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Article ; Online: 3D RNA-scaffolded wireframe origami.

Parsons, Molly F / Allan, Matthew F / Li, Shanshan / Shepherd, Tyson R / Ratanalert, Sakul / Zhang, Kaiming / Pullen, Krista M / Chiu, Wah / Rouskin, Silvi / Bathe, Mark

Nature communications

2023 Volume 14, Issue 1, Page(s) 382

Abstract: Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, ... ...

Abstract	Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
MeSH term(s)	Nanotechnology/methods ; RNA ; Cryoelectron Microscopy ; Nucleic Acid Conformation ; Nanostructures/chemistry ; RNA, Messenger
Chemical Substances	RNA (63231-63-0) ; RNA, Messenger
Language	English
Publishing date	2023-01-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36156-1
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Article ; Online: Random access DNA memory using Boolean search in an archival file storage system.

Banal, James L / Shepherd, Tyson R / Berleant, Joseph / Huang, Hellen / Reyes, Miguel / Ackerman, Cheri M / Blainey, Paul C / Bathe, Mark

Nature materials

2021 Volume 20, Issue 9, Page(s) 1272–1280

Abstract: DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were ... ...

Abstract	DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 10
MeSH term(s)	Archives ; DNA/chemistry ; Fluorescence ; Information Storage and Retrieval ; Plasmids ; Polymerase Chain Reaction ; Silicon Dioxide/chemistry ; Synthetic Biology
Chemical Substances	Silicon Dioxide (7631-86-9) ; DNA (9007-49-2)
Language	English
Publishing date	2021-06-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2088679-2
ISSN	1476-4660 ; 1476-1122
ISSN (online)	1476-4660
ISSN	1476-1122
DOI	10.1038/s41563-021-01021-3
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Article ; Online: Bioproduction of pure, kilobase-scale single-stranded DNA.

Shepherd, Tyson R / Du, Rebecca R / Huang, Hellen / Wamhoff, Eike-Christian / Bathe, Mark

Scientific reports

2019 Volume 9, Issue 1, Page(s) 6121

Abstract: Scalable production of kilobase single-stranded DNA (ssDNA) with sequence control has applications in therapeutics, gene synthesis and sequencing, scaffolded DNA origami, and archival DNA memory storage. Biological production of circular ssDNA (cssDNA) ... ...

Abstract	Scalable production of kilobase single-stranded DNA (ssDNA) with sequence control has applications in therapeutics, gene synthesis and sequencing, scaffolded DNA origami, and archival DNA memory storage. Biological production of circular ssDNA (cssDNA) using M13 addresses these needs at low cost. However, one unmet goal is to minimize the essential protein coding regions of the exported DNA while maintaining its infectivity and production purity to produce sequences less than 3,000 nt in length, relevant to therapeutic and materials science applications. Toward this end, synthetic miniphage with inserts of custom sequence and size offers scalable, low-cost synthesis of cssDNA at milligram and higher scales. Here, we optimize growth conditions using an E. coli helper strain combined with a miniphage genome carrying only an f1 origin and a β-lactamase-encoding (bla) antibiotic resistance gene, enabling isolation of pure cssDNA with a minimum sequence genomic length of 1,676 nt, without requiring additional purification from contaminating DNA. Low-cost scalability of isogenic, custom-length cssDNA is demonstrated for a sequence of 2,520 nt using a bioreactor, purified with low endotoxin levels (<5 E.U./ml). We apply these exonuclease-resistant cssDNAs to the self-assembly of wireframe DNA origami objects and to encode digital information on the miniphage genome for biological amplification.
MeSH term(s)	Bacteriophage M13/genetics ; Bioreactors/economics ; Bioreactors/virology ; DNA, Single-Stranded/biosynthesis ; DNA, Single-Stranded/isolation & purification ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli/virology ; Industrial Microbiology/economics ; Industrial Microbiology/methods ; Nanotechnology/economics ; Nanotechnology/methods ; Plasmids/genetics
Chemical Substances	DNA, Single-Stranded
Language	English
Publishing date	2019-04-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-42665-1
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Article ; Online: Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction.

