ArticleJournal of the American Chemical Society2009
The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 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
56 citing papers in PubMed, 149 citations in OpenAlex.
- The cellular landscape of i-motifs: genomic insights, methodological challenges, and the road ahead.Genome biology · 2026Review
- DNA secondary structures in BCL2 and MYC elicit activation-induced cytidine deaminase binding and activity.Nucleic acids research · 2026Article
- Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at GNature communications · 2026Article
- Ratiometric Detection of pH-Induced i-Motif Folding Based on a Dual Emissive Cytosine Analog.Chembiochem : a European journal of chemical biology · 2025Article
- Effects of flanking regions on DNA i-motif folding and stability.Nucleic acids research · 2025Article
- G-quadruplex and i-motif DNA structures form in the promoter of the key innate immune adaptorCell reports. Physical science · 2025Article
- Biological Regulation StudiedAccounts of chemical research · 2025Article
- i-Motifs as regulatory switches: Mechanisms and implications for gene expression.Molecular therapy. Nucleic acids · 2025Review
- Selective Up-Regulation of Tumor Suppressor Gene Retinoblastoma by Bisacridine Derivative Through Gene Promoter Quadruplex Structures for Cancer Treatment.International journal of molecular sciences · 2025Article
- Metal-Based Drug-DNA Interactions and Analytical Determination Methods.Molecules (Basel, Switzerland) · 2024Review
- The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.Nucleic acids research · 2024Article
- Non-canonical DNA structures in the human ribosomal DNA.Histochemistry and cell biology · 2023Review
- Rapid and Highly Efficient Separation of i-Motif DNA Species by CE-UV and Multivariate Curve Resolution.Analytical chemistry · 2023Article
- Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet.Scientific reports · 2023Article
- In vivo dynamics and regulation of DNA G-quadruplex structures in mammals.Cell & bioscience · 2023Review
- Emerging roles of i-motif in gene expression and disease treatment.Frontiers in pharmacology · 2023Review
- Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice.Nucleic acids research · 2022Article
- Synthesis and Characterization of Bis-Triazolyl-Pyridine Derivatives as Noncanonical DNA-Interacting Compounds.International journal of molecular sciences · 2021Article
- Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides.International journal of molecular sciences · 2021Review
- An Updated Focus on Quadruplex Structures as Potential Therapeutic Targets in Cancer.International journal of molecular sciences · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition.
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.