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Rollo D, Kulkarni A, Yu K, Fabris D. Investigating the Merits of Microfluidic Capillary Zone Electrophoresis-Mass Spectrometry (CZE-MS) in the Bottom-Up Characterization of Larger RNAs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:561-574. [PMID: 38350102 DOI: 10.1021/jasms.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these hydrolytic mixtures calls for the utilization of a front-end separation to facilitate full mass spectrometric (MS) characterization. This report explored the merits of microfluidic capillary zone electrophoresis (CZE) as a possible alternative to common liquid chromatography techniques. An oligonucleotide ladder was initially employed to investigate the roles of fundamental analyte features and experimental parameters in determining the outcome of CZE-MS analyses. The results demonstrated the ability to fully resolve the various rungs into discrete electrophoretic peaks with full-width half-height (FWHH) resolution that was visibly affected by the overall amount of material injected into the system. Analogous results were obtained from a digestion mixture prepared by treating yeast tRNAPhe (75 nt) with RNase T1, which provided several well-resolved peaks in spite of the increasing sample heterogeneity. The regular shapes of such peaks, however, belied the fact that most of them contained sets of comigrating species, as shown by the corresponding MS spectra. Even though it was not possible to segregate each species into an individual electrophoretic peak, the analysis still proved capable of unambiguously identifying a total of 29 hydrolytic products, which were sufficient to cover 96% of the tRNAPhe's sequence. Their masses accurately reflected the presence of modified nucleotides characteristic of this type of substrate. The analysis of a digestion mixture obtained from the 364 nt HIV-1 5'-UTR proved to be more challenging. The electropherogram displayed fewer well-resolved peaks and significantly greater incidence of product comigration. In this case, fractionating the highly heterogeneous mixture into discrete bands helped reduce signal suppression and detection bias. As a result, the corresponding MS data enabled the assignment of 248 products out of the possible 513 predicted from the 5'-UTR sequence, which afforded 100% sequence coverage. This figure represented a significant improvement over the 36 total products identified earlier under suboptimal conditions, which afforded only 57% coverage, or the 83 observed by direct infusion nanospray-MS (72%). These results provided a measure of the excellent potential of the technique to support the bottom-up characterization of progressively larger NA samples, such as putative NA therapeutics and mRNA vaccines.
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Affiliation(s)
- Daniele Rollo
- University of Connecticut, Storrs, Connecticut 06269, United States
| | | | - Kate Yu
- 908 Devices, Boston, Massachusetts 02210, United States
| | - Daniele Fabris
- University of Connecticut, Storrs, Connecticut 06269, United States
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2
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Henderson AN, McDonnell RT, Elcock AH. Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543892. [PMID: 37333149 PMCID: PMC10274748 DOI: 10.1101/2023.06.06.543892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We describe a computational approach to building and simulating realistic 3D models of very large RNA molecules (>1000 nucleotides) at a resolution of one "bead" per nucleotide. The method starts with a predicted secondary structure and uses several stages of energy minimization and Brownian dynamics (BD) simulation to build 3D models. A key step in the protocol is the temporary addition of a 4 th spatial dimension that allows all predicted helical elements to become disentangled from each other in an effectively automated way. We then use the resulting 3D models as input to Brownian dynamics simulations that include hydrodynamic interactions (HIs) that allow the diffusive properties of the RNA to be modelled as well as enabling its conformational dynamics to be simulated. To validate the dynamics part of the method, we first show that when applied to small RNAs with known 3D structures the BD-HI simulation models accurately reproduce their experimental hydrodynamic radii (Rh). We then apply the modelling and simulation protocol to a variety of RNAs for which experimental Rh values have been reported ranging in size from 85 to 3569 nucleotides. We show that the 3D models, when used in BD-HI simulations, produce hydrodynamic radii that are usually in good agreement with experimental estimates for RNAs that do not contain tertiary contacts that persist even under very low salt conditions. Finally, we show that sampling of the conformational dynamics of large RNAs on timescales of 100 µs is computationally feasible with BD-HI simulations.
