Works (66)

Updated: September 20th, 2024 05:00

2024 journal article

A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria

MOLECULAR CELL, 84(14).

By: J. Vento n, D. Durmusoglu n, T. Li n, C. Patinios*, S. Sullivan n, F. Ttofali n, J. Schaik n, Y. Yu* ...

Sources: Web Of Science, NC State University Libraries
Added: September 16, 2024

2024 article

Expanding the flexibility of base editing for high-throughput genetic screens in bacteria

Gawlitt, S., Collins, S. P., Yu, Y., Blackman, S. A., Barquist, L., & Beisel, C. L. (2024, March 18). NUCLEIC ACIDS RESEARCH.

By: S. Gawlitt*, S. Collins n, Y. Yu*, S. Blackman n, L. Barquist* & C. Beisel*

Source: Web Of Science
Added: April 1, 2024

2023 article

Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation

Wimmer, F., Englert, F., Wandera, K. G., Alkhnbashi, O. S., Collins, S. P., Backofen, R., & Beisel, C. L. (2023, November 28). NUCLEIC ACIDS RESEARCH.

TL;DR: Investigation of extensive self-targeting by two CRISPR-Cas systems encoding 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans shows that the native I-C and I-F1 systems are actively expressed and that CRISPR RNAs are properly processed. (via Semantic Scholar)
Source: Web Of Science
Added: December 18, 2023

2023 journal article

Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria

NATURE COMMUNICATIONS, 14(1).

By: D. Collias*, E. Vialetto*, J. Yu*, K. Co*, E. Almasi, A. Ruettiger, T. Achmedov*, T. Strowig*, C. Beisel n

TL;DR: It is shown that systematically attenuating DNA targeting activity enables RecA-mediated repair in different bacteria, allowing chromosomal cleavage to drive genome editing. (via Semantic Scholar)
Source: Web Of Science
Added: July 3, 2023

2022 journal article

A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13

CELL HOST & MICROBE, 30(8), 1151-+.

MeSH headings : Autoimmunity / genetics; Bacteriophages / genetics; CRISPR-Cas Systems; Plasmids; RNA
TL;DR: It was found that endogenous non-essential transcripts targeted by crRNAs rarely elicited autoimmunity, and target expression levels were established as an additional criterion for immune defense by RNA-targeting CRISPR-Cas systems, preventing autoIMmunity and distinguishing pathogenic and benign invaders. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: November 21, 2022

2021 review

CRISPR technologies and the search for the PAM-free nuclease

[Review of ]. NATURE COMMUNICATIONS, 12(1).

By: D. Collias n & C. Beisel n

MeSH headings : Binding Sites / genetics; CRISPR-Associated Protein 9 / classification; CRISPR-Associated Protein 9 / genetics; CRISPR-Associated Protein 9 / metabolism; CRISPR-Cas Systems; Gene Editing / methods; Models, Genetic; Nucleotide Motifs; Phylogeny; Protein Engineering / methods; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / metabolism
Source: Web Of Science
Added: February 22, 2021

2021 article

Coupling smartphone and CRISPR-Cas12a for digital and multiplexed nucleic acid detection

Yu, T., Zhang, S., Matei, R., Marx, W., Beisel, C. L., & Wei, Q. (2021, July 23). AICHE JOURNAL, Vol. 7.

By: T. Yu n, S. Zhang n, R. Matei*, W. Marx n, C. Beisel n & Q. Wei n

author keywords: Cas12a; CRISPR diagnostics; digital assay; point-of-care diagnostics; smartphone device
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 2, 2021

2021 journal article

In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii

ACS SYNTHETIC BIOLOGY, 10(5), 1039–1052.

By: D. Durmusoglu n, I. Al'Abri n, S. Collins n, J. Cheng n, A. Eroglu n, C. Beisel n, N. Crook n

author keywords: Saccharomyces boulardii; probiotic engineering; metabolic engineering; colonization profile; in situ production; beta-carotene
MeSH headings : Animals; Antineoplastic Agents / metabolism; CRISPR-Cas Systems; Feces / chemistry; Female; Gastrointestinal Microbiome; Gastrointestinal Tract / metabolism; Gastrointestinal Tract / microbiology; Gene Editing / methods; Gene Expression; Indoles / metabolism; Male; Metabolic Engineering / methods; Mice; Mice, Inbred C57BL; Microorganisms, Genetically-Modified; Multigene Family; Plasmids / genetics; Probiotics / metabolism; Promoter Regions, Genetic; Provitamins / biosynthesis; Saccharomyces boulardii / genetics; Saccharomyces boulardii / metabolism; Saccharomyces cerevisiae / genetics; beta Carotene / biosynthesis
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 6, 2021

2021 journal article

Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch

NUCLEIC ACIDS RESEARCH, 49(5), 2985–2999.