Liu, Xu / Golden, Lisa C / Lopez, Josue A / Shepherd, Tyson R / Yu, Liping / Fuentes, Ernesto J

Biophysical journal

2019 Volume 116, Issue 12, Page(s) 2314–2330

Abstract: Molecular recognition is critical for the fidelity of signal transduction in biology. Conversely, the disruption of protein-protein interactions can lead to disease. Thus, comprehension of the molecular determinants of specificity is essential for ... ...

Abstract	Molecular recognition is critical for the fidelity of signal transduction in biology. Conversely, the disruption of protein-protein interactions can lead to disease. Thus, comprehension of the molecular determinants of specificity is essential for understanding normal biological signaling processes and for the development of precise therapeutics. Although high-resolution structures have provided atomic details of molecular interactions, much less is known about the influence of cooperativity and conformational dynamics. Here, we used the Tiam2 PSD-95/Dlg/ZO-1 (PDZ) domain and a quadruple mutant (QM), engineered by swapping the identity of four residues important for specificity in the Tiam1 PDZ into the Tiam2 PDZ domain, as a model system to investigate the role of cooperativity and dynamics in PDZ ligand specificity. Surprisingly, equilibrium binding experiments found that the ligand specificity of the Tiam2 QM was switched to that of the Tiam1 PDZ. NMR-based studies indicated that Tiam2 QM PDZ, but not other mutants, had extensive microsecond to millisecond motions distributed throughout the entire domain suggesting structural cooperativity between the mutated residues. Thermodynamic analyses revealed energetic cooperativity between residues in distinct specificity subpockets that was dependent upon the identity of the ligand, indicating a context-dependent binding mechanism. Finally, isothermal titration calorimetry experiments showed distinct entropic signatures along the mutational trajectory from the Tiam2 wild-type to the QM PDZ domain. Collectively, our studies provide unique insights into how structure, conformational dynamics, and thermodynamics combine to modulate ligand-binding specificity and have implications for the evolution, regulation, and design of protein-ligand interactions.
MeSH term(s)	Amino Acid Sequence ; Ligands ; Models, Molecular ; Mutation ; Protein Binding ; Protein Domains ; Substrate Specificity ; T-Lymphoma Invasion and Metastasis-inducing Protein 1/chemistry ; T-Lymphoma Invasion and Metastasis-inducing Protein 1/genetics ; T-Lymphoma Invasion and Metastasis-inducing Protein 1/metabolism ; Thermodynamics
Chemical Substances	Ligands ; T-Lymphoma Invasion and Metastasis-inducing Protein 1
Language	English
Publishing date	2019-05-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2019.05.008
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Article ; Online: Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.

Arrieta-Ortiz, Mario L / Pan, Min / Kaur, Amardeep / Pepper-Tunick, Evan / Srinivas, Vivek / Dash, Ananya / Immanuel, Selva Rupa Christinal / Brooks, Aaron N / Shepherd, Tyson R / Baliga, Nitin S

mSystems

2022 Volume 8, Issue 1, Page(s) e0090422

Abstract: There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant ( ... ...

Abstract	There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (Tet
MeSH term(s)	Escherichia coli/genetics ; Tetracycline Resistance/genetics ; Sertraline/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Tetracycline/pharmacology ; Bacterial Outer Membrane Proteins/pharmacology ; Repressor Proteins/pharmacology ; Escherichia coli Proteins/genetics
Chemical Substances	Sertraline (QUC7NX6WMB) ; Anti-Bacterial Agents ; Tetracycline (F8VB5M810T) ; arcA protein, E coli ; Bacterial Outer Membrane Proteins ; Repressor Proteins ; Escherichia coli Proteins
Language	English
Publishing date	2022-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00904-22
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Article ; Online: In vitro synthesis of gene-length single-stranded DNA.

