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Traykovska M, Otcheva LA, Penchovsky R. Targeting TPP Riboswitches Using Chimeric Antisense Oligonucleotide Technology for Antibacterial Drug Development. ACS APPLIED BIO MATERIALS 2022; 5:4896-4902. [PMID: 36170638 DOI: 10.1021/acsabm.2c00628] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nowadays, the emergence and the transmission of multidrug-resistant pathogenic bacteria are a severe menace mounting a lot of pressure on the healthcare systems worldwide. Many severe outbreaks of bacterial infections have been reported worldwide in recent years. Thus, there is an immediate demand to develop antibiotics. Some riboswitches are potential targets for overcoming bacterial resistance. This paper demonstrates the bacteriostatic effect of an antisense oligonucleotide (ASO) engineered to suppress the growth of pathogenic bacteria such as Listeria monocytogenes by targeting the Thiamine Pyrophosphate (TPP) riboswitch. It does not inhibit the growth of the conditional pathogenic bacteria Escherichia coli, as it lacks the TPP riboswitch, showing the specificity of action of our ASO. It is covalently bonded with the cell-penetrating protein pVEC. We did bioinformatics analyses of the thiamine pyrophosphate riboswitch regarding its role in synthesizing the metabolite thiamine pyrophosphate, which is essential for bacteria. L. monocytogenes is intrinsically resistant to cephalosporins and usually is treated with ampicillin. A dosage of ASO has been established that inhibits 80% of bacterial growth at 700 nM (4.5 μg/mL). Thus, the TPP riboswitch is a valuable antibacterial target.
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Affiliation(s)
- Martina Traykovska
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
| | - Lozena A Otcheva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
| | - Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia 1164, Bulgaria
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An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms. Comput Biol Med 2022; 145:105469. [DOI: 10.1016/j.compbiomed.2022.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
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Penchovsky R. Automated DNA hybridization transfer with movable super-paramagnetic microbeads in a microflow reactor. Biosens Bioelectron 2019; 135:30-35. [PMID: 30991269 DOI: 10.1016/j.bios.2019.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 03/24/2019] [Accepted: 04/06/2019] [Indexed: 12/24/2022]
Abstract
An automated DNA hybridization transfer in a microflow reactor is demonstrated by moving paramagnetic beads between two spatially separate solutions with different pH values. The microbeads-based microfluidic platform is fully automated and programmable. It employs a robust chemical procedure for specific DNA hybridization transfer in microfluidic devices under isothermal conditions based on reversible pH alterations. The method takes advantage of high-speed DNA hybridization and denaturation on beads under flow conditions, high fidelity of DNA hybridization, and small sample volumes. The microfluidic platform presented is saleable and applicable to many areas of modern biotechnology such as DNA hybridization chip microarrays, molecular computation, on-chip selection of functional nucleic acids, high-throughput screening of chemical libraries for drug discovery, and DNA amplification and sequencing.
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Affiliation(s)
- Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164, Sofia, Bulgaria.
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Huang SH, Chang YS, Juang JMJ, Chang KW, Tsai MH, Lu TP, Lai LC, Chuang EY, Huang NT. An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases. Analyst 2019; 143:1367-1377. [PMID: 29423467 DOI: 10.1039/c7an01648d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.
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Affiliation(s)
- Shu-Hong Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
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Pokrzywnicka M, Kamiński J, Michalec M, Koncki R, Tymecki Ł. A multicommutated tester of bioreactors for flow analysis. Talanta 2016; 160:233-240. [DOI: 10.1016/j.talanta.2016.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/28/2016] [Accepted: 07/03/2016] [Indexed: 01/09/2023]
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Ha D, Hong J, Shin H, Kim T. Unconventional micro-/nanofabrication technologies for hybrid-scale lab-on-a-chip. LAB ON A CHIP 2016; 16:4296-4312. [PMID: 27761529 DOI: 10.1039/c6lc01058j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Micro-/nanofabrication-based lab-on-a-chip (LOC) technologies have recently been substantially advanced and have become widely used in various inter-/multidisciplinary research fields, including biological, (bio-)chemical, and biomedical fields. However, such hybrid-scale LOC devices are typically fabricated using microfabrication and nanofabrication processes in series, resulting in increased cost and time and low throughput issues. In this review, after briefly introducing the conventional micro-/nanofabrication technologies, we focus on unconventional micro-/nanofabrication technologies that allow us to produce either in situ micro-/nanoscale structures or master molds for additional replication processes to easily and conveniently create novel LOC devices with micro- or nanofluidic channel networks. In particular, microfabrication methods based on crack-assisted photolithography and carbon-microelectromechanical systems (C-MEMS) are described in detail because of their superior features from the viewpoint of the throughput, batch fabrication process, and mixed-scale channels/structures. In parallel with previously reported articles on conventional micro-/nanofabrication technologies, our review of unconventional micro-/nanofabrication technologies will provide a useful and practical fabrication guideline for future hybrid-scale LOC devices.