By: S. Collins n, W. Rostain*, C. Liao* & C. Beisel n

MeSH headings : CRISPR-Associated Proteins / metabolism; CRISPR-Cas Systems; DNA / chemistry; Endodeoxyribonucleases / metabolism; Escherichia coli / genetics; Phosphotransferases (Alcohol Group Acceptor) / genetics; Protein Biosynthesis; RNA / chemistry; RNA / metabolism; RNA, Messenger / metabolism; Transcription, Genetic
TL;DR: The design framework thus further enables tethering of CRISPR activities to cellular states and could be designed to sense endogenous RNAs expressed only under specific growth conditions, rendering Cas12a targeting activity dependent on cellular metabolism and stress. (via Semantic Scholar)
Source: Web Of Science
Added: June 10, 2021

2020 journal article

A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9

SCIENCE ADVANCES, 6(29).

By: D. Collias n, R. Leenay n, R. Slotkowski n, Z. Zuo*, S. Collins n, B. McGirr n, J. Liu*, C. Beisel n

TL;DR: It is reported that SpyCas9 also recognizes sequences within an N(A/C/T)GG motif, which could have implications for precise editing, off-target predictions, and CRISPR-based immunity. (via Semantic Scholar)
Source: Web Of Science
Added: August 10, 2020

2020 journal article

Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs

NUCLEIC ACIDS RESEARCH, 48(10), 5624–5638.

By: T. Jacobsen n, F. Ttofali n, C. Liao*, S. Manchalu*, B. Gray* & C. Beisel n

MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / classification; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; CRISPR-Associated Proteins / chemistry; CRISPR-Associated Proteins / classification; CRISPR-Associated Proteins / genetics; CRISPR-Associated Proteins / metabolism; DNA Cleavage; Endodeoxyribonucleases / chemistry; Endodeoxyribonucleases / classification; Endodeoxyribonucleases / genetics; Endodeoxyribonucleases / metabolism; HEK293 Cells; Humans; Mutation; Phylogeny; Prevotella / enzymology; Protein Biosynthesis; Protein Domains; Transcription, Genetic
TL;DR: Cas12a nucleases therefore can exhibit widely varying properties between otherwise related orthologs, suggesting selective pressure to diversify PAM recognition and supporting expansion of the CRISPR toolbox through ortholog mining and PAM engineering. (via Semantic Scholar)
Source: Web Of Science
Added: October 5, 2020

2020 journal article

Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 86(7).

author keywords: lactic acid bacteria; bioprotection; food spoilage; manganese starvation; genome editing; Lactobacillus
MeSH headings : Cultured Milk Products / microbiology; Food Microbiology; Fungi / physiology; Lactobacillus / physiology; Yeasts / physiology
TL;DR: Manganese scavenging emerges as a common trait within the Lactobacillus genus, but differences in expression result in some strains showing more bioprotective effect than others, which constitutes an attractive alternative to artificial preservation. (via Semantic Scholar)
Source: Web Of Science
Added: April 20, 2020

2020 article

Methods for characterizing, applying, and teaching CRISPR-Cas systems

Beisel, C. L. (2020, February 1). METHODS, Vol. 172, pp. 1–2.

By: C. Beisel n

MeSH headings : Bacteria / genetics; CRISPR-Cas Systems / genetics; Gene Editing / methods; Molecular Biology / education; Molecular Biology / methods; Teaching
UN Sustainable Development Goal Categories
4. Quality Education (OpenAlex)
Source: Web Of Science
Added: April 6, 2020

2020 journal article

Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

PLOS ONE, 15(4).

By: T. Jacobsen n, G. Yi n, H. Al Asafen n, A. Jermusyk n, C. Beisel n & G. Reeves n

MeSH headings : Animals; Drosophila / genetics; Eukaryota / genetics; Eukaryota / metabolism; Eukaryotic Cells / metabolism; Gene Expression / genetics; Gene Expression / physiology; Gene Expression Regulation / genetics; Gene Expression Regulation / physiology; Genetic Engineering / methods; Nucleic Acid Conformation; Proof of Concept Study; RNA, Catalytic / genetics; RNA, Catalytic / physiology; RNA, Messenger / metabolism; Synthetic Biology / methods
Source: Web Of Science
Added: June 22, 2020

2020 article

Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination

Collins, S. P., & Beisel, C. L. (2020, September 3). MOLECULAR CELL, Vol. 79, pp. 703–704.

By: S. Collins n & C. Beisel n

MeSH headings : CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Cytosine; DNA, Single-Stranded; Deamination; Gene Editing
TL;DR: Jin et al. (2020) engineered new variants of CRISPR base editors that make precise genomic edits in rice protoplasts while minimizing untargeted mutagenesis. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Source: Web Of Science
Added: October 12, 2020

2019 journal article

An educational module to explore CRISPR technologies with a cell-free transcription-translation system

SYNTHETIC BIOLOGY, 4(1).

By: D. Collias n, R. Marshall*, S. Collins n, C. Beisel* & V. Noireaux*

author keywords: CRISPR; Cas9; education modules; synthetic biology; TXTL
TL;DR: Three educational modules intended to expose undergraduate students to CRISPR technologies using TXTL are described and are expected to allow students to experience the power and promise of CRISpr technologies in the classroom and to engage with their instructor and peers about the opportunities and potential risks for society. (via Semantic Scholar)
Source: Web Of Science
Added: February 27, 2020

2019 journal article

An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system

METHODS, 172, 42–50.