Veneziano, Rémi / Shepherd, Tyson R / Ratanalert, Sakul / Bellou, Leila / Tao, Chaoqun / Bathe, Mark

Scientific reports

2018 Volume 8, Issue 1, Page(s) 6548

Abstract: Single-stranded DNA (ssDNA) increases the likelihood of homology directed repair with reduced cellular toxicity. However, ssDNA synthesis strategies are limited by the maximum length attainable, ranging from a few hundred nucleotides for chemical ... ...

Abstract	Single-stranded DNA (ssDNA) increases the likelihood of homology directed repair with reduced cellular toxicity. However, ssDNA synthesis strategies are limited by the maximum length attainable, ranging from a few hundred nucleotides for chemical synthesis to a few thousand nucleotides for enzymatic synthesis, as well as limited control over nucleotide composition. Here, we apply purely enzymatic synthesis to generate ssDNA greater than 15 kilobases (kb) using asymmetric PCR, and illustrate the incorporation of diverse modified nucleotides for therapeutic and theranostic applications.
MeSH term(s)	DNA, Single-Stranded/chemical synthesis ; Nucleotides/chemistry ; Polymerase Chain Reaction/methods
Chemical Substances	DNA, Single-Stranded ; Nucleotides
Language	English
Publishing date	2018-04-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-24677-5
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Article ; Online: Structural and thermodynamic analysis of PDZ-ligand interactions.

Shepherd, Tyson R / Fuentes, Ernesto J

Methods in enzymology

2010 Volume 488, Page(s) 81–100

Abstract: Tiam-family guanine exchange proteins are activators of the Rho GTPase Rac1 and critical for cell morphology, adhesion, migration, and polarity. These modular proteins contain a variety of signaling domains, including a single postsynaptic density-95/ ... ...

Abstract	Tiam-family guanine exchange proteins are activators of the Rho GTPase Rac1 and critical for cell morphology, adhesion, migration, and polarity. These modular proteins contain a variety of signaling domains, including a single postsynaptic density-95/discs large/zonula occludens-1 (PDZ) domain. Here, we show how structural and thermodynamic approaches applied to the Tiam1 PDZ domain can be used to gain unique insights into the affinity and specificity of PDZ-ligand interactions with peptides derived from Syndecan1 and Caspr4 proteins. First, we describe a fluorescence anisotropy-based assay that can be used to determine PDZ-ligand interactions, and describe important considerations in designing binding experiments. Second, we used site-specific mutagenesis in combination with double-mutant cycle analysis to probe the binding energetics and cooperativity of residues in two ligand binding pockets (S(0) and S(-2)) that are involved in Tiam1 PDZ-ligand interactions. Peptide ligand binding results and double-mutant cycle analysis revealed that the S(0) pocket was important for Syndecan1 and Caspr4 peptide interactions and that the S(-2) pocket provided selectivity for the Syndecan1 ligand. Finally, we devised a "peptide evolution" strategy whereby a Model consensus peptide was "evolved" into either the Syndecan1 or Caspr4 peptide by site-directed mutagenesis. These results corroborated the PDZ mutational analysis of the S(0) pocket and identified the P(-4) position in the ligand as critical for Syndecan1 affinity and selectivity. Together, these studies show that a combined structural and thermodynamic approach is powerful for obtaining insights into the origin of Tiam1 PDZ-ligand domain affinity and specificity.
MeSH term(s)	Amino Acid Sequence ; Binding Sites ; Fluorescence Polarization ; Guanine Nucleotide Exchange Factors/chemistry ; Guanine Nucleotide Exchange Factors/metabolism ; Humans ; Ligands ; Molecular Sequence Data ; PDZ Domains ; Peptides/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; T-Lymphoma Invasion and Metastasis-inducing Protein 1 ; Thermodynamics
Chemical Substances	Guanine Nucleotide Exchange Factors ; Ligands ; Peptides ; T-Lymphoma Invasion and Metastasis-inducing Protein 1 ; TIAM1 protein, human
Language	English
Publishing date	2010-12-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/B978-0-12-381268-1.00004-5
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Article ; Online: Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges.

