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

You might also read

Related Articles

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

Sort by
Same author

Network-based framework for studying etiology and phenotypic diversity in primary ciliopathies.

Genome biology·2026
Same author

Airway management in emergency department thoracotomy: A narrative review.

The American journal of emergency medicine·2025
Same author

Tuning the Reactivity of Al@TiO<sub>2</sub> Antenna-Reactor Plasmonic Photocatalysts by Controlling Oxygen Vacancies.

Nano letters·2025
Same author

Tailoring the aluminum nanocrystal surface oxide for all-aluminum-based antenna-reactor plasmonic photocatalysts.

Proceedings of the National Academy of Sciences of the United States of America·2024
Same author

Electrocatalytic activity and surface oxide reconstruction of bimetallic iron-cobalt nanocarbide electrocatalysts for the oxygen evolution reaction.

RSC advances·2023
Same author

Cool carriers: triplet diffusion dominates upconversion yield.

Nanoscale·2023

Related Experiment Video

Updated: Apr 25, 2026

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
12:31

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Published on: February 28, 2015

17.1K

Rationally manipulating aptamer binding affinities in a stem-loop molecular beacon.

Rachel E Armstrong1, Geoffrey F Strouse

  • 1Department of Chemistry and Biochemistry, Florida State University , 95 Chieftan Way, Room 118 DLC, Tallahassee, Florida 32306, United States.

Bioconjugate Chemistry
|August 30, 2014
PubMed
Summary

Aptamer placement in molecular beacons tunes binding affinity over four orders of magnitude. Optimizing aptamer sequence position enhances biosensor sensitivity and enables precise biomolecular tracking.

More Related Videos

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

10.3K
Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction
03:38

Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction

Published on: October 6, 2022

1.6K

Related Experiment Videos

Last Updated: Apr 25, 2026

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
12:31

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Published on: February 28, 2015

17.1K
Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

10.3K
Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction
03:38

Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction

Published on: October 6, 2022

1.6K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biosensor Technology

Background:

  • Aptamers are single-stranded DNA with high ligand specificity.
  • Stem-loop molecular beacons incorporate aptamers for optical biosensing.
  • Aptamer placement within beacons affects binding affinity but lacks defined principles.

Purpose of the Study:

  • To investigate how aptamer sequence placement in molecular beacons influences binding affinity.
  • To establish design principles for optimizing aptamer-based optical biosensors.
  • To explore the relationship between aptamer structure and ligand binding.

Main Methods:

  • Controlled placement of an ATP DNA aptamer within a molecular beacon's stem-loop structure.
  • Tuning binding affinity over a wide range (1.3 nM - 203 μM).
  • Utilizing nanometal surface energy transfer (NSET) probes to monitor ATP binding.

Main Results:

  • Binding affinity is tunable by over four orders of magnitude based on aptamer placement.
  • Fully exposed aptamer sequences show enhanced binding affinity (Kd).
  • Aptamer hybridization within the stem region reduces binding affinity, correlating with ΔG values.
  • NSET detected negative cooperativity and two distinct Kd values for ATP binding.

Conclusions:

  • Aptamer sequence placement is a critical design parameter for tuning binding affinity in molecular beacons.
  • Optimized placement leads to enhanced biosensor performance.
  • NSET is an effective optical method for observing biomolecular interactions and cooperativity.