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Beals N, Farhath MM, Kharel P, Croos B, Mahendran T, Johnson J, Basu S. Rationally designed DNA therapeutics can modulate human TH expression by controlling specific GQ formation in its promoter. Mol Ther 2022; 30:831-844. [PMID: 33992806 PMCID: PMC8822133 DOI: 10.1016/j.ymthe.2021.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 02/04/2023] Open
Abstract
Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the catecholamine (CA) biosynthesis pathway, making TH a molecular target for controlling CA production, specifically dopamine. Dysregulation of dopamine is correlated with neurological diseases such as Parkinson's disease (PD) and post-traumatic stress disorder (PTSD), among others. Previously, we showed that a 49-nucleotide guanine (G)-rich sequence within the human TH promoter adopts two different sets of G-quadruplex (GQ) structures (5'GQ and 3'GQ), where the 5'GQ uses G-stretches I, II, IV, and VI in TH49, which enhances TH transcription, while the 3'GQ utilizes G-stretches II, IV, VI, and VII, which represses transcription. Herein, we demonstrated targeted switching of these GQs to their active state using rationally designed DNA GQ Clips (5'GQ and 3'GQ Clips) to modulate endogenous TH gene expression and dopamine production. As a translational approach, we synthesized a targeted nanoparticle delivery system to effectively deliver the 5'GQ Clip in vivo. We believe this strategy could potentially be an improved approach for controlling dopamine production in a multitude of neurological disorders, including PD.
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Affiliation(s)
- Nathan Beals
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mohamed M. Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Department of Chemical Sciences, Faculty of Applied Sciences, South Eastern University of Sri Lanka, Oluvil, Sri Lanka
| | - Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Brintha Croos
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Thulasi Mahendran
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - John Johnson
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA,Corresponding author: Soumitra Basu, Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
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Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H. Converting FRET Signal into Force Information using Short Looped DNA as Force Transducer. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H. A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. Biosens Bioelectron 2018; 121:34-40. [PMID: 30195120 DOI: 10.1016/j.bios.2018.08.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 01/27/2023]
Abstract
A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged by a DNA hairpin and KCl was titrated to change the applied force. After these proof-of-principle measurements, one of the dsDNA constructs was used to maintain the G-quadruplex (GQ) construct formed by thrombin binding aptamer (TBA) under tension while it interacted with a destabilizing protein and stabilizing small molecule. The force required to unfold TBA-GQ was independently investigated with high-resolution optical tweezers (OT) measurements that established the relevant force to be a few pN, which is consistent with the force generated by the looped dsDNA. The proposed method is particularly promising as it enables studying NAS, protein, and small molecule interactions using a highly-parallel FRET-based assay while the NAS is kept under an approximately constant force.
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Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Cho-Ying Chuang
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - William A Roy
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Mohamed M Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Matthew J Comstock
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, United States.
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Dassanayake RS, Farhath MM, Shelley JT, Basu S, Brasch NE. Kinetic studies on the reaction of cob(II)alamin with hypochlorous acid: Evidence for one electron oxidation of the metal center and corrin ring destruction. J Inorg Biochem 2016; 163:81-87. [PMID: 27567143 DOI: 10.1016/j.jinorgbio.2016.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 07/07/2016] [Accepted: 07/13/2016] [Indexed: 01/16/2023]
Abstract
Kinetic and mechanistic studies on the reaction of a major intracellular vitamin B12 form, cob(II)alamin (Cbl(II)), with hypochlorous acid/hypochlorite (HOCl/OCl-) have been carried out. Cbl(II) (Co(II)) is rapidly oxidized by HOCl to predominately aquacobalamin/hydroxycobalamin (Cbl(III), Co(III)) with a second-order rate constant of 2.4×107M-1s-1 (25.0°C). The stoichiometry of the reaction is 1:1. UHPLC/HRMS analysis of the product mixture of the reaction of Cbl(II) with 0.9mol equiv. HOCl provides support for HOCl being initially reduced to Cl and subsequent H atom abstraction from the corrin macrocycle occurring, resulting in small amounts of corrinoid species with two or four H atoms fewer than the parent cobalamin. Upon the addition of excess (H)OCl further slower reactions are observed. Finally, SDS-PAGE experiments show that HOCl-induced damage to bovine serum albumin does not occur in the presence of Cbl(II), providing support for Cbl(II) being an efficient HOCl trapping agent.
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Affiliation(s)
- Rohan S Dassanayake
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Mohamed M Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Jacob T Shelley
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Nicola E Brasch
- School of Applied Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.
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Farhath MM, Thompson M, Ray S, Sewell A, Balci H, Basu S. G-Quadruplex-Enabling Sequence within the Human Tyrosine Hydroxylase Promoter Differentially Regulates Transcription. Biochemistry 2015; 54:5533-45. [DOI: 10.1021/acs.biochem.5b00209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohamed M. Farhath
- Department
of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Matthew Thompson
- Department
of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Sujay Ray
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Abby Sewell
- Department
of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Hamza Balci
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Soumitra Basu
- Department
of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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