By: K. Wandera*, S. Collins n, F. Wimmer*, R. Marshall*, V. Noireaux* & C. Beisel n

author keywords: Anti-CRISPR proteins; Cas9; Genome editing; sgRNA; TXTL
MeSH headings : Bacteriophages / metabolism; CRISPR-Associated Protein 9 / antagonists & inhibitors; CRISPR-Associated Protein 9 / metabolism; CRISPR-Cas Systems / genetics; Enzyme Assays / instrumentation; Enzyme Assays / methods; Escherichia coli / enzymology; Escherichia coli / genetics; Escherichia coli / immunology; Escherichia coli / virology; Escherichia coli Proteins / antagonists & inhibitors; Escherichia coli Proteins / metabolism; Fluorescence; Gene Editing / methods; Genes, Reporter / genetics; Green Fluorescent Proteins / chemistry; Green Fluorescent Proteins / genetics; Host-Pathogen Interactions / genetics; Host-Pathogen Interactions / immunology; Protein Biosynthesis; Transcription, Genetic; Viral Proteins / metabolism
TL;DR: This work reports a rapid and scalable method for characterizing putative Acrs against Cas nucleases using an E. coli-derived cell-free transcription-translation system and demonstrates how the method can be used to measure the inhibitory activity of individual Acrs in under two days. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: April 6, 2020

2019 review

Barriers to genome editing with CRISPR in bacteria

[Review of ]. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 46(9-10), 1327–1341.

By: J. Vento n, N. Crook n & C. Beisel n

author keywords: Bacteria; Nuclease; Genome editing; CRISPR; Recombineering
MeSH headings : Bacteria / genetics; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; Humans
TL;DR: Existing barriers to implementing CRISPR-based editing across diverse bacterial species are analyzed and guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains are offered. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 28, 2019

2019 article

CRATES: A one-step assembly method for Class 2 CRISPR arrays

TUMOR IMMUNOLOGY AND IMMUNOTHERAPY - MOLECULAR METHODS, Vol. 629, pp. 493–511.

By: C. Liao*, R. Slotkowski n & C. Beisel*

MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA Cleavage; Escherichia coli / genetics; Gene Editing / methods; Plasmids / genetics
TL;DR: The cloning method CRATES (CRISPR Assembly through Trimmed Ends of Spacers) is reported, expected to simplify the study of natural CRISPR arrays and facilitate multiplexed targeting with programmable nucleases from Class 2 Cas nucleases across the myriad applications of CRISpr technologies. (via Semantic Scholar)
Source: Web Of Science
Added: June 29, 2020

2019 journal article

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

BIOTECHNOLOGY AND BIOENGINEERING, 116(5), 1139–1151.

By: A. Westbrook*, X. Tang*, R. Marshall*, C. Maxwell n, J. Chappell*, D. Agrawal*, M. Dunlop*, V. Noireaux* ...

author keywords: Bayesian methods; CRISPRi; model-guided design; RNA-based circuits; sRNA
MeSH headings : CRISPR-Cas Systems; Cell-Free System / chemistry; Cell-Free System / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats; Models, Chemical; RNA / chemistry; RNA / metabolism; Transcription, Genetic; Transcriptional Activation
TL;DR: This work individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and CRISPR interference (CRISPRi), and shows how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: April 15, 2019

2019 journal article

Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis

NATURE COMMUNICATIONS, 10.

By: C. Liao n, F. Ttofali n, R. Slotkowski n, S. Denny n, T. Cecil n, R. Leenay n, A. Keung n, C. Beisel*

MeSH headings : Base Sequence; CRISPR-Associated Proteins / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA / genetics; Endonucleases / metabolism; Gene Library; Genetic Techniques; HEK293 Cells; Humans; Nucleic Acid Conformation; Plasmids / metabolism; RNA / biosynthesis; RNA, Messenger / genetics; RNA, Messenger / metabolism; Saccharomyces cerevisiae / metabolism
TL;DR: A modular, one-pot scheme called CRATES to construct CRISPR arrays and array libraries that can facilitate diverse multiplexing applications and help identify factors impacting crRNA biogenesis is presented. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: July 22, 2019

2019 journal article

Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells

NATURE BIOTECHNOLOGY, 37(12), 1493-+.

By: A. Pickar-Oliver*, J. Black*, M. Lewis*, K. Mutchnick*, T. Klann*, K. Gilcrest*, M. Sitton*, C. Nelson* ...

MeSH headings : CRISPR-Cas Systems / genetics; Escherichia coli / genetics; Genetic Engineering / methods; HEK293 Cells; Humans; Listeria monocytogenes / genetics; RNA, Guide, Kinetoplastida / genetics; Transcription, Genetic / genetics
TL;DR: This study repurposes type I variants of class 1 CRISPR–Cas systems from Escherichia coli and Listeria monocytogenes, which target DNA via a multi-component RNA-guided complex termed Cascade, and demonstrates the use of Cascade as a CRISpr-based technology for targeted eukaryotic gene regulation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 30, 2019

2019 journal article

The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs

FEMS MICROBIOLOGY LETTERS, 366(8).

