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

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

15.3K
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...
15.3K
Ligand Binding Sites02:40

Ligand Binding Sites

14.0K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.0K
Aquaporins01:25

Aquaporins

5.4K
Aquaporins or AQPs are a family of integral membrane proteins whose primary function is to transport water, while some called aquaglyceroporins also transport glycerol. In addition, aquaporins have also been suspected to be involved in transporting volatile substances, such as carbon dioxide and ammonia, across membranes. Such AQPs that act as gas channels are often highly expressed in cells involved in the gaseous exchange, such as red blood cells, epithelial cells, and pulmonary capillaries.
5.4K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

58.3K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
58.3K
Riboswitches01:56

Riboswitches

8.8K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
8.8K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.7K
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...
6.7K

You might also read

Related Articles

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

Sort by
Same author

DNA damaging properties of G-quadruplex ligand QN-302 are potentiated by the DNA repair inhibitor Olaparib and mitigated by the molecular helicase PhpC.

Genome biology·2026
Same author

Cellular adaptations impact the biological activity of naphthalene diimide G-quadruplex ligands in ALT-positive osteosarcoma cells.

Cell death & disease·2025
Same author

Structural and Functional Insights into Targeting GCCG Sites in the EGFR Promoter by Two DNA Intercalators to Inhibit Breast Cancer Metastasis.

Journal of medicinal chemistry·2025
Same author

The G-quadruplex experimental drug QN-302 impairs liposarcoma cell growth by inhibiting MDM2 expression and restoring p53 levels.

Nucleic acids research·2025
Same author

The G-quadruplex experimental drug QN-302 impairs liposarcoma cell growth by inhibiting MDM2 expression and restoring p53 levels.

Nucleic acids research·2025
Same author

Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence.

ACS chemical biology·2025
Same journal

Correction: Jiménez-Sánchez et al. Antioxidant Enzymes Genetic Variants Associated with Urticaria/Angioedema Induced by Cross-Reactive Hypersensitivity to Nonsteroidal Anti-Inflammatory Drugs. <i>Pharmaceuticals</i> 2026, <i>19</i>, 522.

Pharmaceuticals (Basel, Switzerland)·2026
Same journal

Correction: Zhao et al. Multifunctional Gel Films of Marine Polysaccharides Cross-Linked with Poly-Metal Ions for Wound Healing. <i>Pharmaceuticals</i> 2022, <i>15</i>, 750.

Pharmaceuticals (Basel, Switzerland)·2026
Same journal

Intravenous Immunoglobulin Reveals a Novel Protective Mechanism: Targeting the GBP5-Driven Pyroptosis Axis in Experimental Colitis.

Pharmaceuticals (Basel, Switzerland)·2026
Same journal

Icariin Attenuates Renal Injury in Streptozotocin-Induced Diabetic Rats with and Without Adenine-Induced Chronic Kidney Disease.

Pharmaceuticals (Basel, Switzerland)·2026
Same journal

AI-Assisted Identification of a Putative Allosteric Ligand Targeting the CDK4/Cyclin D1 Protein-Protein Interface.

Pharmaceuticals (Basel, Switzerland)·2026
Same journal

Development and Study of Hydrophilic Ointment Compositions with a Dextrin/Polyvinyl Alcohol/Iodine Complex (D/PVA/I).

Pharmaceuticals (Basel, Switzerland)·2026
See all related articles

Related Experiment Video

Updated: Oct 6, 2025

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
08:28

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

8.2K

Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids.

Stephen Neidle1

  • 1The School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK.

Pharmaceuticals (Basel, Switzerland)
|January 21, 2022
PubMed
Summary
This summary is machine-generated.

Structured water molecules are crucial for G-quadruplex ligand binding in cancer drug development. Understanding these water clusters aids in designing effective small molecule G-quadruplex binders.

Keywords:
G-quadruplexacridinescrystal structureshydrogen bondingligandsnaphthalene diimideswater clusters

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

877
Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
05:32

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

1.5K

Related Experiment Videos

Last Updated: Oct 6, 2025

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
08:28

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

8.2K
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

877
Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
05:32

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

1.5K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Medicinal Chemistry

Background:

  • G-quadruplexes are increasingly recognized for their role in human cancers.
  • Small molecules targeting G-quadruplexes are promising drug candidates.
  • Crystal structures reveal insights into G-quadruplex-ligand interactions.

Purpose of the Study:

  • To analyze the role of bound water molecules in G-quadruplex-small molecule complexes.
  • To understand water arrangements mediating ligand-DNA interactions.
  • To inform the design of novel G-quadruplex-targeting drugs.

Main Methods:

  • Analysis of crystal structures of G-quadruplex-ligand complexes.
  • Focus on water molecule arrangements and hydrogen bonding.
  • Comparison of water clusters in native and complexed G-quadruplex structures.

Main Results:

  • Bridging water molecules mediate most hydrogen bonds between ligands and DNA in parallel G-quadruplexes.
  • Clusters of structured water act as essential mediators between ligands and G-quadruplexes.
  • These water clusters are conserved across different complexes and native structures.

Conclusions:

  • Conserved water clusters serve as general platforms for G-quadruplex ligand binding.
  • Water molecule arrangements should be considered in drug design and in silico studies.
  • This understanding can enhance the development of G-quadruplex-based cancer therapeutics.