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

Chirality at Nitrogen, Phosphorus, and Sulfur02:30

Chirality at Nitrogen, Phosphorus, and Sulfur

5.7K
Chirality is most prevalent in carbon-based tetrahedral compounds, but this important facet of molecular symmetry extends to sp3-hybridized nitrogen, phosphorus and sulfur centers, including trivalent molecules with lone pairs. Here, the lone pair behaves as a functional group in addition to the other three substituents to form an analogous tetrahedral center that can be chiral.
A consequence of chirality is the need for enantiomeric resolution. While this is theoretically possible for all...
5.7K
Chirality in Nature02:30

Chirality in Nature

13.5K
Chirality is the most intriguing yet essential facet of nature, governing life’s biochemical processes and precision. It can be observed from a snail shell pattern in a macroscopic world to an amino acid, the minutest building block of life. Most of the snails around the world have right-coiled shells because of the intrinsic chirality in their genes. All the amino acids present in the human body exist in an enantiomerically pure state, except for glycine - the sole achiral amino acid.
13.5K
Molecules with Multiple Chiral Centers02:25

Molecules with Multiple Chiral Centers

11.8K
Molecules that possess multiple chiral centers can afford a large number of stereoisomers. For instance, while some molecules like 2-butanol have one chiral center, defined as a tetrahedral carbon atom with four different substituents attached, several molecules like butane-2,3-diol have multiple chiral centers. A simple formula to predict the number of stereoisomers possible for a molecule with n chiral centers is 2n. However, there can be a lower number where some of the stereoisomers are...
11.8K
Prochirality02:05

Prochirality

3.8K
The concept of prochirality leads to the nomenclature of the individual faces of a molecule and plays a crucial role in the enantioselective reaction. It is a concept where two or more achiral molecules react to produce chiral products. A typical process is the reaction of an achiral ketone to generate a chiral alcohol. Here, the achiral reactant reacts with an achiral reducing agent, sodium borohydride, to generate an equimolar mixture of the chiral enantiomers of the product. For example, an...
3.8K
Chirality02:25

Chirality

24.3K
Chirality is a term that describes the lack of mirror symmetry in an object. In other words, chiral objects cannot be superposed on their mirror images. For example, our feet are chiral, as the mirror image of the left foot, the right foot, cannot be superposed on the left foot.
Chiral objects exhibit a sense of handedness when they interact with another chiral object. For example, our left foot can only fit in the left shoe and not in the right shoe. Achiral objects — objects that have...
24.3K
SN2 Reaction: Stereochemistry02:23

SN2 Reaction: Stereochemistry

9.6K
In an SN2 reaction, the nucleophilic attack on the substrate and departure of the leaving group occurs simultaneously through a transition state. As the nucleophile approaches the substrate from the back-side, the configuration of the substrate carbon changes from tetrahedral to trigonal bipyramidal and then back to tetrahedral, leading to an inversion in the configuration of the product.
If the substrate is an achiral molecule at the α-carbon, the inversion of configuration is not...
9.6K

You might also read

Related Articles

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

Sort by
Same author

Characteristics of specific DNA junction motifs inspired by natural RNA motifs.

International journal of biological macromolecules·2026
Same author

Evolution of IgE sensitization profiles to <i>Artemisia</i> pollen allergens in the allergic pediatric population.

The World Allergy Organization journal·2026
Same author

Hyperthyroidism drives gout risk: A Mendelian randomization observational study.

Medicine·2026
Same author

Comprehensive methylome and transcriptome profiling reveals specific biomarkers for bovine viral diarrhea virus persistent infection in calves.

Frontiers in immunology·2026
Same author

miR-146a-3p drives major depressive disorder pathogenesis via BDNF suppression: a novel diagnostic and therapeutic target.

Gene·2026
Same author

GWAS-Based Mining of Candidate Genes for Low-Nitrogen Tolerance in Maize.

International journal of molecular sciences·2026
Same journal

RETRACTED: Kim et al. The Angiogenesis Inhibitor ALS-L1023 from Lemon-Balm Leaves Attenuates High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease Through Regulating the Visceral Adipose-Tissue Function. <i>Int. J. Mol. Sci.</i> 2017, <i>18</i>, 846.