Jun, Hyungmin / Shepherd, Tyson R / Zhang, Kaiming / Bricker, William P / Li, Shanshan / Chiu, Wah / Bathe, Mark

ACS nano

2019 Volume 13, Issue 2, Page(s) 2083–2093

Abstract: 3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design ... ...

Abstract	3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. In order to test its generality, we apply TALOS to design an in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.
MeSH term(s)	Algorithms ; Automation ; DNA/chemistry ; Nanoparticles/chemistry ; Nucleic Acid Conformation ; Particle Size
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2019-01-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.8b08671
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Article ; Online: Role of nanoscale antigen organization on B-cell activation probed using DNA origami.

Veneziano, Rémi / Moyer, Tyson J / Stone, Matthew B / Wamhoff, Eike-Christian / Read, Benjamin J / Mukherjee, Sayak / Shepherd, Tyson R / Das, Jayajit / Schief, William R / Irvine, Darrell J / Bathe, Mark

Nature nanotechnology

2020 Volume 15, Issue 8, Page(s) 716–723

Abstract: Vaccine efficacy can be increased by arraying immunogens in multivalent form on virus-like nanoparticles to enhance B-cell activation. However, the effects of antigen copy number, spacing and affinity, as well as the dimensionality and rigidity of ... ...

Abstract	Vaccine efficacy can be increased by arraying immunogens in multivalent form on virus-like nanoparticles to enhance B-cell activation. However, the effects of antigen copy number, spacing and affinity, as well as the dimensionality and rigidity of scaffold presentation on B-cell activation remain poorly understood. Here, we display the clinical vaccine immunogen eOD-GT8, an engineered outer domain of the HIV-1 glycoprotein-120, on DNA origami nanoparticles to systematically interrogate the impact of these nanoscale parameters on B-cell activation in vitro. We find that B-cell signalling is maximized by as few as five antigens maximally spaced on the surface of a 40-nm viral-like nanoparticle. Increasing antigen spacing up to ~25-30 nm monotonically increases B-cell receptor activation. Moreover, scaffold rigidity is essential for robust B-cell triggering. These results reveal molecular vaccine design principles that may be used to drive functional B-cell responses.
MeSH term(s)	AIDS Vaccines ; Animals ; Antigens, Viral/chemistry ; Antigens, Viral/immunology ; Antigens, Viral/ultrastructure ; B-Lymphocytes/immunology ; Cell Line ; DNA/chemistry ; DNA/ultrastructure ; Female ; HIV Envelope Protein gp120/chemistry ; HIV Envelope Protein gp120/immunology ; Lymphocyte Activation/immunology ; Mice ; Nanostructures/chemistry ; Nanostructures/ultrastructure ; Nucleic Acid Conformation ; Signal Transduction
Chemical Substances	AIDS Vaccines ; Antigens, Viral ; HIV Envelope Protein gp120 ; gp120 protein, Human immunodeficiency virus 1 ; DNA (9007-49-2)
Keywords	covid19
Language	English
Publishing date	2020-06-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2254964-X
ISSN	1748-3395 ; 1748-3387
ISSN (online)	1748-3395
ISSN	1748-3387
DOI	10.1038/s41565-020-0719-0
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Article ; Online: De novo design and synthesis of a 30-cistron translation-factor module.

Shepherd, Tyson R / Du, Liping / Liljeruhm, Josefine / Samudyata / Wang, Jinfan / Sjödin, Marcus O D / Wetterhall, Magnus / Yomo, Tetsuya / Forster, Anthony C

Nucleic acids research

2017 Volume 45, Issue 18, Page(s) 10895–10905

Abstract: Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to ... ...

Abstract	Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0.
MeSH term(s)	Genes, Synthetic ; Plasmids/genetics ; Protein Biosynthesis ; Ribosomal Proteins/genetics ; Transcription, Genetic
Chemical Substances	Ribosomal Proteins
Language	English
Publishing date	2017-10-13
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx753
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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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