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3
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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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4
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Werner A. Translational and rotational diffusion of short ribonucleic acids. Biochem Biophys Res Commun 2023; 650:17-20. [PMID: 36764208 DOI: 10.1016/j.bbrc.2023.01.028] [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: 12/27/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Inevitable precondition for ribonucleic acids to regulate gene expression and to perform gene editing is diffusion. Free three-dimensional translational diffusion velocity of RNA of up to 200 nucleotides could be predicted with high accuracy by the empirical model D = 4.58 10-10 N-0.39 m2s-1. Furthermore, the biological function of ribonucleic acids is determined by rotational diffusion. In the presented work, an empirical model is derived applying atom-level shell-modeling of electron density maps, Dr = 1.62 109 N-1.20 s-1, to predict the rotational diffusion coefficient of short ribonucleic acids based on the polymer size.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Computer Science and Natural Science, Hamburg University, Germany.
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5
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Werner A. RNA double strand hybridization measured at the single molecule level. Anal Biochem 2023; 660:114959. [PMID: 36341770 DOI: 10.1016/j.ab.2022.114959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
RNA double strand hybridization is a hallmark for gene expression regulation. In this function, single stranded regulatory RNA forms Watson-Crick base pairs with complementary messenger RNA. In the presented work the dissociation constants of complementary equally sized RNA single strands were measured at the single molecule level applying fluorescence correlation spectroscopy (FCS). Dissociation constants of 3.2 nM, 1.4 nM and 1.0 nM were determined for 26 bp, 41 bp and 54 bp dsRNA, respectively. The translational diffusion coefficients of RNA, measured at infinite dilution, could be accurately predicted applying the model D = 4.58 × 10-10 N-0.39 m2s-1.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Computer Science and Natural Science; Hamburg University, Germany.
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6
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Roy S, Sengupta S. The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081227. [PMID: 36013406 PMCID: PMC9410160 DOI: 10.3390/life12081227] [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: 07/14/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes. Despite these advances in our understanding of a primordial RNA-lipid world, key questions remain about the ideal environment for the formation of protocells and its role in regulating the proliferation of functionally complex protocells. The hot spring hypothesis suggests that mineral-rich regions near hot springs, subject to dry-wet cycles, provide an ideal environment for the origin of primitive protocells. We develop a computational model to study protocellular evolution in such environments that are distinguished by the occurrence of three distinct phases, a wet phase, followed by a gel phase, and subsequently by a dry phase. We determine the conditions under which protocells containing multiple types of ribozymes can evolve and proliferate in such regions. We find that diffusion in the gel phase can inhibit the proliferation of complex protocells with the extent of inhibition being most significant when a small fraction of protocells is eliminated during environmental cycling. Our work clarifies how the environment can shape the evolution and proliferation of complex protocells.
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Victorious A, Zhang Z, Chang D, Maclachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022; 61:e202204252. [DOI: 10.1002/anie.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amanda Victorious
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | | | - Richa Pandey
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Jianrun Xia
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Todd Hoare
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Chemical Engineering McMaster University Canada
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Engineering Physics McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
| | - Yingfu Li
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
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8
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Schanke IJ, Xue L, Spustova K, Gözen I. Transport among protocells via tunneling nanotubes. NANOSCALE 2022; 14:10418-10427. [PMID: 35748865 DOI: 10.1039/d2nr02290g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We employ model protocell networks for evaluation of molecular transport through lipid nanotubes as potential means of communication among primitive cells on the early Earth. Network formation is initiated by deposition of lipid reservoirs onto a SiO2 surface in an aqueous environment. These reservoirs autonomously develop into surface-adhered protocells interconnected via lipid nanotubes while encapsulating solutes from the ambient buffer. We observe the uptake of DNA and RNA, and their diffusive transport between the lipid compartments via the interconnecting nanotubes. By means of an analytical model we determine key physical parameters affecting the transport, such as nanotube diameter and compartment size. We conclude that nanotube-mediated transport could have been a possible pathway of communication between primitive cells on the early Earth, circumventing the necessity for crossing the membrane barrier. We suggest this transport as a feasible means of RNA and DNA exchange under primitive prebiotic conditions, possibly facilitating early replication.
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Affiliation(s)
- Ingrid Jin Schanke
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway.
| | - Lin Xue
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway.
| | - Karolina Spustova
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway.
| | - Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway.
