利用DNA Assembly方法构建重组腺病毒载体

目的:建立一种基于DNA Assembly方法的重组腺病毒载体构建方法。方法:首先,通过设计合适的酶切位点及同源臂,采用了传统的限制性内切核酸酶连接方法和DNA Assembly方法获得63型猩猩腺病毒(Chimpanzee adenovirus serotype 63,ChAd63)的骨架质粒pChAd63。随后,采用Sca I单酶切携带EGFP基因的穿梭pShuttle63/EGFP,Hpa I单酶切pChAd63,以DNA Assembly方法,获得重组腺病毒载体pChAd63/EGFP。最后,在293细胞中拯救获得重组腺病毒rChAd63/EGFP。结果:采用DNA Assembly方法成功构建了重组腺病毒载体pChAd63/EGFP,并拯救出重组腺病毒rChAd63/EGFP。结论:DNA Assembly可用于重组腺病毒载体的构建,有利于提高重组腺病毒载体的构建效率。

A flexible,modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

Streptomyces has enormous potential to produce novel natural products(NPs)as it harbors a huge reservoir of uncharacterized and silent natural product biosynthetic gene clusters(BGCs).However,the lack of efficient gene cluster engineering strategies has hampered the pace of new drug discovery.Here,we developed an easy-to-use,highly flexible DNA assembly toolkit for gene cluster engineering.The DNA assembly toolkit is compatible with various DNA assembling approaches including Biobrick,Golden Gate,CATCH,yeast homologous recombination-based DNA assembly and homing endonuclease-mediated assembly.This compatibility offers great flexibility in handling multiple genetic parts or refactoring large gene clusters.To demonstrate the utility of this toolkit,we quantified a library of modular regulatory parts,and engineered a gene cluster(act)using characterized promoters that led to increased production.Overall,this work provides a powerful part assembly toolkit that can be used for natural product discovery and optimization in Streptomyces.

Efficient de novo assembly and modification of large DNA fragments

Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes.The construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints significantly.But for the synthesis and assembly of such large-scale genomes,the development of new or expanded methods is required.In this study,we develop an efficient pipeline for the construction of large DNA fragments sized 100 kilobases(kb)or above from scratches and describe an efficient method for“scar-free”engineering of the assembled sequences.Our method,therefore,should provide a standard framework for producing long DNA molecules,which are critical materials for synthetic genomics and metabolic engineering.

Assembly of long DNA sequences using a new synthetic Escherichia coli-yeast shuttle vector

Synthetic biology is a newly developed field of research focused on designing and rebuilding novel biomolecular components, circuits, and networks. Synthetic biology can also help understand biological principles and engineer complex artificial metabolic systems. DNA manipulation on a large genome-wide scale is an inevitable challenge, but a necessary tool for synthetic biology. To improve the methods used for the synthesis of long DNA fragments, here we constructed a novel shuttle vector named p GF(plasmid Genome Fast) for DNA assembly in vivo. The BAC plasmid p CC1 BAC, which can accommodate large DNA molecules, was chosen as the backbone. The sequence of the yeast artificial chromosome(YAC) regulatory element CEN6-ARS4 was synthesized and inserted into the plasmid to enable it to replicate in yeast. The selection sequence HIS3, obtained by polymerase chain reaction(PCR) from the plasmid p BS313, was inserted for screening. This new synthetic shuttle vector can mediate the transformation-associated recombination(TAR) assembly of large DNA fragments in yeast, and the assembled products can be transformed into Escherichia coli for further amplification. We also conducted in vivo DNA assembly using p GF and yeast homologous recombination and constructed a 31-kb long DNA sequence from the cyanophage PP genome. Our findings show that this novel shuttle vector would be a useful tool for efficient genome-scale DNA reconstruction.

RPA functions as a platform for coupling of nucleosome assembly to DNA replication

Subject Code:C05 With the support by the National Natural Science Foundation of China,the research team led by Dr.Li Qing(李晴)at the State Key Laboratory of Protein and Plant Gene Research,School of Life Sciences and Peking-Tsinghua Center for Life Sciences,Peking University,Beijing,recently reported that

Gel electrophoresis as a nanoseparation tool serving DNA nanotechnology

The past years have witnessed a rapid development of DNA nanotechnology in nanomaterials science with a central focus on programmable material construction on the nanoscale. An efficient method is therefore highly desirable（but challenging） for analytical/preparative purification of DNA-conjugated nano-objects and their DNA-assemblies. In this regard, agarose gel electrophoresis, a traditional technique that has been invented for biomacromolecule separation, has found many innovative uses.This includes shape, size, charge, and ligand-valence separations of nanoparticle building blocks as well as monitoring a self-assembly process towards product identification and purification.

