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Chen H, Gu Z, Yang L, Liu F, An R, Ge Y, Liang X. Direct dsRNA preparation by promoter-free RCT and RNase H cleavage using one circular dsDNA template with a mismatched bubble. RNA (NEW YORK, N.Y.) 2023; 29:1691-1702. [PMID: 37536954 PMCID: PMC10578470 DOI: 10.1261/rna.079670.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023]
Abstract
Double-stranded RNA (dsRNA) has aroused widespread interest due to its effects on immunity and applications based on RNAi. However, the in vitro preparation of dsRNA is costly and laborious. In this study, we have developed a novel and interesting method designated as pfRCT (promoter-free rolling-circle transcription) for direct, facile, and efficient dsRNA preparation. This method generates equal amounts of sense and antisense strands simultaneously from a single circular dsDNA template. To initiate transcription by T7 RNA polymerase without directional preference, a 9-15-bp bubble (mismatched duplex with strong sequence symmetry) is introduced into the template. During RCT, all the necessary reagents, including the template, NTPs, RNA polymerase, RNase H, and Helpers, are present in one pot; and the just-transcribed RNA is immediately truncated by RNase H to monomers with the desired size. The ends of the dsRNA product can also be simply sealed by T4 RNA ligase 1 after pfRCT. This new approach is expected to promote the applications of dsRNA.
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Affiliation(s)
- Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266550, Shandong, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, Shandong, China
| | - Zhenzhu Gu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266550, Shandong, China
| | - Liu Yang
- Department of Biochemistry and Molecular Biology School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong, China
| | - Feng Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266550, Shandong, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266550, Shandong, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, Shandong, China
| | - Yinlin Ge
- Department of Biochemistry and Molecular Biology School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266550, Shandong, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, Shandong, China
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2
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Mosley RJ, Rucci B, Byrne ME. Recent advancements in design of nucleic acid nanocarriers for controlled drug delivery. J Mater Chem B 2023; 11:2078-2094. [PMID: 36806872 DOI: 10.1039/d2tb02325c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Research of nanoscale nucleic acid carriers has garnered attention in recent years due to their distinctive and controllable properties. However, current knowledge is limited in how we can efficiently utilize these systems for clinical applications. Several researchers have pioneered new and innovative nanocarrier drug delivery systems, but understanding physiochemical properties and behavior in vivo is vital to implementing them as clinical drug delivery platforms. In this review, we outline the most significant innovations in the synthesis, physical properties, and utilization of nucleic acid nanocarriers in the past 5 years, addressing the crucial properties which improve nanocarrier characteristics, delivery, and drug release. The challenges of controlling the transport of nucleic acid nanocarriers and therapeutic release for biological applications are outlined. Barriers which inhibit effective transport into tissue are discussed with emphasis on the modifications needed to overcome such obstacles. The novel strategies discussed in this work summarize the pivotal features of modern nucleic nanocarriers and postulate where future developments could revolutionize the translation of these tools into a clinical setting.
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Affiliation(s)
- Robert J Mosley
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA.
| | - Brendan Rucci
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA.
| | - Mark E Byrne
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA. .,Department of Chemical Engineering, Rowan University, Glassboro, NJ, 08028, USA
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3
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Bremer J, Richter C, Schwalbe H, Richert C. Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly. Chembiochem 2022; 23:e202200352. [PMID: 35867587 PMCID: PMC9542650 DOI: 10.1002/cbic.202200352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/21/2022] [Indexed: 12/02/2022]
Abstract
Peptidoyl RNAs are the products of ribosome‐free, single‐nucleotide translation. They contain a peptide in the backbone of the oligoribonucleotide and are interesting from a synthetic and a bioorganic point of view. A synthesis of a stabilized version of peptidoyl RNA, with an amide bond between the C‐terminus of a peptide and a 3′‐amino‐2′,3′‐dideoxynucleoside in the RNA chain was developed. The preferred synthetic route used an N‐Teoc‐protected aminonucleoside support and involved a solution‐phase coupling of the amino‐terminal oligonucleotide to a dipeptido dinucleotide. Exploratory UV‐melting and NMR analysis of the hairpin 5′‐UUGGCGAAAGCdC‐LeuLeu‐AA‐3′ indicated that the peptide‐linked RNA segments do not fold in a cooperative fashion. The synthetic access to doubly RNA‐linked peptides on a scale sufficient for structural biology opens the door to the exploration of their structural and biochemical properties.