By: T. Jacobsen n, C. Liao* & C. Beisel n

author keywords: Cas nuclease; Cpf1; CRISPR-Cas systems; PAM; TIDE; TXTL
MeSH headings : Acidaminococcus / enzymology; Acidaminococcus / genetics; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; CRISPR-Associated Proteins / genetics; CRISPR-Associated Proteins / metabolism; CRISPR-Cas Systems; Catalytic Domain; DNA Cleavage; Endodeoxyribonucleases / genetics; Endodeoxyribonucleases / metabolism; Endonucleases / genetics; Endonucleases / metabolism; Escherichia coli / genetics; Gene Editing; HEK293 Cells; Humans; Nucleotide Motifs; Plasmids / genetics
TL;DR: Results show that wild-type AsCas12a can recognize non-canonical GTTV and GCTV motifs and exemplify why the range of PAMs recognized by Cas nucleases are poorly captured with a consensus sequence. (via Semantic Scholar)
Source: Web Of Science
Added: September 9, 2019

2018 journal article

A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs

Methods, 143, 48–57.

By: C. Maxwell n, T. Jacobsen n, R. Marshall*, V. Noireaux* & C. Beisel n

author keywords: Cas9; Cas12a; PAM; sgRNA; crRNA; TXTL
MeSH headings : Amino Acid Motifs; Biotechnology / methods; CRISPR-Associated Protein 9 / genetics; CRISPR-Associated Protein 9 / metabolism; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Computational Biology / methods; DNA / genetics; Escherichia coli; Gene Library; Green Fluorescent Proteins / chemistry; Green Fluorescent Proteins / metabolism; High-Throughput Nucleotide Sequencing / instrumentation; High-Throughput Nucleotide Sequencing / methods; Neisseria meningitidis; Plasmids / genetics; Protein Biosynthesis / genetics; RNA, Guide, Kinetoplastida / genetics; Sequence Analysis, DNA / instrumentation; Sequence Analysis, DNA / methods; Transcription, Genetic / genetics
TL;DR: An in vitro method based on an E. coli cell-free transcription-translation system to rapidly elucidate PAMs recognized by Cas nucleases, with the potential to greatly accelerate the ability to characterize and harness novel CRISPR nucleases across their many uses. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2018 journal article

Advances in CRISPR Technologies for Microbial Strain Engineering

Biotechnology Journal, 13(9), 1800460.

By: H. Alper* & C. Beisel*

MeSH headings : Bacteria / genetics; CRISPR-Cas Systems; Fungi / genetics; Gene Editing / methods; Genetic Engineering / methods
TL;DR: This special issue in Biotechnology Journal addresses the forefront of CRISPR technologies and their application to microbial strain engineering with a collection of five review articles and eleven original research articles highlighting what has been achieved withCRISPR to-date and what challenges await new discoveries and developments. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2018 journal article

Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus LESymbiosis

CELL HOST & MICROBE, 24(1), 109-+.

By: M. Martino*, P. Joncour*, R. Leenay n, H. Gervais*, M. Shah n, S. Hughes*, B. Gillet*, C. Beisel n, F. Leulier*

MeSH headings : Acetate Kinase / genetics; Acetate Kinase / metabolism; Adaptation, Physiological; Animals; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Drosophila melanogaster / microbiology; Evolution, Molecular; Glutamine / analogs & derivatives; Glutamine / metabolism; Host Microbial Interactions; Lactobacillus plantarum / genetics; Lactobacillus plantarum / growth & development; Larva / microbiology; Microbiota; Mutation; Symbiosis
TL;DR: It is found that the diet of the host, rather than the host itself, is a predominant driving force in the evolution of this symbiosis, and a mechanism resulting from the bacterium's adaptation to the diet, which confers growth benefits to the colonized host is identified. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2018 journal article

CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9

MOLECULAR CELL, 69(5), 893-+.

By: G. Dugar*, R. Leenay n, S. Eisenbart*, T. Bischler*, B. Aul*, C. Beisel n, C. Sharma*

MeSH headings : CRISPR-Associated Protein 9 / genetics; CRISPR-Associated Protein 9 / metabolism; CRISPR-Cas Systems / physiology; Campylobacter jejuni / enzymology; Campylobacter jejuni / genetics; DNA, Bacterial / genetics; DNA, Bacterial / metabolism; Protein Domains; RNA Stability / physiology; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism
TL;DR: Findings suggest that C. jejuni Cas9 is a promiscuous nuclease that can coordinately target both DNA and RNA and was programmable in vitro. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2018 journal article

CRISPR tool puts RNA on the record

Nature, 562(7727), 347–349.

By: C. Beisel*

MeSH headings : CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; RNA
TL;DR: The bacterial-defence system CRISPR–Cas can store DNA snippets that correspond to encountered viral RNA sequences that can be recorded in bacterial cells to record gene expression over time in bacteria. (via Semantic Scholar)
Source: Crossref
Added: November 21, 2020

2018 journal article

Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods

BIOTECHNOLOGY JOURNAL, 14(3).

author keywords: genome editing; lactobacilli; recombineering; shuttle plasmids
MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Gene Editing / methods; Lactobacillus plantarum / genetics; Plasmids / genetics; Recombinases / genetics; Recombination, Genetic / genetics
TL;DR: Surprising differences for Cas9-mediated genome editing between methods and related strains are highlighted, arguing for the need for multiple, distinct methods when performing CRISPR-based editing in bacteria. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: March 18, 2019