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9
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Victorious A, Zhang Z, Chang D, Malachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Dingran Chang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | | | | | - Jianrun Xia
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMurry University Biochemistry and Biomedical Sciences CANADA
| | - Todd Hoare
- McMurry University Chemical Engineering CANADA
| | - Leyla Soleymani
- McMastser University Engineering Physics 1280 Main Street W. L8S 4M1 Hamilton CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
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10
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Wei B, Wang J, Cadang L, Goyon A, Chen B, Yang F, Zhang K. Development of an ion pairing reversed-phase liquid chromatography-mass spectrometry method for characterization of clustered regularly interspaced short palindromic repeats guide ribonucleic acid. J Chromatogr A 2022; 1665:462839. [PMID: 35093620 DOI: 10.1016/j.chroma.2022.462839] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 12/20/2022]
Abstract
Guide ribonucleic acid (gRNA) is a critical reagent in clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing. The single stranded guide RNA (sgRNA) is the most commonly used gRNA in application. Evaluation of the impurity profile of synthetic sgRNA is important for any CRISPR genome editing experiments. However, the large molecular size, complex impurity profile and unique secondary structure pose many challenges in the analysis of sgRNA by ion pairing reversed-phase liquid chromatography (IP-RPLC), the commonly used method. In this work, we developed a generic IP-RPLC method for guide RNA analysis. We found that large pore size of stationary phase was the most critical column parameter to achieve high resolution separation of sgRNA while particle structure, particle size and surface chemistry had less impact. Our results indicated that charge interaction was the most critical mechanism for retention and mass transfer had less impact on the performance of separation. An IP-RPLC/mass spectrometry (MS) method was also developed with a specific practice to reduce adducts and enable intact MS analysis of sgRNAs. The generic IP-RPLC method demonstrates its feasibility to serve as a release, stability, characterization and in-process control testing method for synthetic sgRNA products.
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Affiliation(s)
- Bingchuan Wei
- Genentech Research and Early Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Jenny Wang
- Genentech Research and Early Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lance Cadang
- Pharma Technical Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexandre Goyon
- Genentech Research and Early Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Bifan Chen
- Genentech Research and Early Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Feng Yang
- Pharma Technical Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Genentech Research and Early Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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11
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Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MC, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z. Fundamental behaviors emerge from simulations of a living minimal cell. Cell 2022; 185:345-360.e28. [PMID: 35063075 PMCID: PMC9985924 DOI: 10.1016/j.cell.2021.12.025] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/01/2021] [Accepted: 12/17/2021] [Indexed: 01/18/2023]
Abstract
We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.
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Affiliation(s)
- Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David M. Bianchi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler M. Earnest
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcelo C.R. Melo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nataliya Safronova
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - James P. Sáenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | | | - Kim S. Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | | | | | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NSF Center for the Physics of Living Cells, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.
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12
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De Masi A, Scognamiglio PL, Battista E, Netti PA, Causa F. PEG-based Cleavable Hydrogel Microparticles with controlled porosity for permiselective trafficking of biomolecular complexes in biosensing applications. J Mater Chem B 2022; 10:1980-1990. [PMID: 35229850 DOI: 10.1039/d1tb02751d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the last decade, PEG-based hydrogels have been extensively used for the production of microparticles for biosensing applications. The biomolecule accessibility and mass transport rate represent key parameters for the...
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Affiliation(s)
- Alessandra De Masi
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
| | - Pasqualina L Scognamiglio
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
| | - Edmondo Battista
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy.
| | - Paolo A Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy.
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy.
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13
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Vezeau GE, Salis HM. Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression. ACS Synth Biol 2021; 10:2508-2519. [PMID: 34498860 DOI: 10.1021/acssynbio.1c00136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The composition of cell-free expression systems (TX-TL) is adjusted by adding macromolecular crowding agents and salts. However, the effects of these cosolutes on the dynamics of individual gene expression processes have not been quantified. Here, we carry out kinetic mRNA and protein level measurements on libraries of genetic constructs using the common cosolutes PEG-8000, Ficoll-400, and magnesium glutamate. By combining these measurements with biophysical modeling, we show that cosolutes have differing effects on transcription initiation, translation initiation, and translation elongation rates with trade-offs between time delays, expression tunability, and maximum expression productivity. We also confirm that biophysical models can predict translation initiation rates in TX-TL using Escherichia coli lysate. We discuss how cosolute composition can be tuned to maximize performance across different cell-free applications, including biosensing, diagnostics, and biomanufacturing.