International journal of molecular sciences·2026
Same journal

Correction: Mahmud et al. Thymoquinone Attenuates NF-κβ Signalling Activation in Retinal Pigment Epithelium Cells Under AMD-Mimicking Conditions. <i>Int. J. Mol. Sci.</i> 2025, <i>26</i>, 11473.

International journal of molecular sciences·2026
Same journal

Correction: Borovikov et al. The Twisting and Untwisting of Actin and Tropomyosin Filaments Are Involved in the Molecular Mechanisms of Muscle Contraction, and Their Disruption Can Result in Muscle Disorders. <i>Int. J. Mol. Sci</i>. 2025, <i>26</i>, 6705.

International journal of molecular sciences·2026
Same journal

Correction: Molagoda et al. Flavonoid Glycosides from <i>Ziziphus jujuba</i> var. <i>inermis</i> (Bunge) Rehder Seeds Inhibit α-Melanocyte-Stimulating Hormone-Mediated Melanogenesis. <i>Int. J. Mol. Sci.</i> 2021, <i>22</i>, 7701.

International journal of molecular sciences·2026
Same journal

Correction: Guo et al. Integrated Transcriptomic and Metabolomic Analysis Reveals the Molecular Regulatory Mechanism of Flavonoid Biosynthesis in Maize Roots Under Lead Stress. <i>Int. J. Mol. Sci.</i> 2024, <i>25</i>, 6050.

International journal of molecular sciences·2026
Same journal

Correction: Chang et al. Improvement of Carbon Tetrachloride-Induced Acute Hepatic Failure by Transplantation of Induced Pluripotent Stem Cells Without Reprogramming Factor c-Myc. <i>Int. J. Mol. Sci.</i> 2012, <i>13</i>, 3598-3617.

International journal of molecular sciences·2026
See all related articles

Related Experiment Video

Updated: Jul 11, 2025

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
09:26

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

4.2K

Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.

Tong Qin1, Bei Hu1, Qianwei Zhao1,2

  • 1Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.

International Journal of Molecular Sciences
|November 14, 2023
PubMed
Summary
This summary is machine-generated.

This study visualizes DNA synthesis stereochemistry using a selenium-modified probe, revealing an SN2 mechanism. Findings highlight the critical role of metal ions in DNA polymerase catalysis and drug design.

Keywords:
configuration inversionmetal ionsphosphodiester bond formationpolymerasesingle selenium atom

More Related Videos

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

688
Self-assembling Morphologies Obtained from Helical Polycarbodiimide Copolymers and Their Triazole Derivatives
09:22

Self-assembling Morphologies Obtained from Helical Polycarbodiimide Copolymers and Their Triazole Derivatives

Published on: February 7, 2017

7.9K

Related Experiment Videos

Last Updated: Jul 11, 2025

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
09:26

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

4.2K
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

688
Self-assembling Morphologies Obtained from Helical Polycarbodiimide Copolymers and Their Triazole Derivatives
09:22

Self-assembling Morphologies Obtained from Helical Polycarbodiimide Copolymers and Their Triazole Derivatives

Published on: February 7, 2017

7.9K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA polymerase catalyzes DNA synthesis, a fundamental biological process.
  • Phosphodiester bond formation involves phosphorus center inversion, crucial for DNA replication.
  • Understanding DNA polymerase reaction mechanisms is key for developing therapeutics.

Purpose of the Study:

  • To visualize the stereochemistry and catalysis of DNA synthesis.
  • To provide explicit evidence for the in-line attacking SN2 mechanism in DNA polymerization.
  • To investigate the impact of diastereomeric modifications on DNA polymerase binding and catalysis.

Main Methods:

  • Utilized a single-selenium-atom-modified deoxyribonucleoside triphosphate (dNTP) probe.
  • Captured pre- and post-reaction states to analyze stereochemical outcomes.
  • Performed kinetic and thermodynamic studies to assess binding affinity and reaction selectivity.

Main Results:

  • Visualized the center inversion and confirmed the SN2 mechanism of DNA polymerization.
  • Determined the absolute configurations of diastereomers.
  • Demonstrated that Mg2+ or Mn2+ ions significantly influence substrate binding and catalysis, with specific diastereomers being disruptive.

Conclusions:

  • The study provides direct evidence for the stereochemical course of DNA polymerization.
  • Highlights the critical role of the third metal ion in substrate recognition and phosphodiester bond formation.
  • Offers insights for designing improved polymerase inhibitors and therapeutics.