1
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Xiang Z, Zheng JY, Ma X, Chu Y, Song Q, Zhou G, Zou B, Wu H, Wang C. FEN1-assisted DNA logic amplifier circuit for fast and compact DNA computing. Chem Commun (Camb) 2024; 60:4593-4596. [PMID: 38577866 DOI: 10.1039/d4cc00203b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
This work developed DNA amplifier logic gates (AND-OR, OR-AND, FAN-IN, FAN-OUT, and 4-bit square-root circuits) using a flap endonuclease 1 (FEN1)-catalyzed signal amplification reaction, for the fastest and compact DNA computing. Moreover, the logic circuit can use input strands with concentrations of less than 1 nM, which is more than 100 times lower than the input concentration of other DNA logic circuits, providing a promising methodology for constructing fast and compact DNA computations.
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Affiliation(s)
- Zheng Xiang
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jia-Yi Zheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Xueping Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Yanan Chu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Qinxin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Haiping Wu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Chen Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
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2
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Gulzar A, Noetzel J, Forbert H, Marx D. Elucidating the Self-cleavage Dynamics of Hairpin Ribozyme by Mode-decomposed Infrared Spectroscopy. J Phys Chem Lett 2023; 14:7940-7945. [PMID: 37646493 DOI: 10.1021/acs.jpclett.3c01724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
While catalytic reactions of biomolecular processes play an indispensable role in life, extracting the underlying molecular picture often remains challenging. Based on ab initio simulations of the self-cleavage reaction of hairpin ribozyme, mode-decomposed infrared spectra, and cosine similarity analysis to correlate the product with reactant IR spectra, we demonstrate a strategy to extract molecular details from characteristic spectral changes. Our results are in almost quantitative agreement with the experimental IR band library of nucleic acids and suggest that the spectral range of 800-1200 cm-1 is particularly valuable to monitor self-cleavage. Importantly, the cosine similarities also disclose that IR peaks subject to slight shifts due to self-cleavage might be unrelated, while strongly shifting resonances can correspond to the same structural dynamics. This framework of correlating complex IR spectra at the molecular level along biocatalytic reaction pathways is broadly applicable.
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Affiliation(s)
- Adnan Gulzar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jan Noetzel
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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3
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Kaloudas D, Pavlova N, Penchovsky R. GHOST-NOT and GHOST-YES: Two programs for generating high-speed biosensors with randomized oligonucleotide binding sites with NOT or YES Boolean logic functions based on experimentally validated algorithms. J Biotechnol 2023; 373:82-89. [PMID: 37499876 DOI: 10.1016/j.jbiotec.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
High-speed allosteric hammerhead ribozymes can be engineered to distinguish well between a perfectly matching effector and the nucleic acid sequences with a few mismatches under physiologically relevant conditions. Such ribozymes can be designed to control the expression of exogenous mRNAs and can be used to develop new gene therapies, including anticancer treatments. The in vivo selection of such ribozymes is a complicated and lengthy procedure with no guarantee of success. Thus, in silico selection of high-speed ribozymes can be employed using secondary RNA structure computation based on the partition function of the RNA folding in combination with random search algorithms. This approach has already been proven very accurate in designing allosteric hammerhead ribozymes. Herein, we present two programs for the computational design of allosteric ribozymes sensing randomized oligonucleotides based on the extended version of the hammerhead ribozyme. A Generator for High-speed Oligonucleotide Sensing allosteric ribozymes with NOT logic function (GHOST-NOT) and a Generator for High-speed Oligonucleotide Sensing allosteric ribozymes with YES logic function (GHOST-YES) for computational design of high-speed allosteric ribozymes are described. The allosteric hammerhead ribozymes had a high self-cleavage rate of about 1.8 per minute and were very selective in sensing an effector sequence.
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Affiliation(s)
- Dimitrios Kaloudas
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 1164 Sofia, 8 Dragan Tsankov Blvd., Sofia, Bulgaria
| | - Nikolet Pavlova
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 1164 Sofia, 8 Dragan Tsankov Blvd., Sofia, Bulgaria
| | - Robert Penchovsky
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 1164 Sofia, 8 Dragan Tsankov Blvd., Sofia, Bulgaria.
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4
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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: 8] [Impact Index Per Article: 4.0] [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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5
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Pavlova N, Penchovsky R. Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics (Basel) 2022; 11:antibiotics11091177. [PMID: 36139956 PMCID: PMC9495176 DOI: 10.3390/antibiotics11091177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.
