ArticleNucleic acids research2018
Loop permutation affects the topology and stability of G-quadruplexes.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed.
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
- How loop lengths shape topological preferences of two-tetrad G-quadruplexes.Nucleic acids research · 2026Article
- QuaDB: A streamlined web tool for identifier-based rapid prediction of putative quadruplex sequences.Human genomics · 2026Article
- Investigation of possible G-quadruplex formation by GU- and GA-rich repeats and their role in translation.RNA biology · 2025Article
- Deciphering the intermolecular interactions between G-quadruplex (G4)-forming sequences.Nucleic acids research · 2025Article
- Sequence Determinants of G-Quadruplex Thermostability: Aligning Evidence from High-Precision Biophysics and High-Throughput Genomics.Biomolecules · 2025Review
- Functional and Structural Analyses of Diverse G-Quadruplex and Non-G-Quadruplex Structures Formed by Guanine-Rich Nucleic Acids: A Study on the Insulin Aptamer.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Large-Scale Conformational Analysis Explains G-Quadruplex Topological Landscape.The journal of physical chemistry. B · 2025Article
- G-quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides.Nucleic acids research · 2025Article
- Three- and four-stranded nucleic acid structures and their ligands.RSC chemical biology · 2025Review
- G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation.Science (New York, N.Y.) · 2025Article
- Identifying G-quadruplex-interacting proteins in cancer-related gene promoters.Communications chemistry · 2025Article
- Imperfect G-quadruplex as an emerging candidate for transcriptional regulation.Nucleic acids research · 2025Article
- Article
- Chronic RNA G-quadruplex Accumulation in Aging and Alzheimer's Disease.bioRxiv : the preprint server for biology · 2025Article
- Immunostimulatory Effects of Guanine-Quadruplex Topologies as Scaffolds for CpG Oligodeoxynucleotides.Biomolecules · 2025Article
- RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed?Nucleic acids research · 2024Article
- Quantitative Effects of the Loop Region on Topology, Thermodynamics, and Cation Binding of DNA G-quadruplexes.ACS omega · 2024Article
- Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsiveChemical science · 2024Article
- Why Are Left-Handed G-Quadruplexes Scarce?The journal of physical chemistry letters · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on Tm as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.
Indexed as
Identifiers
What OpenQuestion holds
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.