title: Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL.
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.
authors.affiliation: Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA.
authors.forename: Yunxi
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Koirala
authors.affiliation: College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, AZ 85721, USA.
authors.forename: HyunJin
authors.initials: H
authors.lastname: Kang
authors.affiliation: Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA.
authors.forename: Soma
authors.initials: S
authors.lastname: Dhakal
authors.affiliation: Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA.
authors.forename: Philip
authors.initials: P
authors.lastname: Yangyuoru
authors.affiliation: College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, AZ 85721, USA Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, AZ 85724, USA BIO5 Institute, 1657 East Helen Street, Tucson, AZ 85721, USA.
authors.forename: Laurence H
authors.initials: LH
authors.lastname: Hurley
authors.affiliation: Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA hmao@kent.edu.
authors.forename: Hanbin
authors.initials: H
authors.lastname: Mao
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D048588:Benzoxazines / Q000737:chemistry*; D002776:Cholestanes / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D005786:Gene Expression Regulation / Q000187:drug effects*; D019254:Genes, bcl-2; D034664:Heterogeneous-Nuclear Ribonucleoprotein L / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D010363:Pattern Recognition, Automated; D010880:Piperidines / Q000737:chemistry*; D011278:Pregnanes / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D011485:Protein Binding
chemical_list: D048588:Benzoxazines; D002776:Cholestanes; D034664:Heterogeneous-Nuclear Ribonucleoprotein L; C000589552:IMC-48; C000589551:IMC-76; D010880:Piperidines; D011278:Pregnanes; D004247:DNA