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Affiliation(s)
- Grace E. Vezeau
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Howard M. Salis
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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14
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Pandey R, Chang D, Smieja M, Hoare T, Li Y, Soleymani L. Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform. Nat Chem 2021; 13:895-901. [PMID: 34168325 DOI: 10.1038/s41557-021-00718-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/29/2021] [Indexed: 11/09/2022]
Abstract
The detection and identification of bacteria currently rely on enrichment steps such as bacterial culture and nucleic acid amplification to increase the concentration of target analytes. These steps increase assay time, cost and complexity, making it difficult to realize a truly rapid point-of-care test. Here we report the development of an electrical assay that uses electroactive RNA-cleaving DNAzymes (e-RCDs) to identify specific bacterial targets and subsequently release a DNA barcode for transducing a signal onto an electrical chip. Integrating e-RCDs into a two-channel electrical chip with nanostructured electrodes provides the analytical sensitivity and specificity needed for clinical analysis. The e-RCD assay is capable of detecting 10 CFU (equivalent to 1,000 CFU ml-1) of Escherichia coli selectively from a panel containing multiple non-specific bacterial species. Clinical evaluation of this assay using 41 patient urine samples demonstrated a diagnostic sensitivity of 100% and specificity of 78% at an analysis time of less than one hour compared with the several hours needed for currently used culture-based methods.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, Hamilton, Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, Hamilton, Canada
| | - Todd Hoare
- Department of Chemical Engineering, McMaster University, Hamilton, Canada.,School of Biomedical Engineering, McMaster University, Hamilton, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, Hamilton, Canada. .,School of Biomedical Engineering, McMaster University, Hamilton, Canada.
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Hamilton, Canada. .,School of Biomedical Engineering, McMaster University, Hamilton, Canada.
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15
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NMR analysis of nucleotide π-stacking in prebiotically relevant crowded environment. Commun Chem 2020; 3:51. [PMID: 36703483 PMCID: PMC9814533 DOI: 10.1038/s42004-020-0300-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 04/07/2020] [Indexed: 01/29/2023] Open
Abstract
The prebiotic soup of a putative 'RNA World' would have been replete with a plethora of molecules resulting from complex chemical syntheses and exogeneous delivery. The presence of background molecules could lead to molecular crowding, potentially affecting the course of the reactions facilitated therein. Using NMR spectroscopy, we have analyzed the effect of crowding on the stacking ability of RNA monomers. Our findings corroborate that the purines stack more efficiently than the pyrimidine ribonucleotides. This competence is further enhanced in the presence of a crowding agent. This enhanced stacking could result in greater sequestration of the purine monomers, putting their ready availability for relevant nonenzymatic reactions into question. Thus, this study demonstrates the need for systematic characterization of molecular crowding in the context of prebiotically pertinent processes. Unraveling such phenomena is essential for our understanding of the transition from abiotic to biotic, during the origin of life.
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16
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Manzano I, Vezeau G, Salis H, Zydney AL. RNA size and 3-dimensional structure determine ultrafiltration behavior of small RNA molecules. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2019.116372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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17
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Lin Y, Jing H, Liu Z, Chen J, Liang D. Dynamic Behavior of Complex Coacervates with Internal Lipid Vesicles under Nonequilibrium Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1709-1717. [PMID: 32004005 DOI: 10.1021/acs.langmuir.9b03561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
During the evolution of life on earth, the emergence of lipid membrane-bounded compartments is one of the most enigmatic events. Endosymbiosis has been hypothesized as one of the solutions. In this work, using a coacervate droplet formed by single-stranded oligonucleotides (ss-oligo) and poly(l-lysine) (PLL) as the protocell model, we monitored the uptake of liposomes of different types and studied the dynamic behavior of the resulting composite droplet under the electric field. The coacervate droplet exhibits affinity for the liposomes of varying charges. However, the permeation of liposome is also controlled by electrostatic interactions. Dominated by electrostatic attraction, the positively charged liposome is retained inside the droplet as growing fibrous structures, while the negatively charged liposome is mainly coated on the droplet surface. Permeation and even distribution occur when the liposome and the droplet carry the same charges, or at least one of them is neutral. As an electric field is applied to trigger repetitive cycles of vacuolization in the ss-oligo/PLL droplet, the fibrous structure formed by the positively charged liposome is basically intact, while a new phase is generated together with uneven mass transport as the negatively charged liposome is internalized. Interestingly, the release of daughter droplets with similar components occurs on the droplet containing neutral liposomes. Our work not only provides a step toward creating protocells with hierarchical structures and biofunctions using a biogenetic material via simple mixing but also sheds light on the possible origin of the lipid structure inside a living organism.
