ArticleNucleic acids research2009
Stability of intramolecular quadruplexes: sequence effects in the central loop.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Modulating G-quadruplexes for therapeutic intervention: Structural diversity, stability, and emerging nucleic-acid-based strategies.Molecular therapy. Nucleic acids · 2026Review
- Tri-mode fluorescence/colorimetric/strip aptasensor with CRISPR/Cas12a-driven cascade strategy for mycotoxin.Current research in food science · 2026Article
- Sequence Determinants of G-Quadruplex Thermostability: Aligning Evidence from High-Precision Biophysics and High-Throughput Genomics.Biomolecules · 2025Review
- Spectroscopic studies of sequence-dependent conformational transitions in asymmetric G/C rich double-stranded DNA.European biophysics journal : EBJ · 2025Article
- 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
- NMR Screen Reveals the Diverse Structural Landscape of a G-Quadruplex Library.Chemistry (Weinheim an der Bergstrasse, Germany) · 2024Article
- G-quadruplex structural dynamics at MAPK12 promoter dictates transcriptional switch to determine stemness in breast cancer.Cellular and molecular life sciences : CMLS · 2024Article
- Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection.Nucleic acids research · 2022Article
- Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment.Chembiochem : a European journal of chemical biology · 2021Review
- RNA G-quadruplexes (rG4s): genomics and biological functions.Nucleic acids research · 2021Review
- G-quadruplex structural variations in human genome associated with single-nucleotide variations and their impact on gene activity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences inMicroorganisms · 2019Article
- Involvement of G-quadruplex regions in mammalian replication origin activity.Nature communications · 2019Article
- Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes.Molecules (Basel, Switzerland) · 2019Article
- Loop permutation affects the topology and stability of G-quadruplexes.Nucleic acids research · 2018Article
- Encoding canonical DNA quadruplex structure.Science advances · 2018Article
- Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.Nucleic acids research · 2018Article
- Stability of the NaACS omega · 2018Article
- The effects of DNA supercoiling on G-quadruplex formation.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hundreds of thousands of putative quadruplex sequences have been found in the human genome. It is important to understand the rules that govern the stability of these intramolecular structures. In this report, we analysed sequence effects in a 3-base-long central loop, keeping the rest of the quadruplex unchanged. A first series of 36 different sequences were compared; they correspond to the general formula GGGTTTGGGHNHGGGTTTGGG. One clear rule emerged from the comparison of all sequence motifs: the presence of an adenine at the first position of the loop was significantly detrimental to stability. In contrast, adenines have no detrimental effect when present at the second or third position of the loop. Cytosines may either have a stabilizing or destabilizing effect depending on their position. In general, the correlation between the T(m) or DeltaG degrees in sodium and potassium was weak. To determine if these sequence effects could be generalized to different quadruplexes, specific loops were tested in different sequence contexts. Analysis of 26 extra sequences confirmed the general destabilizing effect of adenine as the first base of the loop(s). Finally, analysis of some of the sequences by microcalorimetry (DSC) confirmed the differences found between the sequence motifs.
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