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Affiliation(s)
- Jennifer Bremer
- University of Stuttgart: Universitat Stuttgart, Chemistry, GERMANY
| | - Christian Richter
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Harald Schwalbe
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, GERMANY
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4
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Yang Z, Zhang C, Lian G, Dong S, Song M, Shao H, Wang J, Zhong T, Luo Z, Jin S, Ding C. Direct adenylation from 5'-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase. Nucleic Acids Res 2022; 50:7560-7569. [PMID: 35819229 PMCID: PMC9303275 DOI: 10.1093/nar/gkac604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022] Open
Abstract
5′-Adenylated oligonucleotides (AppOligos) are widely used for single-stranded DNA/RNA ligation in next-generation sequencing (NGS) applications such as microRNA (miRNA) profiling. The ligation between an AppOligo adapter and target molecules (such as miRNA) no longer requires ATP, thereby minimizing potential self-ligations and simplifying library preparation procedures. AppOligos can be produced by chemical synthesis or enzymatic modification. However, adenylation via chemical synthesis is inefficient and expensive, while enzymatic modification requires pre-phosphorylated substrate and additional purification. Here we cloned and characterized the Pfu RNA ligase encoded by the PF0353 gene in the hyperthermophilic archaea Pyrococcus furiosus. We further engineered fusion enzymes containing both Pfu RNA ligase and T4 polynucleotide kinase. One fusion enzyme, 8H-AP, was thermostable and can directly catalyze 5′-OH-terminated DNA substrates to adenylated products. The newly discovered Pfu RNA ligase and the engineered fusion enzyme may be useful tools for applications using AppOligos.
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Affiliation(s)
- Zhengquan Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chengliang Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.,Department of Clinical Laboratory, Kunming Third People's Hospital, Kunming, Yunnan, 650041, China
| | - Guojun Lian
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shijie Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Menghui Song
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Hengrong Shao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jingmei Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Tao Zhong
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Zhenni Luo
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shengnan Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chunming Ding
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
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5
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Abstract
Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.
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6
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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7
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Shahsavari S, Eriyagama DNAM, Halami B, Begoyan V, Tanasova M, Chen J, Fang S. Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection. Beilstein J Org Chem 2019; 15:1116-1128. [PMID: 31164948 PMCID: PMC6541367 DOI: 10.3762/bjoc.15.108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023] Open
Abstract
Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, α-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within the ODN sequences without using any sequence- or functionality-specific conditions and procedures.
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Affiliation(s)
- Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Dhananjani N A M Eriyagama
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Bhaskar Halami
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Vagarshak Begoyan
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Marina Tanasova
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Jinsen Chen
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
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8
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Milisavljevič N, Perlíková P, Pohl R, Hocek M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org Biomol Chem 2019; 16:5800-5807. [PMID: 30063056 DOI: 10.1039/c8ob01498a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We synthesized a small library of eighteen 5-substituted pyrimidine or 7-substituted 7-deazapurine nucleoside triphosphates bearing methyl, ethynyl, phenyl, benzofuryl or dibenzofuryl groups through cross-coupling reactions of nucleosides followed by triphosphorylation or through direct cross-coupling reactions of halogenated nucleoside triphosphates. We systematically studied the influence of the modification on the efficiency of T7 RNA polymerase catalyzed synthesis of modified RNA and found that modified ATP, UTP and CTP analogues bearing smaller modifications were good substrates and building blocks for the RNA synthesis even in difficult sequences incorporating multiple modified nucleotides. Bulky dibenzofuryl derivatives of ATP and GTP were not substrates for the RNA polymerase. In the case of modified GTP analogues, a modified procedure using a special promoter and GMP as initiator needed to be used to obtain efficient RNA synthesis. The T7 RNA polymerase synthesis of modified RNA can be very efficiently used for synthesis of modified RNA but the method has constraints in the sequence of the first three nucleotides of the transcript, which must contain a non-modified G in the +1 position.
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Affiliation(s)
- Nemanja Milisavljevič
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic.
