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Literature DB >> 18640907

Computationally Optimised DNA Assembly of synthetic genes.

Liza S Z Larsen¹, Christopher D Wassman, G Wesley Hatfield, Richard H Lathrop.

Abstract

Gene synthesis is hampered by two obstacles: improper assembly of oligonucleotides; oligonucleotide defects incurred during chemical synthesis. To overcome the first problem, we describe the employment of a Computationally Optimised DNA Assembly (CODA) algorithm that uses the degeneracy of the genetic code to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product. To address the second problem, we describe a hierarchical assembly strategy that reduces the incorporation of defective oligonucleotides into full-length gene constructs. The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes.

Entities: Chemical

Mesh：

Substances：
DNA

Year: 2008 PMID： 18640907 PMCID： PMC2668710 DOI： 10.1504/IJBRA.2008.019578

Source DB: PubMed Journal: Int J Bioinform Res Appl ISSN： 1744-5485

23 in total

Computationally Optimised DNA Assembly of synthetic genes.

Review 1. DNA engineering and its application to nanotechnology.

2. Investigating the relationship between genome structure, composition, and ecology in prokaryotes.

3. eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.

4. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

Review 5. DNA nanotechnology: novel DNA constructions.

6. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

7. Predicting DNA duplex stability from the base sequence.

8. Optimization of ligation reaction conditions in gene synthesis.

9. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides.

10. Codon pairs in the genome of Escherichia coli.

1. In vitro targeting of strand transfer by the Ty3 retroelement integrase.

2. Novel TUTase associates with an editosome-like complex in mitochondria of Trypanosoma brucei.

3. Making green.

4. Mechanism of U insertion RNA editing in trypanosome mitochondria: the bimodal TUTase activity of the core complex.

5. A vector set for systematic metabolic engineering in Saccharomyces cerevisiae.

6. All-codon scanning identifies p53 cancer rescue mutations.

7. High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides.

8. Incorporation of a horizontally transferred gene into an operon during cnidarian evolution.

9. Directed DNA shuffling of retrovirus and retrotransposon integrase protein domains.