ArticleNucleic acids research2014
Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 35 citations in OpenAlex.
- Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures.Nucleic acids research · 2024Article
- Emerging roles of i-motif in gene expression and disease treatment.Frontiers in pharmacology · 2023Review
- Rational design of small-molecules to recognize G-quadruplexes of c-MYC promoter and telomere and the evaluation of their in vivo antitumor activity against breast cancer.Nucleic acids research · 2022Article
- Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment.iScience · 2022Article
- Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy.Biomolecules · 2021Review
- G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders.Nucleic acids research · 2020Review
- Duplex DNA Is Weakened in Nanoconfinement.Journal of the American Chemical Society · 2020Article
- Folding/unfolding kinetics of G-quadruplexes upstream of the P1 promoter of the humanThe Journal of biological chemistry · 2019Article
- Systematic investigation of sequence requirements for DNA i-motif formation.Nucleic acids research · 2019Article
- Homoduplex to i-motif structural switch exhibited by a cytosine rich strand of theRSC advances · 2018Article
- N-Terminomics TAILS Identifies Host Cell Substrates of Poliovirus and Coxsackievirus B3 3C Proteinases That Modulate Virus Infection.Journal of virology · 2018Article
- Fluorescence-based tools to probe G-quadruplexes in cell-free and cellular environments.RSC advances · 2018Article
- Preferential targeting of i-motifs and G-quadruplexes by small molecules.Chemical science · 2017Article
- Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression.Journal of the American Chemical Society · 2017Article
- Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH.Nucleic acids research · 2017Article
- Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery.Biochemistry. Biokhimiia · 2016Article
- GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1.Scientific reports · 2015Article
- Nascent RNA transcripts facilitate the formation of G-quadruplexes.Nucleic acids research · 2014Article
- The dynamic character of the BCL2 promoter i-motif provides a mechanism for modulation of gene expression by compounds that bind selectively to the alternative DNA hairpin structure.Journal of the American Chemical Society · 2014Article
- The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules.Journal of the American Chemical Society · 2014Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Minute difference in free energy change of unfolding among structures in an oligonucleotide sequence can lead to a complex population equilibrium, which is rather challenging for ensemble techniques to decipher. Herein, we introduce a new method, molecular population dynamics (MPD), to describe the intricate equilibrium among non-B deoxyribonucleic acid (DNA) structures. Using mechanical unfolding in laser tweezers, we identified six DNA species in a cytosine (C)-rich bcl-2 promoter sequence. Population patterns of these species with and without a small molecule (IMC-76 or IMC-48) or the transcription factor hnRNP LL are compared to reveal the MPD of different species. With a pattern recognition algorithm, we found that IMC-48 and hnRNP LL share 80% similarity in stabilizing i-motifs with 60 s incubation. In contrast, IMC-76 demonstrates an opposite behavior, preferring flexible DNA hairpins. With 120-180 s incubation, IMC-48 and hnRNP LL destabilize i-motifs, which has been previously proposed to activate bcl-2 transcriptions. These results provide strong support, from the population equilibrium perspective, that small molecules and hnRNP LL can modulate bcl-2 transcription through interaction with i-motifs. The excellent agreement with biochemical results firmly validates the MPD analyses, which, we expect, can be widely applicable to investigate complex equilibrium of biomacromolecules.
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