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9
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Efficient Genome Engineering of a Virulent Klebsiella Bacteriophage Using CRISPR-Cas9. J Virol 2018; 92:JVI.00534-18. [PMID: 29899105 DOI: 10.1128/jvi.00534-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is one of the most common nosocomial opportunistic pathogens and usually exhibits multiple-drug resistance. Phage therapy, a potential therapeutic to replace or supplement antibiotics, has attracted much attention. However, very few Klebsiella phages have been well characterized because of the lack of efficient genome-editing tools. Here, Cas9 from Streptococcus pyogenes and a single guide RNA (sgRNA) were used to modify a virulent Klebsiella bacteriophage, phiKpS2. We first evaluated the distribution of sgRNA activity in phages and proved that it is largely inconsistent with the predicted activity from current models trained on eukaryotic cell data sets. A simple CRISPR-based phage genome-editing procedure was developed based on the discovery that homologous arms as short as 30 to 60 bp were sufficient to introduce point mutation, gene deletion, and swap. We also demonstrated that weak sgRNAs could be used for precise phage genome editing but failed to select random recombinants, possibly because inefficient cleavage can be tolerated through continuous repair by homologous recombination with the uncut genomes. Small frameshift deletion was proved to be an efficient way to evaluate the essentiality of phage genes. By using the abovementioned strategies, a putative promoter and nine genes of phiKpS2 were successfully deleted. Interestingly, the holin gene can be deleted with little effect on phiKpS2 infection, but the reason is not yet clear. This study established an efficient, time-saving, and cost-effective procedure for phage genome editing, which is expected to significantly promote the development of bacteriophage therapy.IMPORTANCE In the present study, we have addressed efficient, time-saving, and cost-effective CRISPR-based phage genome editing of Klebsiella phage, which has the potential to significantly expand our knowledge of phage-host interactions and to promote applications of phage therapy. The distribution of sgRNA activity was first evaluated in phages. Short homologous arms were proven to be enough to introduce point mutation, small frameshift deletion, gene deletion, and swap into phages, and weak sgRNAs were proven useful for precise phage genome editing but failed to select random recombinants, all of which makes the CRISPR-based phage genome-editing method easier to use.
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10
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Lietard J, Hassler MR, Fakhoury J, Damha MJ. An orthogonal photolabile linker for the complete "on-support" synthesis/fast deprotection/hybridization of RNA. Chem Commun (Camb) 2015; 50:15063-6. [PMID: 25329642 DOI: 10.1039/c4cc07153k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The preparation of a polystyrene solid support decorated with a photolabile linker is described. The entire post-synthetic processing of RNA can be carried out in the solid phase in a minimum amount of time. The deprotected RNA is available for "on-support" hybridization and photolysis releases siRNA duplexes under mild, neutral conditions.
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Affiliation(s)
- Jory Lietard
- Department of Chemistry, McGill University, Montréal, Québec H3A 0B8, Canada.
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11
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Krause A, Hertl A, Muttach F, Jäschke A. Phosphine-free Stille-Migita chemistry for the mild and orthogonal modification of DNA and RNA. Chemistry 2014; 20:16613-9. [PMID: 25322724 DOI: 10.1002/chem.201404843] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 12/31/2022]
Abstract
An optimized catalyst system of [Pd2 (dba)3 ] and AsPh3 efficiently catalyzes the Stille reaction between a diverse set of functionalized stannanes and halogenated mono-, di- and oligonucleotides. The methodology allows for the facile conjugation of short and long nucleic acid molecules with moieties that are not compatible with conventional chemical or enzymatic synthesis, among them acid-, base-, or fluoride-labile protecting groups, fluorogenic and synthetically challenging moieties with good to near-quantitative yields. Notably, even azides can be directly introduced into oligonucleotides and (deoxy)nucleoside triphosphates, thereby giving direct access to "clickable" nucleic acids.
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Affiliation(s)
- André Krause
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg
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12
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Li Y, Liu X. Tunable acid-sensitive ester protecting groups in oligosaccharide synthesis. Chem Commun (Camb) 2014; 50:3155-8. [DOI: 10.1039/c3cc49205b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Vazquez-Anderson J, Contreras LM. Regulatory RNAs: charming gene management styles for synthetic biology applications. RNA Biol 2013; 10:1778-97. [PMID: 24356572 DOI: 10.4161/rna.27102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions.
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Affiliation(s)
- Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
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