2018 journal article

Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression

ACS SYNTHETIC BIOLOGY, 7(5), 1219–1228.

author keywords: RNA; feedback; gene expression; mathematical modeling; control; sensitivity analysis
MeSH headings : CRISPR-Cas Systems; Computational Biology / methods; Feedback, Physiological / physiology; Gene Expression Regulation; Models, Theoretical; RNA / chemistry; Synthetic Biology / methods
TL;DR: This work presents mathematical models of biomolecular controllers that enable reference tracking, disturbance rejection, and tuning of the temporal response of gene expression and indicates that RNA regulators are well-suited for building robust and precise feedback controllers for gene expression. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2018 journal article

Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

MOLECULAR CELL, 69(1), 146-+.

By: R. Marshall*, C. Maxwell n, S. Collins n, T. Jacobsen n, M. Luo n, M. Begemann*, B. Gray*, E. January* ...

MeSH headings : CRISPR-Cas Systems / genetics; Cell-Free System / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA, Bacterial / genetics; Endonucleases / metabolism; Escherichia coli / genetics; Genetic Engineering / methods; Oryza / genetics; Protein Biosynthesis / genetics; RNA, Guide, Kinetoplastida / genetics; Transcription, Genetic / genetics
TL;DR: The use of E. coli cell-free transcription-translation (TXTL) systems are presented to vastly improve the speed and scalability of CRISPR characterization and validation. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2018 article

Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications

ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 20, Vol. 20, pp. 277–300.

By: J. Bober*, C. Beisel n & N. Nair*

author keywords: probiotics; genetic tools; CRISPR; genome engineering; microbiome
MeSH headings : Animals; Bacteroides; CRISPR-Cas Systems; Gene Editing; Genetic Engineering; Genomics; Humans; Immune System; Lactic Acid / chemistry; Microbiota; Probiotics / chemistry; Probiotics / therapeutic use; Synthetic Biology / methods
TL;DR: Recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes are discussed, and a perspective on the future potential of these technologies is provided. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2018 journal article

The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays

RNA BIOLOGY, 16(4), 404–412.

By: C. Liao n, R. Slotkowski n, T. Achmedov* & C. Beisel n

author keywords: Cpf1; CRISPR; RNA structure; terminator; TXTL
MeSH headings : CRISPR-Associated Proteins / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA Cleavage; DNA, Intergenic / genetics; Francisella / genetics; Nucleic Acid Conformation; RNA Processing, Post-Transcriptional / genetics; RNA, Guide, Kinetoplastida / metabolism; Rho Factor / metabolism; Terminal Repeat Sequences / genetics; Transcription Termination, Genetic
TL;DR: It is shown that a structured hairpin located immediately downstream of the 3ʹ repeat interferes with utilization of the adjacent encoded guide RNA by Francisella novicida (Fn)Cas12a, revealing that sequences surrounding a CRISPR array can interfere with the function of aCRISPR nuclease. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: May 20, 2019

2017 journal article

Advancing the design and delivery of CRISPR antimicrobials

Current Opinion in Biomedical Engineering, 4, 57–64.

By: J. Fagen n, D. Collias n, A. Singh n & C. Beisel n

author keywords: Bacteriophage; Cas9; CRISPR-Cas systems; sgRNA; Tail-fiber proteins
TL;DR: The current efforts toward repurposing CRISPR nucleases as programmable antimicrobials may help quell the spread of antimicrobial resistance and provide a tool for the manipulation of complex microbial communities. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Crossref
Added: February 24, 2020

2017 review

Deciphering, Communicating, and Engineering the CRISPR PAM

[Review of ]. JOURNAL OF MOLECULAR BIOLOGY, 429(2), 177–191.

By: R. Leenay n & C. Beisel n

author keywords: Cas9; Cpf1; CRISPR-Cas systems; PFS; rPAM
MeSH headings : Amino Acid Motifs; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA, Bacterial / genetics; Gene Library; Genetic Loci; Plasmids / genetics; Protein Engineering; RNA / genetics; RNA / metabolism; Staphylococcus epidermidis / genetics; Streptococcus thermophilus / genetics
TL;DR: The properties of the CRISPR PAM and the emerging tools for determining, visualizing, and engineering PAM recognition are discussed and a standard means of orienting the PAM is proposed to simplify how its location and sequence are communicated. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2017 journal article

Short DNA Containing chi Sites Enhances DNA Stability and Gene Expression in E-coli Cell-Free Transcription-Translation Systems

BIOTECHNOLOGY AND BIOENGINEERING, 114(9), 2137–2141.

By: R. Marshall*, C. Maxwell n, S. Collins n, C. Beisel n & V. Noireaux*

author keywords: Escherichia coli; gene circuits; prototyping; RecBCD; synthetic biology; TXTL
MeSH headings : Cell-Free System / physiology; DNA, Bacterial / genetics; Escherichia coli / genetics; Exodeoxyribonuclease V / genetics; Gene Expression Regulation, Bacterial / genetics; Genetic Engineering / methods; Protein Biosynthesis / genetics; Transcription, Genetic / genetics
TL;DR: It is shown that double-stranded DNA encoding χ sites-eight base-pair sequences preferentially bound by the RecBCD recombination machinery-stabilizes linear DNA and greatly enhances the TXTL-based expression and activity of a fluorescent reporter gene, simple regulatory cascades, and T7 bacteriophage particles. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2017 journal article

Toward a genetic tool development pipeline for host-associated bacteria

Current Opinion in Microbiology, 38, 156–164.

