

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.6K
Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

7.1K

Related Experiment Videos

Last Updated: Jul 26, 2025

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

11.7K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.6K
Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

7.1K

Area of Science:

  • Computational Biology
  • Synthetic Biology
  • Biochemistry

Background:

  • DNA secondary structure prediction and design are crucial for synthetic biology applications.
  • Current algorithms primarily use the standard A-T and G-C base pairing rules.
  • Expanding the base pairing alphabet offers potential for more accurate and robust DNA design.

Conclusions:

  • Extending the DNA base pairing alphabet beyond A-T and G-C to include P-Z pairs significantly enhances in silico secondary structure design.
  • The new thermodynamic parameters and software integration enable more accurate prediction and design of DNA structures.
  • This work establishes a pipeline for incorporating novel nucleotides into computational DNA design workflows, paving the way for more complex synthetic biology applications.