生物信息学技术

Bacteriophage T4 has proven itself readily amenable to phage-based DNA and protein packaging, expression, and display systems due to its physical resiliency and genomic flexibility. As a large dsDNA phage with dispensable internal proteins and dispensable outer capsid proteins it c ...

One challenge in the development of cancer therapies is the availability of cancer-specific ligands. Recently, phage-displayed peptide libraries have been used for the selection of peptide-based cell-targeting ligands, especially cancer cell ligands. Here we describe the meth ...

Edible vaccines must survive digestive process and preserve the specific structure of the antigenic peptide to elicit effective immune response. The stability of a protein to digestive process can be predicted by subjecting it to the in vitro assay with simulated gastric fluid (SGF) and sim ...

Adenoviral (Ad) vectors are commonly used for various gene therapy applications. Significant advances in the genetic engineering of Ad vectors in recent years has highlighted their potential for the treatment of metastatic disease. There are several methods to genetically modify t ...

Here we report the genetic engineering and chemical modification of potato virus X (PVX) for the presentation of various peptides, proteins, and fluorescent dyes, or other chemical modifiers. Three different ways of genetic engineering are described and by these means, peptides are succ ...

One of the dominant approaches in synthetic biology is the development and implementation of minimal circuits that generate reproducible and controllable system behavior. However, most biological systems are highly complicated and the design of sustainable minimal circuits c ...

Synthetic biology gives researchers the opportunity to rationally (re-)design cellular activities to achieve a desired function. The design of networks of pathways towards accomplishing this calls for the application of engineering principles, often using model-based tools. ...

DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, co ...

Bacterial noncoding small RNAs (sRNAs) modulate expression of numerous genes through antisense interactions with mRNAs. This chapter describes an in vivo screening strategy to engineer artificial sRNAs that can posttranscriptionally regulate desired endogenous genes in E ...

Large numbers of well-described components are essential for advanced synthetic biology and model-guided design of pathways and regulatory networks. Here a method is presented for the creation of libraries of novel control elements. From these libraries, parts with well-defined pr ...

The complexity of even small gene networks makes them hardly amenable to rational design. Testing random combinations of genetic elements in a directed evolution procedure is thus of interest for many applications including metabolic engineering. Here we describe how the recombina ...

The construction of stable and functional synthetic circuits in bacteria is necessary in the areas of systems and synthetic biology. The common approach using plasmids to carry foreign genetic circuits offers convenience in genetic construction but is poor in genetic stability (e.g., v ...

A basic requirement for synthetic biology is the availability of efficient DNA assembly methods. We have previously reported the development of Golden Gate cloning, a method that allows parallel assembly of multiple DNA fragments in a one-tube reaction. Golden Gate cloning can be used for di ...

A robust protocol to generate recombinant DNA containing multigene expression cassettes by using sequence and ligation independent cloning (SLIC) followed by multiplasmid Cre-LoxP recombination in tandem for multiprotein complex research is described. The protocol incl ...

As an emerging discipline, synthetic biology is becoming increasingly important to design, construct, and optimize metabolic pathways leading to desired phenotypes such as overproduction of biofuels and pharmaceuticals in genetically tractable organisms. We have recently ...

The One-Step Isothermal DNA Assembly method allows for the efficient assembly of DNA constructs using fragments up to several hundred kilobases in as little as 15 min. Applications of this method range from the addition of promoters to expression constructs to the assembly of bacterial geno ...

Rising demand for recombinant proteins has motivated the development of efficient and reliable cloning methods. Here we show how a beginner can clone virtually any DNA insert into a plasmid of choice without the use of restriction endonucleases or T4 DNA ligase. Chimeric primers encoding pl ...

Synthetic biologists assemble genetic circuits from standardized biological parts called BioBricks™. BioBrick™ examples include promoters, ribosome binding sites, DNA or RNA-coding sequences, and transcriptional terminators. Standard BioBrick™ assembly normally ...

Gene synthesis by chemical methods provides a powerful tool for modifying genes and exploring their structure, expression, and function in the post-genomic era. However, a bottleneck in recent gene synthesis technologies is the high cost of oligonucleotide synthesis and post-synth ...

Synthetic biology is a rapidly developing field that aims to engineer new biological systems that do not already exist in Nature or redesign existing systems from scratch. The emergence of synthetic biology has been supported by a number of enabling technologies and what has developed is a bro ...