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6
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Versatile tools of synthetic biology applied to drug discovery and production. Future Med Chem 2022; 14:1325-1340. [PMID: 35975897 DOI: 10.4155/fmc-2022-0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although synthetic biology is an emerging research field, which has come to prominence within the last decade, it already has many practical applications. Its applications cover the areas of pharmaceutical biotechnology and drug discovery, bringing essential novel methods and strategies such as metabolic engineering, reprogramming the cell fate, drug production in genetically modified organisms, molecular glues, functional nucleic acids and genome editing. This review discusses the main avenues for synthetic biology application in pharmaceutical biotechnology. The authors believe that synthetic biology will reshape drug development and drug production to a similar extent as the advances in organic chemical synthesis in the 20th century. Therefore, synthetic biology already plays an essential role in pharmaceutical, biotechnology, which is the main focus of this review.
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7
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A High-Pressure, High-Temperature Flow Reactor Simulating the Hadean Earth Environment, with Application to the Pressure Dependence of the Cleavage of Avocado Viroid Hammerhead Ribozyme. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081224. [PMID: 36013404 PMCID: PMC9410335 DOI: 10.3390/life12081224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
The RNA world hypothesis suggests that chemical networks consisting of functional RNA molecules could have constructed a primitive life-like system leading a first living system. The chemical evolution scenario of RNA molecules should be consistent with the Hadean Earth environment. We have demonstrated the importance of the environment at both high temperature and high pressure, using different types of hydrothermal flow reactor systems and high-pressure equipment. In the present study, we have attempted to develop an alternative easy-to-implement method for high-pressure measurements and demonstrate that the system is applicable as an efficient research tool for high-pressure experiments at pressures up to 30 MPa. We demonstrate the usefulness of the system by detecting the high-pressure influence for the self-cleavage of avocado hammerhead ribozyme (ASBVd(−):HHR) at 45–65 °C. A kinetic analysis of the high-pressure behavior of ASBVd(−):HHR shows that the ribozyme is active at 30 MPa and its activity is sensitive to pressures between 0.1–30 MPa. The surprising finding that such a short ribozyme is effective for self-cleavage at a high pressure suggests the importance of pressure as a factor for selection of adaptable RNA molecules towards an RNA-based life-like system in the Hadean Earth environment deep in the ocean.
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8
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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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9
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Davis AN, Samlali K, Kapadia JB, Perreault J, Shih SCC, Kharma N. Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions. ACS OMEGA 2021; 6:22514-22524. [PMID: 34514224 PMCID: PMC8427639 DOI: 10.1021/acsomega.1c00239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/22/2021] [Indexed: 06/08/2023]
Abstract
In this paper, we describe the design and performance of two digital microfluidics (DMF) chips capable of executing multiple ribozymatic reactions, with proper controls, in response to short single-stranded DNA inducers. Since the fluorescence output of a reaction is measurable directly from the chip, without the need for gel electrophoresis, a complete experiment involving up to eight reactions (per chip) can be carried out reliably, relatively quickly, and efficiently. The ribozymes can also be used as biosensors of the concentration of oligonucleotide inputs, with high sensitivity, low limits of quantification and of detection, and excellent signal-to-noise ratio. The presented chips are readily usable devices that can be used to automate, speed up, and reduce the costs of ribozymatic reaction experiments.
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Affiliation(s)
- Alen N. Davis
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Kenza Samlali
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
| | - Jay B. Kapadia
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Jonathan Perreault
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
- Armand-Frappier
Health Biotechnology Center, Institut national
de la recherche scientifique, Laval, Québec H7V 1B7, Canada
| | - Steve C. C. Shih
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Nawwaf Kharma
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
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10
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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11
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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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12
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Pavlova N, Penchovsky R. Genome-wide bioinformatics analysis of FMN, SAM-I, glmS, TPP, lysine, purine, cobalamin, and SAH riboswitches for their applications as allosteric antibacterial drug targets in human pathogenic bacteria. Expert Opin Ther Targets 2019; 23:631-643. [DOI: 10.1080/14728222.2019.1618274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nikolet Pavlova
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
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13
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Zakrevsky P, Bindewald E, Humbertson H, Viard M, Dorjsuren N, Shapiro BA. A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E615. [PMID: 30991728 PMCID: PMC6526476 DOI: 10.3390/nano9040615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 01/16/2023]
Abstract
Several varieties of small nucleic acid constructs are able to modulate gene expression via one of a number of different pathways and mechanisms. These constructs can be synthesized, assembled and delivered to cells where they are able to impart regulatory functions, presenting a potential avenue for the development of nucleic acid-based therapeutics. However, distinguishing aberrant cells in need of therapeutic treatment and limiting the activity of deliverable nucleic acid constructs to these specific cells remains a challenge. Here, we designed and characterized a collection of nucleic acids systems able to generate and/or release sequence-specific oligonucleotide constructs in a conditional manner based on the presence or absence of specific RNA trigger molecules. The conditional function of these systems utilizes the implementation of AND and NOT Boolean logic elements, which could ultimately be used to restrict the release of functionally relevant nucleic acid constructs to specific cellular environments defined by the high or low expression of particular RNA biomarkers. Each system is generalizable and designed with future therapeutic development in mind. Every construct assembles through nuclease-resistant RNA/DNA hybrid duplex formation, removing the need for additional 2'-modifications, while none contain any sequence restrictions on what can define the diagnostic trigger sequence or the functional oligonucleotide output.