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Affiliation(s)
- Ya'nan Lin
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Hairong Jing
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
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18
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T Magalhães B, Lourenço A, Azevedo NF. Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae. Brief Bioinform 2019; 22:219-231. [PMID: 31879749 DOI: 10.1093/bib/bbz149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/16/2019] [Accepted: 10/30/2019] [Indexed: 11/13/2022] Open
Abstract
This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.
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Affiliation(s)
| | - Anália Lourenço
- Department of Computer Science, University of Vigo, Spain, Centre of Biological Engineering, University of Minho, Portugal
| | - Nuno F Azevedo
- Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Portugal
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19
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Drobot B, Iglesias-Artola JM, Le Vay K, Mayr V, Kar M, Kreysing M, Mutschler H, Tang TYD. Compartmentalised RNA catalysis in membrane-free coacervate protocells. Nat Commun 2018; 9:3643. [PMID: 30194374 PMCID: PMC6128941 DOI: 10.1038/s41467-018-06072-w] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022] Open
Abstract
Phase separation of mixtures of oppositely charged polymers provides a simple and direct route to compartmentalisation via complex coacervation, which may have been important for driving primitive reactions as part of the RNA world hypothesis. However, to date, RNA catalysis has not been reconciled with coacervation. Here we demonstrate that RNA catalysis is viable within coacervate microdroplets and further show that these membrane-free droplets can selectively retain longer length RNAs while permitting transfer of lower molecular weight oligonucleotides. Phase separation of mixtures of oppositely charged polymers provides a simple and direct route to compartmentalisation via coacervation. Here authors demonstrate that a coacervate microenvironment supports RNA catalysis whilst selectively sequestering RNA based on length.
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Affiliation(s)
- Björn Drobot
- Max-Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Juan M Iglesias-Artola
- Max-Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Kristian Le Vay
- Max-Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Viktoria Mayr
- Max-Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Mrityunjoy Kar
- Max-Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Moritz Kreysing
- Max-Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany.
| | - Hannes Mutschler
- Max-Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - T-Y Dora Tang
- Max-Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany.
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20
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Wang Y, Carta G. Rapid and Sensitive Detection of the Interaction of Human Papillomavirus Virus-Like Particles with Yeast Whole Cell RNA Using Biolayer Interferometry. Biotechnol J 2018; 14:e1800303. [PMID: 30076738 DOI: 10.1002/biot.201800303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/21/2018] [Indexed: 11/06/2022]
Abstract
RNA is a potential contaminant encountered in the production of recombinant yeast products such as proteins and virus-like particles (VLPs) and can be a particular concern when RNA associates with the product of interest. In this study a method to monitor and quantify the interaction of RNA with yeast-expressed human papillomavirus (HPV) VLPs using biolayer interferometry (BLI) is developed. Both biosensors with immobilized VLPs as well as biosensors with immobilized RNA are tested. Two types of recombinantly expressed HPV VLPs are used, Type 18 and Type 11. The data show that yeast whole cell RNA associates with Type 18 but not with Type 11 (maximum binding signal of 0.20 ± 0.02 nm on immobilized VLP probes for Type 18 vs. 0.03 ± 0.01 nm for Type 11). Additionally, the results show that a higher ionic strength weakens the affinity by both decreasing the association rate and increasing the dissociation rate, resulting in the dissociation constant increasing from 0.48 × 10-9 to 2.1 × 10-9 M, with phosphate ions having a greater effect on the reduction of association compared to chloride ions.
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Affiliation(s)
- Yiran Wang
- Department of Chemical Engineering, University of Virginia, 102 Engineers' Way, 22904, Charlottesville, Virginia
| | - Giorgio Carta
- Department of Chemical Engineering, University of Virginia, 102 Engineers' Way, 22904, Charlottesville, Virginia
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21
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Giraud L, Viricel W, Leblond J, Giasson S. Single stranded siRNA complexation through non-electrostatic interactions. Biomaterials 2017; 113:230-242. [DOI: 10.1016/j.biomaterials.2016.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/19/2016] [Accepted: 10/23/2016] [Indexed: 11/24/2022]
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22
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Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R. Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. Biophys J 2016; 111:2077-2085. [PMID: 27851933 PMCID: PMC5113152 DOI: 10.1016/j.bpj.2016.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/25/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022] Open
Abstract
Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with nonrepeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. To test whether a branched polymer model can estimate the overall sizes of large RNAs, we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long noncoding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation-one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of maximum ladder distance. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low ionic-strength sizes. These results suggest that sizes of long RNA molecules are determined by the branching pattern of their secondary structures. We also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs.