By: M. Waller n, J. Bober*, N. Nair* & C. Beisel n

MeSH headings : Bacteria / genetics; Gastrointestinal Microbiome; Genetics, Microbial / methods; Host-Pathogen Interactions; Humans; Molecular Biology / methods; Symbiosis
TL;DR: The current challenges to rendering culturable, non-model members of microbial communities genetically tractable are discussed - including overcoming barriers to DNA delivery, achieving predictable gene expression, and applying CRISPR-based tools - and recent efforts to create generalized pipelines that simplify and expedite the tool-development process are details. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2017 journal article

What is the role of circuit design in the advancement of synthetic biology? Part 1 enabling real-world applications and therapeutics

Cell Systems, 4(4), 370–372.

By: Y. Chen, M. Shapiro, W. Ruder, H. Ye, S. Kiani, T. Moon, S. Raman, C. Beisel, C. Barnes

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

Engineering genes with CRISPR-Cas9

Chemical Engineering Progress , 112(9), 36–41.

By: M. Luo & C. Beisel

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems

MOLECULAR CELL, 62(1), 137–147.

By: R. Leenay n, K. Maksimchuk n, R. Slotkowski n, R. Agrawal n, A. Gomaa n, A. Briner, R. Barrangou n, C. Beisel n

MeSH headings : Bacillus / chemistry; Bacillus / metabolism; CRISPR-Associated Proteins / chemistry; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems; Escherichia coli / chemistry; Escherichia coli / metabolism; Francisella / chemistry; Francisella / metabolism; High-Throughput Screening Assays / methods; Protein Structure, Tertiary; Streptococcus thermophilus / chemistry; Streptococcus thermophilus / metabolism
TL;DR: An in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities to accelerate ability to understand and exploit the multitude of CRISPR-Cas systems in nature. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers

NUCLEIC ACIDS RESEARCH, 44(15), 7385–7394.

MeSH headings : CRISPR-Associated Proteins / metabolism; CRISPR-Cas Systems / genetics; DNA / metabolism; Escherichia coli / genetics; Escherichia coli Proteins / metabolism; Gene Expression Regulation, Bacterial; Gene Silencing; Macromolecular Substances / chemistry; Macromolecular Substances / metabolism; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Guide, Kinetoplastida / chemistry; RNA, Guide, Kinetoplastida / genetics; Transcription, Genetic
TL;DR: It is found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA, and spacer length can be modified to fine-tune Cascade activity. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Cover Picture: Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing (Angew. Chem. Int. Ed. 41/2015)

Angewandte Chemie International Edition, 54(41), 11877–11877.

By: W. Sun n, W. Ji n, J. Hall n, Q. Hu n, C. Wang n, C. Beisel n, Z. Gu n

Source: Crossref
Added: February 24, 2020

2015 review

Current and future prospects for CRISPR-based tools in bacteria

[Review of ]. BIOTECHNOLOGY AND BIOENGINEERING, 113(5), 930–943.

By: M. Luo n, R. Leenay n & C. Beisel n

author keywords: antimicrobials; Cas9; genetic control; genetic circuits; genome engineering; undomesticated microbes
MeSH headings : Anti-Bacterial Agents / pharmacology; Bacteria / drug effects; Bacteria / genetics; Bacterial Infections / drug therapy; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Drug Discovery; Drug Resistance, Bacterial; Gene Editing / methods; Gene Expression Regulation, Bacterial; Genetic Engineering / methods; Genome, Bacterial; Humans
TL;DR: Overall, CRISPR‐Cas systems have formed the basis of an ever‐expanding genetic toolbox and hold tremendous potential for the future understanding and engineering of the bacterial world. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Impact of Residual Inducer on Titratable Expression Systems

PLOS ONE, 10(9).

By: T. Afroz n, M. Luo n & C. Beisel n

MeSH headings : Arabinose / biosynthesis; Arabinose / genetics; Bacterial Proteins / biosynthesis; Bacterial Proteins / genetics; Escherichia coli; Flow Cytometry; Gene Expression Regulation, Bacterial; Models, Theoretical; Plasmids; Promoter Regions, Genetic; Riboswitch / genetics; Thiamine / genetics; Thiamine Pyrophosphate / biosynthesis; Thiamine Pyrophosphate / genetics
TL;DR: It is found that residual inducer had a distinct effect on “all-or-none” systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2015 article

Rethinking the Hierarchy of Sugar Utilization in Bacteria

Beisel, C. L., & Afroz, T. (2016, February). JOURNAL OF BACTERIOLOGY, Vol. 198, pp. 374–376.

By: C. Beisel n & T. Afroz n

MeSH headings : Bacteria / metabolism; Carbohydrate Metabolism / physiology; Carbohydrates / classification; Gene Expression Regulation, Bacterial
TL;DR: Findings from studying the preferential consumption of l-arabinose over d-xylose in Escherichia coli can guide efforts to engineer the simultaneous utilization of multiple sugars. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing

Angewandte Chemie International Edition, 54(41), 12029–12033.

