ArticleRNA (New York, N.Y.)2005
In vitro RNA random pools are not structurally diverse: a computational analysis.
Article in RNA (New York, N.Y.), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
52 citing papers in PubMed.
- CompELS vs SELEX: Comparative Aptamer Discovery Integrating Rational Libraries and Enzymatic Elution.ACS nano medicine · 2026Article
- RNA and proteins joined up at the Origins of Life: Persistence is the point.bioRxiv : the preprint server for biology · 2026Article
- A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements.Biochemistry · 2025Article
- Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Selection-diversification interplay in oligonucleotide chemical evolution.Biophysics and physicobiology · 2025Article
- An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.bioRxiv : the preprint server for biology · 2024Article
- Aptamer-Based Strategies to Address Challenges in COVID-19 Diagnosis and Treatments.Interdisciplinary perspectives on infectious diseases · 2023Review
- SELEX: Critical factors and optimization strategies for successful aptamer selection.Biotechnology and applied biochemistry · 2022Review
- Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety.Sensors (Basel, Switzerland) · 2022Review
- The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.Molecular therapy. Nucleic acids · 2021Article
- Comparison of protein capture from a human cancer cell line by genomic G-quadruplex DNA sequences toward aptamer discovery.Analytical and bioanalytical chemistry · 2021Article
- Diagrammatic approaches to RNA structures with trinucleotide repeats.Biophysical journal · 2021Article
- Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.Biophysical journal · 2021Article
- Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element.bioRxiv : the preprint server for biology · 2020Article
- Aptamers: A Review of Their Chemical Properties and Modifications for Therapeutic Application.Molecules (Basel, Switzerland) · 2019Review
- Inside the Black Box: What Makes SELEX Better?Molecules (Basel, Switzerland) · 2019Review
- Key Aspects of Nucleic Acid Library Design for in Vitro Selection.International journal of molecular sciences · 2018Review
- Article
- Aptamer Bioinformatics.International journal of molecular sciences · 2017Review
- Improving the odds: Influence of starting pools on in vitro selection outcomes.Methods (San Diego, Calif.) · 2016Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In vitro selection of functional RNAs from large random sequence pools has led to the identification of many ligand-binding and catalytic RNAs. However, the structural diversity in random pools is not well understood. Such an understanding is a prerequisite for designing sequence pools to increase the probability of finding complex functional RNA by in vitro selection techniques. Toward this goal, we have generated by computer five random pools of RNA sequences of length up to 100 nt to mimic experiments and characterized the distribution of associated secondary structural motifs using sets of possible RNA tree structures derived from graph theory techniques. Our results show that such random pools heavily favor simple topological structures: For example, linear stem-loop and low-branching motifs are favored rather than complex structures with high-order junctions, as confirmed by known aptamers. Moreover, we quantify the rise of structural complexity with sequence length and report the dominant class of tree motifs (characterized by vertex number) for each pool. These analyses show not only that random pools do not lead to a uniform distribution of possible RNA secondary topologies; they point to avenues for designing pools with specific simple and complex structures in equal abundance in the goal of broadening the range of functional RNAs discovered by in vitro selection. Specifically, the optimal RNA sequence pool length to identify a structure with x stems is 20x.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.