Pairwise selection assembly for sequence-independent construction of long-length DNA

@article{Blake2010PairwiseSA,
  title={Pairwise selection assembly for sequence-independent construction of long-length DNA},
  author={William J. Blake and Brad A. Chapman and Anuradha Zindal and Michael E. Lee and Shaun M. Lippow and Brian M. Baynes},
  journal={Nucleic Acids Research},
  year={2010},
  volume={38},
  pages={2594 - 2602}
}
The engineering of biological components has been facilitated by de novo synthesis of gene-length DNA. Biological engineering at the level of pathways and genomes, however, requires a scalable and cost-effective assembly of DNA molecules that are longer than ∼10 kb, and this remains a challenge. Here we present the development of pairwise selection assembly (PSA), a process that involves hierarchical construction of long-length DNA through the use of a standard set of components and operations… 
View PDF
47 Citations
Highly Influential Citations
4
Background Citations
13
Methods Citations
9

Figures and Tables from this paper

47 Citations

DNA assembly for synthetic biology: from parts to pathways and beyond.

This review provides a critical examination of recent DNA assembly strategies and considers how this important facilitating aspect of synthetic biology may proceed in the future.

A solid-phase platform for combinatorial and scarless multipart gene assembly.

This work has developed a method for scarless ligation of multipart gene segments in a truly sequence-independent fashion, allowing the generation of all combinations of several variants of two or more modules to be ligated in less than a day.

Reiterative Recombination for the in vivo assembly of libraries of multigene pathways

The design and construction of the first Reiterative Recombination system in Saccharomyces cerevisiae are described, and it is shown that it can be used to assemble multigene constructs and can construct large mock libraries of at least 104 biosynthetic pathways.

The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly

A novel method designated ‘MASTER Ligation’ is described, by which multiple DNA sequences can be seamlessly assembled through a simple and sequence-independent hierarchical procedure.

Methods and applications for assembling large DNA constructs.

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

This work describes a synthetic yeast genome project, Sc2.0, and the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL, and shows the utility of SCRaMbLE as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes.

In Vitro Seamless Stack Enzymatic Assembly of DNA Molecules Based on a Strategy Involving Splicing of Restriction Sites

An in vitro Seamless Stack Enzymatic Assembly (SSEA) method involving a seamless strategy of splicing restriction sites via a stepwise process of multiple enzymatic reactions that does not leave nucleotide scars at the junction sites is proposed.

A Rapid Cloning Method Employing Orthogonal End Protection

A novel in vitro cloning strategy that combines standard tools in molecular biology with a basic protecting group concept to create a versatile framework for the rapid and seamless assembly of modular DNA building blocks into functional open reading frames for single-molecule force spectroscopy is described.

iBrick: A New Standard for Iterative Assembly of Biological Parts with Homing Endonucleases

A new standard is introduced, namely iBrick, which uses two homing endonucleases of I-SceI and PI-PspI, their sites are extremely rare in natural DNA sources, thus providing additional convenience, especially in handling large pieces of DNA fragments.

Bricks and blueprints: methods and standards for DNA assembly

Standards such as the modular cloning system, GoldenBraid, modular overlap-directed assembly with linkers and PaperClip are discussed, which have been developed to facilitate a streamlined assembly workflow to aid the exchange of material between research groups and to create modular reusable DNA parts.

References

SHOWING 1-10 OF 28 REFERENCES

Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.

Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides

Conditions are established for the rapid assembly of the complete infectious genome of bacteriophage φX174 from a single pool of chemically synthesized oligonucleotides and sequence analysis of several infectious isolates verified the accuracy of these synthetic genomes.

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments, and studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMad.

Total synthesis of multi-kilobase DNA sequences from oligonucleotides

Synthetic fragments are assembled in pairs to generate the final construct using vectors that allow selection of desired clones with two unique antibiotic resistance markers, and this eliminates the need for purification of fragments after digestion with restriction endonucleases.

Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster.

This work has developed and implemented a strategy for the high-throughput synthesis of long, accurate DNA sequences and validated the approach by building a synthetic 31,656-bp polyketide synthase gene cluster whose functionality was demonstrated by its ability to produce the megaenzyme and itspolyketide product in Escherichia coli.

Protein-mediated error correction for de novo DNA synthesis.

A DNA mismatch-binding protein, MutS (from Thermus aquaticus) is employed to remove failure products from synthetic genes, which reduces errors by >15-fold relative to conventional gene synthesis techniques, yielding DNA with one error per 10 000 base pairs.

FokI method of gene synthesis.

Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously.

A procedure for precise assembly of linear DNA constructs as long as 20 kb, using Pfu polymerase mix, which has a proofreading activity, is proposed, offering an additional improvement on the combination of long PCR and overlap extension PCR.

Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model

A full-length infectious construct of transmissible gastroenteritis virus (TGEV) is assembled, conclusively demonstrating the marker mutations and restriction sites that were engineered into the component clones that will permit the precise genetic modification of the coronavirus genome.

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.