By: W. Sun n, W. Ji n, J. Hall n, Q. Hu n, C. Wang n, C. Beisel n, Z. Gu n

author keywords: CRISPR-Cas9; DNA; drug delivery; genome editing; nanoparticles
MeSH headings : Animals; CRISPR-Associated Proteins / administration & dosage; CRISPR-Associated Proteins / chemistry; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems; Cell Line; Clustered Regularly Interspaced Short Palindromic Repeats; DNA / administration & dosage; DNA / chemistry; DNA / genetics; Green Fluorescent Proteins / genetics; Humans; Mice, Nude; Nanoparticles / chemistry; Neoplasms / genetics; Neoplasms / therapy; RNA, Guide, Kinetoplastida / administration & dosage; RNA, Guide, Kinetoplastida / chemistry; RNA, Guide, Kinetoplastida / genetics; Streptococcus pyogenes / chemistry; Streptococcus pyogenes / genetics
TL;DR: The biologically inspired vehicles were efficiently loaded with Cas9/sgRNA complexes and delivered the complexes to the nuclei of human cells, thus enabling targeted gene disruption while maintaining cell viability. (via Semantic Scholar)
Sources: Crossref, Web Of Science
Added: August 6, 2018

2014 article

A CRISPR design for next-generation antimicrobials

GENOME BIOLOGY, Vol. 15.

By: C. Beisel n, A. Gomaa n & R. Barrangou n

MeSH headings : Animals; Anti-Infective Agents / administration & dosage; CRISPR-Cas Systems; Drug Resistance, Microbial / genetics; Enterohemorrhagic Escherichia coli / genetics; Gene Targeting; RNA, Guide, Kinetoplastida / genetics; Ribonucleases / genetics
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 journal article

Bacterial sugar utilization gives rise to distinct single-cell behaviours

MOLECULAR MICROBIOLOGY, 93(6), 1093–1103.

By: T. Afroz n, K. Biliouris*, Y. Kaznessis* & C. Beisel n

MeSH headings : Carbohydrate Metabolism; Escherichia coli / cytology; Escherichia coli / metabolism; Gene Expression Regulation, Bacterial; Metabolic Networks and Pathways; Models, Biological; Single-Cell Analysis / methods
TL;DR: The findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Construction of ligand-responsive microRNAs that operate through inhibition of Drosha processing

Artificial Riboswitches: Methods and Protocols, 1111, 259–267.

By: C. Beisel, R. Bloom & C. Smolke

Source: NC State University Libraries
Added: August 6, 2018

2014 journal article

Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality

MOLECULAR CELL, 56(2), 333–339.

By: A. Briner, P. Donohoue*, A. Gomaa n, K. Selle n, E. Slorach*, C. Nye*, R. Haurwitz*, C. Beisel n, A. May*, R. Barrangou n

MeSH headings : Bacterial Proteins / chemistry; CRISPR-Associated Protein 9; CRISPR-Associated Proteins / chemistry; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; DNA / chemistry; DNA Cleavage; Endonucleases / chemistry; Genetic Engineering / methods; HEK293 Cells; Humans; Nucleic Acid Conformation; RNA, Guide, Kinetoplastida / chemistry; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / ultrastructure
TL;DR: Six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs that direct Cas9 endonuclease activity are identified and characterized and it is shown the bulge and nexus are necessary for DNA cleavage and the nexus and hairpins are instrumental in defining orthogonality between systems. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 journal article

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

MBIO, 5(1).

By: A. Gomaa n, H. Klumpe n, M. Luo n, K. Selle n, R. Barrangou n & C. Beisel n

MeSH headings : CRISPR-Cas Systems; DNA, Bacterial / genetics; DNA, Bacterial / metabolism; Escherichia coli / genetics; Genome, Bacterial; Hydrolysis; Microbial Viability
TL;DR: It is demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

NUCLEIC ACIDS RESEARCH, 43(1), 674–681.

By: M. Luo n, A. Mullis n, R. Leenay n & C. Beisel n

MeSH headings : CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems; Cell Engineering; Escherichia coli / genetics; Gene Deletion; Transcription, Genetic
TL;DR: It is found that deletion of the signature cas3 gene converted this immune system in Escherichia coli into a programmable gene regulator capable of reversible gene silencing of heterologous and endogenous genes. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control

ACS SYNTHETIC BIOLOGY, 4(2), 141–149.

By: T. Afroz n, K. Biliouris*, K. Boykin n, Y. Kaznessis* & C. Beisel n

author keywords: carbon catabolism; Escherichia coli; feedback; inducible systems; linearization; systems biology
MeSH headings : Arabinose / metabolism; Carbohydrate Metabolism / physiology; Escherichia coli / metabolism; Metabolic Engineering; Models, Theoretical
TL;DR: Overall, the findings indicate that there is no ideal set of typical alterations when co-opting natural utilization pathways for titratable control and suggest design rules for manipulating these pathways to advance basic genetic studies and the metabolic engineering of microorganisms for optimized chemical production. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2013 journal article

Understanding and exploiting feedback in synthetic biology

CHEMICAL ENGINEERING SCIENCE, 103, 79–90.

