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

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
DNA as a Genetic Template02:05

DNA as a Genetic Template

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...
Southern Blot02:57

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...
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...

You might also read

Related Articles

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

Sort by
Same author

Cutting the cord: virtual machines for real instrumental analysis not just at the instrument.

Analytical and bioanalytical chemistry·2018
Same author

[Effect of perioperative treatment with ambroxol on lung cancer patients after video-assisted thoracic surgery lobectomy].

Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences·2014
Same author

Overexpression of FABP7 promotes cell growth and predicts poor prognosis of clear cell renal cell carcinoma.

Urologic oncology·2014
Same author

Preparation and pharmacokinetics study on gastro-floating sustained-release tablets of troxipide.

Drug development and industrial pharmacy·2014
Same author

De novo design of an endohedral heteronuclear dimetallofullerene (U-Gd)@C60 with exceptional structural and electronic properties.

Chemphyschem : a European journal of chemical physics and physical chemistry·2014
Same author

Accelerating Multiagent Reinforcement Learning by Equilibrium Transfer.

IEEE transactions on cybernetics·2014

Related Experiment Video

Updated: Jul 13, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison.

Yang Gao1, Lauren K Wolf, Rosina M Georgiadis

  • 1Department of Chemistry, Metcalf Center for Science and Engineering, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA.

Nucleic Acids Research
|July 11, 2006
PubMed
Summary

Secondary structure in DNA probes and targets significantly slows hybridization kinetics. This effect is consistent in solution and on surfaces, impacting biosensor design.

More Related Videos

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
07:44

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes

Published on: July 6, 2016

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
08:00

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

Related Experiment Videos

Last Updated: Jul 13, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
07:44

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes

Published on: July 6, 2016

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
08:00

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • Hybridization kinetics are crucial for nucleic acid interactions.
  • Secondary structures in probes and targets can influence hybridization efficiency.
  • Understanding these effects is vital for applications like biosensing.

Purpose of the Study:

  • To quantify the impact of secondary structure on hybridization kinetics.
  • To compare hybridization kinetics in solution versus surface-bound environments.
  • To assess the implications for biosensor design.

Main Methods:

  • Designed 25mer probe-target pairs with varying secondary structures.
  • Measured hybridization kinetics using UV absorbance spectroscopy (solution).
  • Measured hybridization kinetics using surface plasmon resonance (SPR) spectroscopy (surface).

Main Results:

  • Increased probe and target secondary structure decreased hybridization rate constants.
  • Three intramolecular base pairs slowed hybridization by a factor of two.
  • Hybridization of strands with >=4 intramolecular base pairs deviated from a two-state model.
  • Surface hybridization was 20-40 fold slower than solution hybridization for identical sequences.

Conclusions:

  • Secondary structure significantly impedes hybridization kinetics for nucleic acid probes and targets.
  • Surface-based hybridization is considerably slower than solution-based hybridization.
  • Findings provide quantitative insights for designing improved biosensors, especially those utilizing designed secondary structures.