Hybridization chain reaction triggered controllable one-dimensional assembly of gold nanoparticles

Assembling and ordering nanomaterials into desirable patterns are considerably significant,since the properties of nanomaterials depend not only on the size and shape,but also on the spatial arrangement among the collective building blocks.In this work,the DNA self-assembly technology of hybridization chain reaction(HCR) provided a convenient method to yield long double-strand DNA(dsDNA) to install gold nanoparticles(AuNPs) into one dimensional assembly along the skeleton of dsDNA.Interestingly,the tunable length of AuNPs assemblies along dsDNA chain could be achieved by adjusting the reaction time of HCR,which is based on the formation of covalent bond between Au and the-SH group of DNA.Compared with weak light scattering of single AuNP,these AuNPs assemblies could be clearly imaged under the dark field microscopy,indicating that the light scattering was greatly improved after assembling.

RNA nanostructure transformation into DNA ones

RNAs and their assemblies can form diverse nano-structures and nano-shapes,offering various biological functions.However,by simply mimicking RNA sequences,DNAs cannot normally form the corresponding nanostructures,which makes the natureinspired transformations and designs challenging.To understand the possible designs and connections between related RNA and DNA nano-shapes,herein we have reported several DNA squares transformed and derived from an RNA assembled square,by gradually replacing RNA with DNA nucleotides.We have found that there were key RNA nucleotides:Their presences maintained the square,while their absences disrupted it.Interestingly,we have revealed that as long as the conditions of higher ionic strengths or longer duplexes were included,the square RNA assembly could be completely replaced with DNA nucleotides,still offering the stable DNA nano-shapes.Our experimental results have demonstrated that similar RNA nanostructure can be easily transformed into DNA ones via designing and increasing ionic strengths or duplex lengths.

The formation of fibers via complementary base pairing of DNA-conjugated bovine serum albumin

Assembled protein-based substances are emerging and promising classes of materials that provide unique properties for various applications in biotechnology and nanotechnolegy. Self-assembly is an effective way to immobilize protein. In this study, DNAs-conjugated bovine serum albumin （BSA） assembled into fibers via DNA hybridization is demonstrated. The morphology of fibers was observed by optical microscopy, scanning electron microscopy （SEM）, and atomic force microscopy （AFM）, and the assembly mechanism was then analysed and discussed. BSA molecules were first linked by DNA molecule and formed linear chains. These chains then were parallelly linked through additional DNA hybridization. Finally, several BSA chains further assembled into fibers by layering lamellae in a parallel manner. This work perhaps will provide a guide to the immobilization of enzyme, which could be applied to increase its catalytic efficiency in biomedicine and nanotechnology.

Autonomous DNA walker： probing cell membrane dynamics

We are all familiar with DNA as the substance that encodes the genomes of all living things.In addition to genetic function,DNA is one of the smartest building blocks for innovative nanostructures.DNA walker is a kind of self-assembled molecular machine that mimics the movement of protein motors in living systems.Usually,DNA walker consists of three parts：a single stranded DNA track,

Building biological foundries for next-generation synthetic biology

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Rapid Shape Memory and p H-modulated Spontaneous Actuation of Dopamine Containing Hydrogels

The dopamine containing hydrogels with rapid responsive shape memory capability were synthesized by a one-pot method. The temporary shape of hydrogel was fixed within 20 s in Na OH solution by the tris-complex crosslinking of metalligand complex between Fe3＋ ions and catechol groups, while the permanent shape was recovered completely in HCl solution within 60 s upon the change from tris-complex to mono-complex. The hydrogel showed unique spontaneous actuation behavior. It could curl spontaneously without further external force deformation when immersed in Na OH solution again after the first shape recovery in HCl solution. This might be attributed to the competitive result of swelling and additional tris-complex crosslinking formation when immersed in Na OH solution. In addition, the hydrogels also had proper modulus, elongation ratio and tensile strength. Such hydrogel provides a new candidate material for designing soft actuators and robots modulated with spontaneous actuating.