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

Size, constant sequences, and optimal selection.

Michal Legiewicz1, Catherine Lozupone, Rob Knight

  • 1Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 80309-0347, USA.

RNA (New York, N.Y.)
|September 24, 2005
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

The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.

Microbiome·2026
Same author

Amoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungs.

bioRxiv : the preprint server for biology·2026
Same author

Gut microbiome composition influences immunologic alterations in the blood and gut of HIV-positive and HIV-negative men who have sex with men.

Frontiers in immunology·2026
Same author

EXPLANA: a user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies.

Bioinformatics (Oxford, England)·2025
Same author

Agrarian diet improves metabolic health in HIV-positive men with <i>Prevotella</i>-rich microbiomes: results from a randomized trial.

mSystems·2025
Same author

A capsular polysaccharide from a healthy human microbiota member activates a Lag-3-NK cell axis to restrain colon cancer and augment immunotherapy.

Cell reports·2025
Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026
Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026
Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026
Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026
Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026
Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026
See all related articles

Optimal RNA selection requires careful consideration of randomized tract length. Shorter or longer sequences hinder motif recovery, with 50-70 nucleotides yielding the highest abundance of the isoleucine aptamer.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • RNA Therapeutics

Background:

  • Exploring functional molecules in RNA sequence space is crucial.
  • Affinity selection is a key method for discovering RNA aptamers.
  • Understanding factors influencing selection outcomes is vital for aptamer design.

Purpose of the Study:

  • To compare the impact of varying randomized tract lengths on RNA selection outcomes.
  • To identify the optimal randomized region length for isolating specific RNA motifs.
  • To investigate the influence of primer sets on aptamer selection efficiency.

Main Methods:

  • Performed 11 independent RNA affinity selections targeting the isoleucine aptamer.
  • Utilized contiguous randomized regions of diverse lengths (16-90 nucleotides).

Related Experiment Videos

  • Compared different primer sets designed to favor distinct structural conformations.

    • Main Results:

    • The isoleucine aptamer was dominant except in the 16-nucleotide tract, where no motif was selected.
    • Optimal motif recovery occurred with 50-70 nucleotide randomized regions, showing 20-40 fold higher abundance.
    • Pre-formed primer stems negatively impacted motif abundance by 5-10 fold.
    • Random tract length influenced motif permutation and helix lengths.

    Conclusions:

    • Randomized tract length significantly impacts RNA selection success and motif abundance.
    • An optimal length range (50-70 nucleotides) exists for efficient selection of the isoleucine aptamer.
    • Primer sequence design plays a role, but randomized tract length is a more dominant factor in selection outcomes.