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Affiliation(s)
- Dogyeong Ha
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Jisoo Hong
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Heungjoo Shin
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Taesung Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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Sun H. A multi-layer microchip for high-throughput single-cell gene expression profiling. Anal Biochem 2016; 508:1-8. [DOI: 10.1016/j.ab.2016.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
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Penchovsky R, Traykovska M. Designing drugs that overcome antibacterial resistance: where do we stand and what should we do? Expert Opin Drug Discov 2015; 10:631-50. [PMID: 25981754 DOI: 10.1517/17460441.2015.1048219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION In recent years, infections caused by multidrug-resistant bacterial pathogens have become a huge issue to public healthcare systems. Indeed, the misuse of antibiotics has led to, over the past 30 years, the emergence of a number of resistant bacterial strains including Staphylococcus aureus, Neisseria gonorrhoeae, Escherichia coli and Mycobacterium tuberculosis. Unfortunately, efforts to produce new antibiotics have not been sufficient to cope with the emergence of these new antibiotic-resistant (AR) strains. AREAS COVERED There is an urgent need to invent and employ unconventional strategies for antimicrobial drug development to tackle the rising global threats imposed by the spread of antimicrobial resistance. Herein, the authors discuss these novel design strategies and provide their expert perspective on the subject. EXPERT OPINION To deal with the growing threat of AR, it is important to cut down the use of antibiotics to the very minimum to diminish the risk of unknown drug-resistant bacteria and increase antibacterial vaccination programs. Furthermore, it is important to develop new classes of antibiotics that can deal with multidrug-resistant bacterial pathogens.
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Affiliation(s)
- Robert Penchovsky
- Sofia University "St. Kliment Ohridski", Department of Genetics, Faculty of Biology , 8 Dragan Tzankov Blvd., 1164 Sofia , Bulgaria +35928167340 ; +35928167340 ;
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Culbertson CT, Mickleburgh TG, Stewart-James SA, Sellens KA, Pressnall M. Micro total analysis systems: fundamental advances and biological applications. Anal Chem 2014; 86:95-118. [PMID: 24274655 PMCID: PMC3951881 DOI: 10.1021/ac403688g] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Tom G. Mickleburgh
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | | | - Kathleen A. Sellens
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Melissa Pressnall
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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Penchovsky R. Nucleic Acids-Based Nanotechnology. HANDBOOK OF RESEARCH ON NANOSCIENCE, NANOTECHNOLOGY, AND ADVANCED MATERIALS 2014. [DOI: 10.4018/978-1-4666-5824-0.ch016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nanobiotechnology is emerging as a valuable field that integrates research from science and technology to create novel nanodevices and nanostructures with various applications in modern nanotechnology. Applications of nanobiotechnology are employed in biomedical and pharmaceutical research, biosensoring, nanofluidics, self-assembly of nanostructures, nanopharmaceutics, molecular computing, and others. It has been proven that nucleic acids are a very suitable medium for self-assembly of diverse nanostructures and catalytic nanodevices for various applications. In this chapter, the authors discuss various applications of nucleic-based nanotechnology. The areas discussed here include building nanostructures using DNA oligonucleodite, self-assembly of integrated RNA-based nanodevices for molecular computing and diagnostics, antibacterial drug discovery, exogenous control of gene expression, and gene silencing.
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Penchovsky R, Kostova GT. Computational selection and experimental validation of allosteric ribozymes that sense a specific sequence of human telomerase reverse transcriptase mRNAs as universal anticancer therapy agents. Nucleic Acid Ther 2013; 23:408-17. [PMID: 24206267 PMCID: PMC3868306 DOI: 10.1089/nat.2013.0446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/07/2013] [Indexed: 12/19/2022] Open
Abstract
High expression levels of telomerase reverse transcriptase messenger RNAs in differentiated cells can be used as a common marker for cancer development. In this paper, we describe a novel computational method for selection of allosteric ribozymes that sense a specific sequence of human telomerase reverse transcriptase mRNAs. The in silico selection employed is based on computing secondary structures of RNA using the partition function in combination with a random search algorithm. We selected one of the ribozymes for experimental validation. The obtained results demonstrate that the tested ribozyme has a high-speed (∼1.8 per minute) of self-cleavage and is very selective. It can distinguish well between perfectly matching effector and the closest expressed RNA sequence in the human cell with 10 mismatches, with a ∼300-fold difference under physiologically relevant conditions. The presented algorithm is universal since the allosteric ribozymes can be designed to sense any specific RNA or DNA sequence of interest. Such designer ribozymes may be used for monitoring the expression of mRNAs in the cell and for developing novel anticancer gene therapies.
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Affiliation(s)
- Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University St. Kliment Ohridski , Sofia, Bulgaria
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