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Affiliation(s)
- Paul Zakrevsky
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Eckart Bindewald
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Hadley Humbertson
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Nomongo Dorjsuren
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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14
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Kaloudas D, Pavlova N, Penchovsky R. EBWS: Essential Bioinformatics Web Services for Sequence Analyses. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:942-953. [PMID: 29993817 DOI: 10.1109/tcbb.2018.2816645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The Essential Bioinformatics Web Services (EBWS) are implemented on a new PHP-based server that provides useful tools for analyses of DNA, RNA, and protein sequences applying a user-friendly interface. Nine Web-based applets are currently available on the Web server. They include reverse complementary DNA and random DNA/RNA/peptide oligomer generators, a pattern sequence searcher, a DNA restriction cutter, a prokaryotic ORF finder, a random DNA/RNA mutation generator. It also includes calculators of melting temperature (TM) of DNA/DNA, RNA/RNA, and DNA/RNA hybrids, a guide RNA (gRNA) generator for the CRISPR/Cas9 system and an annealing temperature calculator for multiplex PCR. The pattern-searching applet has no limitations in the number of motif inputs and applies a toolbox of Regex quantifiers that can be used for defining complex sequence queries of RNA, DNA, and protein sequences. The DNA enzyme digestion program utilizes a large database of 1502 restriction enzymes. The gRNA generator has a database of 25 bacterial genomes searchable for gRNA target sequences and has an option for searching in any genome sequence given by the user. All programs are permanently available online at http://penchovsky.atwebpages.com/applications.php without any restrictions.
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15
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Abstract
Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code.
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16
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Otero TF. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics. Phys Chem Chem Phys 2017; 19:1718-1730. [DOI: 10.1039/c6cp06735b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ea,k,αandβfrom reactions driving molecular polymeric motors constituting dense gels include quantitative conformational and structural information.
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Affiliation(s)
- Toribio F. Otero
- Centre for Electrochemistry and Intelligent Materials (CEMI)
- Universidad Politécnica de Cartagena Aulario II
- Cartagena
- Spain
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17
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Nomura Y, Chien HC, Yokobayashi Y. Direct screening for ribozyme activity in mammalian cells. Chem Commun (Camb) 2017; 53:12540-12543. [DOI: 10.1039/c7cc07815c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using deep sequencing, 3001 natural and synthetic ribozymes were screened for self-cleaving activity directly in mammalian cells.
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Affiliation(s)
- Yoko Nomura
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Japan
| | - Hsiao-Chiao Chien
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Japan
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18
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Felletti M, Hartig JS. Ligand-dependent ribozymes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27687155 DOI: 10.1002/wrna.1395] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 12/20/2022]
Abstract
The discovery of catalytic RNA (ribozymes) more than 30 years ago significantly widened the horizon of RNA-based functions in natural systems. Similarly to the activity of protein enzymes that are often modulated by the presence of an interaction partner, some examples of naturally occurring ribozymes are influenced by ligands that can either act as cofactors or allosteric modulators. Recent discoveries of new and widespread ribozyme motifs in many different genetic contexts point toward the existence of further ligand-dependent RNA catalysts. In addition to the presence of ligand-dependent ribozymes in nature, researchers have engineered ligand dependency into natural and artificial ribozymes. Because RNA functions can often be assembled in a truly modular way, many different systems have been obtained utilizing different ligand-sensing domains and ribozyme activities in diverse applications. We summarize the occurrence of ligand-dependent ribozymes in nature and the many examples realized by researchers that engineered ligand-dependent catalytic RNA motifs. We will also highlight methods for obtaining ligand dependency as well as discuss the many interesting applications of ligand-controlled catalytic RNAs. WIREs RNA 2017, 8:e1395. doi: 10.1002/wrna.1395 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michele Felletti
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
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Coulovoltammetric and Dynamovoltammetric Responses from Conducting Polymers and Bilayer Muscles as Tools to Identify Reaction-driven Structural Changes. A review. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Gaines CS, York DM. Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation. J Am Chem Soc 2016; 138:3058-65. [PMID: 26859432 PMCID: PMC4904722 DOI: 10.1021/jacs.5b12061] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present results from molecular dynamics simulations and free energy calculations of the twister ribozyme at different stages along the reaction path to gain insight into its mechanism. The results, together with recent biochemical experiments, provide support for a mechanism involving general-acid catalysis by a conserved adenine residue in the active site. Although adenine has been previously implicated as a general acid acting through the N1 position in other ribozymes such as the hairpin and VS ribozymes, in the twister ribozyme there may be a twist. Biochemical experiments suggest that general acid catalysis may occur through the N3 position, which has never before been implicated in this role; however, currently, there is a lack of a detailed structural model for the active state of the twister ribozyme in solution that is consistent with these and other experiments. Simulations in a crystalline environment reported here are consistent with X-ray crystallographic data, and suggest that crystal packing contacts trap the RNA in an inactive conformation with U-1 in an extruded state that is incompatible with an in-line attack to the scissile phosphate. Simulations in solution, on the other hand, reveal this region to be dynamic and able to adopt a conformation where U-1 is stacked with G33. In this state, the nucleophile is in line with the scissile phosphate, and the N1 position of G33 and N3 position of A1 are poised to act as a general base and acid, respectively, as supported by mutational experiments. Free energy calculations further predict the electrostatic environment causes a shift of the microscopic pKa at the N3 position of A1 toward neutrality by approximately 5 pKa units. These results offer a unified interpretation of a broad range of currently available experimental data that points to a novel mode of general acid catalysis through the N3 position of an adenine nucleobase, thus expanding the repertoire of known mechanistic strategies employed by small nucleolytic ribozymes.
