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 Experiment Videos

A nicked duplex decamer DNA with a PEG(6) tether.

L Kozerski1, A P Mazurek, R Kawecki

  • 1Drug Institute, 00-725 Warszawa, Chetmska 30/34, Poland, Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warszawa, Kasprzaka 44, Poland. lkoz@ichf.edu.pl

Nucleic Acids Research
|February 27, 2001
PubMed
Summary
This summary is machine-generated.

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

Thickness measurement of nm HfO<sub>2</sub> films.

Metrologia·2024
Same author

Standard clinical computed tomography fails to precisely visualise presence, course and branching points of deep cerebral perforators.

Folia morphologica·2021
Same author

Menisco-fibular ligament - an overview: cadaveric dissection, clinical and magnetic resonance imaging diagnosis, arthroscopic visualisation and treatment.

Folia morphologica·2020
Same author

Opioid receptors expression in the skin of haemodialysis patients suffering from uraemic pruritus.

Journal of the European Academy of Dermatology and Venereology : JEADV·2020
Same author

Dynamics of excited state proton transfer in nitro substituted 10-hydroxybenzo[h]quinolines.

Physical chemistry chemical physics : PCCP·2017
Same author

Human skull translucency: post mortem studies.

Biomedical optics express·2016

A synthesized dumbbell DNA decamer (DDSDPEG) with a nick maintains a stable B-DNA helix. Potassium ions enhance stability and reduce conformational heterogeneity, with T1 times indicating stabilization.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Oligonucleotide synthesis and characterization are crucial for understanding DNA structure-function relationships.
  • The impact of modifications like nicks and linkers on DNA stability and conformation requires detailed investigation.

Purpose of the Study:

  • To synthesize and characterize a dumbbell double-stranded DNA decamer tethered with a hexaethylene glycol linker (DDSDPEG) containing a central nick.
  • To elucidate the structural and conformational properties of DDSDPEG using NMR spectroscopy and molecular modeling.
  • To assess the influence of the PEG linker and a central nick on DNA stability and geometry.

Main Methods:

  • Synthesis of a dumbbell double-stranded DNA decamer with a hexaethylene glycol linker and a central nick.

Related Experiment Videos

  • Nuclear Magnetic Resonance (NMR) spectroscopy, including E.COSY, TOCSY, NOESY, and HMQC, to measure spectral parameters.
  • Molecular modeling with replica-exchange molecular dynamics (rMD)-simulated annealing to compute the three-dimensional structure.

    • Main Results:

    • The DDSDPEG molecule adopts a right-handed B-DNA helix in solution, confirmed by scalar couplings and dipolar contacts.
    • High melting temperature indicates good base stacking and duplex stability, attributed to the PEG(6) linker restricting dynamics.
    • The nick minimally affects overall tertiary structure but significantly impacts local geometry at the nick site.
    • Potassium ions sharpen (1)H NMR resonances and increase T1 times, suggesting reduced conformational heterogeneity and stabilization.

    Conclusions:

    • The synthesized DDSDPEG is a stable B-DNA duplex, with the PEG linker enhancing stability without distorting the overall geometry.
    • The central nick primarily affects local DNA structure, with minimal impact on global B-DNA conformation.
    • Potassium ions stabilize the DDSDPEG structure, offering a sensitive NMR parameter (T1 times) for monitoring stabilization.