By: T. Afroz n & C. Beisel n

author keywords: Biological engineering; Feedback; Genetic circuit; Mathematical modeling; Process control; Synthetic biology
TL;DR: It is argued that biological feedback represents a powerful yet underutilized tool that can advance the construction of biological systems. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2012 journal article

Multiple factors dictate target selection by Hfq-binding small RNAs

The EMBO Journal, 31(8), 1961–1974.

author keywords: base-pairing; Escherichia coli; Spot 42; target prediction
MeSH headings : Base Pairing; Binding Sites; Escherichia coli / physiology; Escherichia coli Proteins / metabolism; Gene Expression Regulation, Bacterial; Host Factor 1 Protein / metabolism; MicroRNAs / metabolism; Nucleic Acid Conformation; Protein Binding; Sequence Analysis
TL;DR: Using the Hfq‐binding sRNA Spot 42 of Escherichia coli as a model, it is found that predictions using only the three unstructured regions of Spot 42 substantially improved the identification of previously known and novel Spot 42 targets. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

2011 journal article

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

Nucleic Acids Research, 39(7), 2981–2994.

By: C. Beisel CL, C. Yy, . Hoff KG & S. Cd

Source: NC State University Libraries
Added: August 6, 2018

2011 article

Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression

RNA Biology, Vol. 8, pp. 1–5.

By: C. Beisel & G. Storz

Source: NC State University Libraries
Added: August 6, 2018

2011 journal article

The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli

Molecular Cell, 41(3), 286–297.

By: C. Beisel* & G. Storz*

MeSH headings : Base Pairing; Base Sequence; Escherichia coli / chemistry; Escherichia coli / genetics; Escherichia coli / growth & development; Escherichia coli / metabolism; Gene Expression Regulation, Bacterial; Microbial Viability; Molecular Sequence Data; Operon; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Messenger / chemistry; RNA, Messenger / genetics
TL;DR: It is found that the base-pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse nonpreferred carbon sources. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

2011 journal article

The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

Molecular Cell, 41, 1–12.

By: B. Cl & S. G

Source: NC State University Libraries
Added: August 6, 2018

2010 review

Base pairing small RNAs and their roles in global regulatory networks

[Review of ]. FEMS MICROBIOLOGY REVIEWS, 34(5), 866–882.

By: C. Beisel* & G. Storz*

author keywords: sRNAs; regulatory circuits; gene regulation; Hfq; network motifs
MeSH headings : Bacteria / genetics; Base Pairing / genetics; Gene Expression Regulation, Bacterial; Gene Regulatory Networks; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Small Untranslated / genetics; RNA, Small Untranslated / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR: This review describes the specific regulatory circuits that incorporate base-pairing sRNAs and the importance of each circuit in global regulation and discusses why s RNAs may be used over protein transcription factors to help transduce environmental signals. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2009 journal article

Conformational analysis of gossypol and its derivatives by molecular mechanics

Journal of Molecular Structure [Including Theochem], 3(1).

By: H. Bayer TS, L. Beisel CL & S. Cd

Source: NC State University Libraries
Added: August 6, 2018

2009 journal article

Design Principles for Riboswitch Function

PLOS COMPUTATIONAL BIOLOGY, 5(4).

By: C. Beisel* & C. Smolke*

MeSH headings : Base Sequence; Gene Expression Regulation / genetics; Models, Genetic; Molecular Sequence Data; RNA, Messenger / genetics; Regulatory Sequences, Ribonucleic Acid; Ribosomes / genetics
TL;DR: Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms, and developed a set of general design principles for synthetic riboswitches. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Model-guided design of ligand-regulated RNAi for programmable control of gene expression

Molecular Systems Biology, 4, 224.

By: B. Beisel CL, . Hoff KG & S. Cd

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Model‐guided design of ligand‐regulated RNAi for programmable control of gene expression

Molecular Systems Biology, 4(1), 224.

By: C. Beisel*, T. Bayer*, K. Hoff* & C. Smolke*

author keywords: aptamer; mathematical modelling; RNA; shRNA; synthetic biology
MeSH headings : Aptamers, Nucleotide / chemistry; Biotechnology / methods; Drug Design; Ligands; RNA Interference / drug effects; RNA, Small Interfering / chemical synthesis; RNA, Small Interfering / pharmacology
TL;DR: An RNA‐based platform that provides for integrated ligand control of RNA interference by modular coupling of an aptamer, competing strand, and small hairpin stem into a single component that links ligand concentration and target gene expression levels is engineered. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

2005 journal article

Conformational analysis of gossypol and its derivatives by molecular mechanics

Journal of Molecular Structure: THEOCHEM, 730(1-3), 51–58.

By: C. Beisel*, M. Dowd* & P. Reilly*

Source: Crossref
Added: August 28, 2020

2005 journal article

Conformational analysis of gossypol and its derivatives by molecular mechanics

Journal of Molecular Structure, 730, 51–58.

By: D. Beisel CL & R. Pj

Source: NC State University Libraries
Added: August 6, 2018

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