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Affiliation(s)
- Alexander Borodavka
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Surendra W Singaram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter G Stockley
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Avinoam Ben-Shaul
- The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roman Tuma
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
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23
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Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res 2016; 45:926-937. [PMID: 27625389 PMCID: PMC5314786 DOI: 10.1093/nar/gkw787] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 07/29/2016] [Accepted: 08/20/2016] [Indexed: 11/21/2022] Open
Abstract
Transfer RNA (tRNA) links messenger RNA nucleotide sequence with amino acid sequence during protein synthesis. Despite the importance of tRNA for translation, its subcellular distribution and diffusion properties in live cells are poorly understood. Here, we provide the first direct report on tRNA diffusion localization in live bacteria. We internalized tRNA labeled with organic fluorophores into live bacteria, applied single-molecule fluorescence imaging with single-particle tracking and localized and tracked single tRNA molecules over seconds. We observed two diffusive species: fast (with a diffusion coefficient of ∼8 μm2/s, consistent with free tRNA) and slow (consistent with tRNA bound to larger complexes). Our data indicate that a large fraction of internalized fluorescent tRNA (>70%) appears to diffuse freely in the bacterial cell. We also obtained the subcellular distribution of fast and slow diffusing tRNA molecules in multiple cells by normalizing for cell morphology. While fast diffusing tRNA is not excluded from the bacterial nucleoid, slow diffusing tRNA is localized to the cell periphery (showing a 30% enrichment versus a uniform distribution), similar to non-uniform localizations previously observed for mRNA and ribosomes.
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Affiliation(s)
- Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
| | - Ian Farrell
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA.,Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Zeev Smilansky
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
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24
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Guo J, Lian X, Zhong J, Wang T, Zhang G. Length-dependent translation initiation benefits the functional proteome of human cells. MOLECULAR BIOSYSTEMS 2016; 11:370-8. [PMID: 25353704 DOI: 10.1039/c4mb00462k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We previously found that shorter mRNAs are preferably translated in various eukaryotic cells. However, the theoretical basis of this phenomenon is unclear. We hypothesize that shorter mRNA length correlates to the decreased translational error rate to reduce the energy consumption on defective protein degradation. In this study, we established a computational model to explain the length-dependent translation initiation efficiency. We provided mathematical evidence that this translational preference, rather than the protein degradation, is a major factor to shape the genome-wide length-dependent protein abundance. As deducted, we simulated that shorter mRNA length is a determinant of initiation circularization time. Furthermore, our model unveiled that preferentially translating shorter mRNAs benefits the energy efficiency on the proteome functionality. We proposed that cancer cells tend to hijack this evolutionary mechanism by counteracting the higher translational error rate. In conclusion, our model provides insights into the nature of the global length-dependent translational control and its biological significance.
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Affiliation(s)
- Jieming Guo
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou 510632, China.
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25
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Berasaluce A, Matthys L, Mujika J, Antoñana-Díez M, Valero A, Agirregabiria M. Bead beating-based continuous flow cell lysis in a microfluidic device. RSC Adv 2015. [DOI: 10.1039/c5ra01251a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This paper describes a bead beating-based miniaturized cell lysis device that works in continuous flow allowing the analysis of large volumes of samples without previous treatment.
