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

SSCP primer design based on single-strand DNA structure predicted by a DNA folding program

D A Nielsen1, A Novoradovsky, D Goldman

  • 1Section of Molecular Genetics, NIAAA, NIH, Bethesda, MD 20892-0001, USA.

Nucleic Acids Research
|June 25, 1995
PubMed
Summary

This study modified an RNA folding program to predict single-strand DNA folding and mobility shifts in gels. The new DNA-Fold 1.0 program accurately predicts DNA secondary structure alterations.

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

Markers of Negative Emotionality in Individuals With Comorbid Alcohol Use Disorder and Post-Traumatic Stress Disorder: Role of Childhood Trauma.

Addiction biology·2025
Same author

Pain in alcohol use disorder: Evaluating effects of childhood trauma, perceived stress, and psychological comorbidity.

Alcohol (Fayetteville, N.Y.)·2024
Same author

Val/Met BDNF as a genetic risk for a false sense of security in post-discharge suicide risk.

Journal of affective disorders·2024
Same author

Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells.

Nature communications·2023
Same author

Emotional self-regulation, impulsivity, 5-HTTLPR and tobacco use behavior among psychiatric inpatients.

Journal of affective disorders·2022
Same author

The oral microbiome in alcohol use disorder: a longitudinal analysis during inpatient treatment.

Journal of oral microbiology·2021

Area of Science:

  • Molecular Biology
  • Biophysics

Background:

  • Predicting single-strand DNA (ssDNA) secondary structure and mobility in non-denaturing gels is crucial for analyzing genetic variations.
  • Existing RNA folding algorithms require modification to accurately model DNA thermodynamics and base pairing rules.

Purpose of the Study:

  • To adapt an existing RNA folding algorithm for predicting ssDNA secondary structure and conformational changes.
  • To develop a computational tool for designing primers that induce or abolish Single-Strand Conformation Polymorphism (SSCP) mobility shifts.

Main Methods:

  • Modified Zuker's RNA folding program (LRNA) by adjusting energy files for DNA thermodynamics, disallowing G-T pairing, and removing loop constraints.
  • Applied the modified algorithm (DNA-Fold 1.0) to predict folding of PCR-generated ssDNA from human ALDH2 and TPH alleles.

Related Experiment Videos

  • Designed primers using DNA-Fold 1.0 to create or eliminate SSCP mobility shifts, altering 5' tag sequences or internal complementarity.

    • Main Results:

    • The DNA-Fold 1.0 program successfully predicted alterations in ssDNA secondary structure.
    • SSCP analysis confirmed that predicted conformational changes corresponded to observed mobility shifts.
    • Primer design based on DNA-Fold 1.0 predictions effectively manipulated SSCP mobility.

    Conclusions:

    • The modified RNA folding algorithm, DNA-Fold 1.0, is a viable tool for predicting ssDNA secondary structure and conformational alterations.
    • This approach enables the design of primers for targeted manipulation of SSCP mobility shifts, aiding in genetic analysis.