Codon optimizer: a freeware tool for codon optimization

Fuglsang, Anders

doi:10.1016/s1046-5928(03)00213-4

Cited by 73 publications

(49 citation statements)

References 21 publications

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“…Using the MC1 amino acid sequence as a template, a synthetic gene with the natural codon bias of E. coli was designed using the codon optimization tool (Fuglsang 2003) at Integrated DNA Technologies (IDT; http://www.idtdna.com/CodonOpt). BamH1 and HindIII sites were added at the 5 ′ and 3 ′ ends, respectively, to enable cloning into the IPTG (Isopropyl β-D-1-thiogalactopyranoside)-inducible expression cassette of the pET22b vector (EMD-Millipore).…”

Section: Designing Synthetic Gene and Cloningmentioning

confidence: 99%

“…However, such engineered tRNAs can be undermodified (Krivos et al 2011), which may impact their efficiency during translation. To overcome these limitations, a codon optimization tool was designed to adjust the codon usage of a target gene to resemble that of highly expressed genes (ribosomal proteins and elongation factors) of a host cell (Fuglsang 2003). Such an approach should enhance overexpression of plant-based genes within an E. coli host.…”

Section: Introductionmentioning

confidence: 99%

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Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 fromMomordica charantia

Addepalli

Lesner

Limbach

2015

RNA

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A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNA Tyr I . Analysis of MC1 digestion products by ion-pairing reverse phase liquidchromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5 ′ -termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated.

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Section: Designing Synthetic Gene and Cloningmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 fromMomordica charantia

Addepalli

Lesner

Limbach

2015

RNA

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“…In order to improve such heterologous gene expression, customized artificial genes can be designed by matching the codon preference of the host based on several design parameters adjusted for codon optimization [10][11][12][13][14][15]. To perform codon optimization, the codon usage bias of the expression host is first established.…”

Section: Introductionmentioning

confidence: 99%

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli

Pek¹,

Klement²,

Ang³

et al. 2015

Enzyme and Microbial Technology

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“…A number of published software tools are capable of codon optimization, including DNA Works [8], Codon Optimizer [2], GeMS [9], Gene Designer [17], JCat [4], OPTIMIZER [12], the Synthetic Gene Designer [18], UpGene [3] and a method by Satya et. al [13].…”

Section: Introductionmentioning

confidence: 99%

Efficient Codon Optimization with Motif Engineering

Condon

Thachuk

2011

Lecture Notes in Computer Science

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Abstract. It is now common to add protein coding genes into cloning vectors for expression within non-native host organisms. Codon optimization supports translational efficiency of the desired protein product, by exchanging codons which are rarely found in the host organism with more frequently observed codons. Motif engineering, such as removal of restriction enzyme recognition sites or addition of immuno-stimulatory elements, is also often necessary. We present an algorithm for optimizing codon bias of a gene with respect to a well motivated measure of bias, while simultaneously performing motif engineering. The measure is the previously studied codon adaptation index, which favors the use, in the gene to be optimized, of the most abundant codons found in the host genome. We demonstrate the efficiency and effectiveness of our algorithm on the GENCODE dataset and provide a guarantee that the solution found is always optimal.

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Codon optimizer: a freeware tool for codon optimization

Cited by 73 publications

References 21 publications

Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 fromMomordica charantia

Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 fromMomordica charantia

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli

Efficient Codon Optimization with Motif Engineering

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