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Affiliation(s)
- A. Berasaluce
- CIC-Microgune
- Polo Garaia
- 20500 Arrasate
- Spain
- IK4-Ikerlan
| | - L. Matthys
- IK4-Ikerlan
- Polo Garaia
- 20500 Arrasate
- Spain
| | - J. Mujika
- IK4-Ikerlan
- Polo Garaia
- 20500 Arrasate
- Spain
| | | | - A. Valero
- CIC-Microgune
- Polo Garaia
- 20500 Arrasate
- Spain
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26
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Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin J. Rate-limiting steps in yeast protein translation. Cell 2013; 153:1589-601. [PMID: 23791185 PMCID: PMC3694300 DOI: 10.1016/j.cell.2013.05.049] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 02/11/2013] [Accepted: 05/29/2013] [Indexed: 12/04/2022]
Abstract
Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We leverage these data to parameterize a computational model of translation, keeping track of every ribosome, tRNA, and mRNA molecule in a yeast cell. We determine the parameter regimes in which fast initiation or high codon bias in a transgene increases protein yield and infer the initiation rates of endogenous Saccharomyces cerevisiae genes, which vary by several orders of magnitude and correlate with 5′ mRNA folding energies. Our model recapitulates the previously reported 5′-to-3′ ramp of decreasing ribosome densities, although our analysis shows that this ramp is caused by rapid initiation of short genes rather than slow codons at the start of transcripts. We conclude that protein production in healthy yeast cells is typically limited by the availability of free ribosomes, whereas protein production under periods of stress can sometimes be rescued by reducing initiation or elongation rates. Computational model of translation tracks all ribosomes, tRNAs, and mRNAs in a cell Translation is generally limited by initiation, not elongation Model allows inference of initiation rates for all yeast genes Ramp of 5′ ribosomes is caused by rapid initiation of short genes
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Affiliation(s)
- Premal Shah
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yang Ding
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Malwina Niemczyk
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH3 9LP, UK
| | - Grzegorz Kudla
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH3 9LP, UK
| | - Joshua B. Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
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27
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Tjong V, Yu H, Hucknall A, Chilkoti A. Direct fluorescence detection of RNA on microarrays by surface-initiated enzymatic polymerization. Anal Chem 2012. [PMID: 23194025 DOI: 10.1021/ac303132j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the first demonstration of surface-initiated enzymatic polymerization (SIEP) for the direct detection of RNA in a fluorescence microarray format. This new method incorporates multiple fluorophores into an RNA strand using the two-step sequential and complementary reactions catalyzed by yeast poly(A) polymerase (PaP) to incorporate deoxyadenosine triphosphate (dATP) at the 3'-OH of an RNA molecule, followed by terminal deoxynucleotidyl transferase (TdT) to catalyze the sequential addition of a mixture of natural and fluorescent deoxynucleotides (dNTPs) at the 3'-OH of an RNA-DNA hybrid. We found that the 3'-end of RNA can be efficiently converted into DNA (∼50% conversion) by polymerization of dATP using yeast PaP, and the short DNA strand appended to the end of the RNA by PaP acts as the initiator for the TdT-catalyzed polymerization of longer DNA strands from a mixture of natural and fluorescent dNTPs that contain up to ∼45 Cy3 fluorophores per 1 kb DNA. We obtained an ∼2 pM limit of detection (LOD) and a 3 log-linear dynamic range for hybridization of a short 21 base-long RNA target to an immobilized peptide nucleic acid probe, while fragmented mRNA targets from three different full length mRNA transcripts yielded a ∼10 pM LOD with a similar dynamic range in a microarray format.
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Affiliation(s)
- Vinalia Tjong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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28
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Kalwarczyk T, Tabaka M, Holyst R. Biologistics--diffusion coefficients for complete proteome of Escherichia coli. ACTA ACUST UNITED AC 2012; 28:2971-8. [PMID: 22942021 PMCID: PMC3496334 DOI: 10.1093/bioinformatics/bts537] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Motivation: Biologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type. Results: We demonstrate a method for the determination of in vivo DCs for any molecule—regardless of its molecular weight, size and structure—in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. Contact:rholyst@ichf.edu.pl Supplementary information:Supplementary data are available at Bioinformatics Online.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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29
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Roy S, Soh JH, Gao Z. A microfluidic-assisted microarray for ultrasensitive detection of miRNA under an optical microscope. LAB ON A CHIP 2011; 11:1886-94. [PMID: 21526238 DOI: 10.1039/c0lc00638f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this article, we report on direct detection of microRNAs (miRNAs) on a microarray by differential interference contrast (DIC) imaging technique. While the best resolution achieved with a fluorescence scanner is ∼1 μm, the DIC imaging technique adopted in our study offers the possibility of imaging individual reporting gold nanoparticles, or, in other words, individual miRNA strands. Due to its unrivalled resolution, the present technique could detect as low as 300 copies of target miRNAs in a sample volume of 1.0 μl. With the greatly improved sensitivity, the amount of total RNA needed in the assay is reduced to only a few nanograms, offering an excellent opportunity for fast and direct miRNA profiling without engaging any labeling and amplification procedure. Expression patterns of hsa-let-7 family members in healthy versus cancer cells analyzed on our microarray, are found to be consistent with the patterns obtained on a commercial microarray and those reported in the literature.
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Affiliation(s)
- Somenath Roy
- Institute of Bioengineering and Nanotechnology, the Nanos, Singapore
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