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Affiliation(s)
- Colin S. Gaines
- Center for Integrative Proteomics Research and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
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Lee TS, Radak BK, Harris ME, York DM. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 2016; 6:1853-1869. [PMID: 27774349 DOI: 10.1021/acscatal.5b02158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path. Building upon recent crystallographic data, our results provide a dynamic model of the HDVr reaction mechanism involving a conformational switch between multiple non-canonical G25:U20 base pair conformations in the active site. These local nucleobase dynamics play an important role in catalysis by modulating the metal binding environments of two Mg2+ ions that support catalysis at different steps of the reaction pathway. The first ion plays a structural role by inducing a base pair flip necessary to obtain the catalytic fold in which C75 moves towards to the scissile phosphate in the active site. Ejection of this ion then permits a second ion to bind elsewhere in the active site and facilitate nucleophile activation. The simulations collectively describe a mechanistic scenario that is consistent with currently available experimental data from crystallography, phosphorothioate substitutions, and chemical probing studies. Avenues for further experimental verification are suggested.
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Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Brian K. Radak
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
- Argonne National Laboratory, Argonne, Illinois 60439, United State
| | - Michael E. Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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22
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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: 47] [Impact Index Per Article: 5.2] [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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Panteva MT, Dissanayake T, Chen H, Radak BK, Kuechler ER, Giambaşu GM, Lee TS, York DM. Multiscale methods for computational RNA enzymology. Methods Enzymol 2015; 553:335-74. [PMID: 25726472 PMCID: PMC4739856 DOI: 10.1016/bs.mie.2014.10.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA catalysis is of fundamental importance to biology and yet remains ill-understood due to its complex nature. The multidimensional "problem space" of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence on potentially correlated protonation states of key residues, and bond breaking/forming in the chemical steps of the reaction. The goal of this chapter is to summarize and apply multiscale modeling methods in an effort to target the different parts of the RNA catalysis problem space while also addressing the limitations and pitfalls of these methods. Classical molecular dynamics simulations, reference interaction site model calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics, and quantum mechanical/molecular mechanical simulations will be discussed in the context of the study of RNA backbone cleavage transesterification. This reaction is catalyzed by both RNA and protein enzymes, and here we examine the different mechanistic strategies taken by the hepatitis delta virus ribozyme and RNase A.
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Affiliation(s)
- Maria T Panteva
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Thakshila Dissanayake
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Haoyuan Chen
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Brian K Radak
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Erich R Kuechler
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - George M Giambaşu
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Tai-Sung Lee
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.
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Frommer J, Appel B, Müller S. Ribozymes that can be regulated by external stimuli. Curr Opin Biotechnol 2014; 31:35-41. [PMID: 25146171 DOI: 10.1016/j.copbio.2014.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022]
Abstract
Ribozymes have been known for about 30 years, and nowadays are understood well enough to be turned into useful tools for a number of applications in vitro and in vivo. Allosteric ribozymes switch on and off their activity in response to a specific chemical (ligand) or physical (temperature, light) signal. The possibility of controlling ribozyme activity by external stimuli is of particular relevance for applications in different fields, such as environmental and medicinal diagnostics, molecular computing, control of gene expression and others. Herein, we review recent advances and describe selected examples of addressable ribozymes.
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Affiliation(s)
- Jennifer Frommer
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany
| | - Bettina Appel
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany
| | - Sabine Müller
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany.
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