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 ...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.展开更多
Lung cancer-derived exosomes are a kind of valuable and clinically-predictable biomarkers for lung cancer, but they have the limitations in individual differences when being applied in liquid biopsy. To improve their ...Lung cancer-derived exosomes are a kind of valuable and clinically-predictable biomarkers for lung cancer, but they have the limitations in individual differences when being applied in liquid biopsy. To improve their application value and accuracy in clinical diagnosis, a dual-labelled electrochemical method is herein reported for precise assessment of lung cancer-derived exosomes. To do so, two probes are prepared for the dual labeling of exosome membrane to run DNA assembly reactions: One is modified with cholesterol and can insert into exosome membrane through hydrophobic interaction;another one is linked with programmed death ligand-1(PD-L1) antibody and can bind to exosome surface-expressing PD-L1 via specific immunoreaction. Quantum dots-tagged signal strands are used to collect respective DNA products, and produce stripping signals corresponding to the amounts of total exosome and surfaceexpressing PD-L1, respectively. A wide linear relationship is established for the quantitative determination of lung cancer-derived exosomes in the range from 103to 1010particles/m L, whereas the ratiometric value of the two stripping signals is proven to have a better diagnostic use in screening and staging of lung cancer when being applied to clinical samples. Therefore, our method might provide a new insight into precise diagnosis of lung cancer, and offer sufficient information to refiect the biomarker level and guide the personalized treatment level even at an early stage in clinic.展开更多
DNA synthesis and assembly technology is the fundamental enabling technology of synthetic biology,providing methods for humans to understand and modify organisms.Oligonucleotide chains and long DNA fragments synthesiz...DNA synthesis and assembly technology is the fundamental enabling technology of synthetic biology,providing methods for humans to understand and modify organisms.Oligonucleotide chains and long DNA fragments synthesized through DNA synthesis and assembly technology are becoming increasingly widely used in fields such as biomedicine,energy,new materials,and information storage,with strong application prospects.This review provides a comprehensive and systematic introduction and exposition of current DNA synthesis and assembly technologies,discussing current challenges and future research prospects.展开更多
Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology.In this study,we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate asse...Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology.In this study,we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate assembly technique,utilizing Escherichia coli as the model organism.Through polymerase chain reaction(PCR)amplification,restriction enzyme digestion,ligation,transformation,and Sanger sequencing,we assessed the operational efficiency and cloning fidelity of both strategies.Our results demonstrated that Golden Gate assembly,leveraging type IIS restriction enzymes and simultaneous ligation,significantly enhanced cloning efficiency and precision,particularly for seamless multi-fragment assembly.In contrast,the classical cloning approach maintained certain advantages in simplicity and robustness for specific experimental conditions.Challenges encountered during transformation and sequencing highlighted the critical impact of technical accuracy on experimental outcomes.This study underscores the importance of selecting appropriate cloning methodologies tailored to experimental objectives and laboratory capabilities,providing a foundation for optimized molecular cloning workflows in future synthetic biology and biotechnology applications.展开更多
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 des...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.展开更多
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 immo...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.展开更多
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 understandin...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.展开更多
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 gen...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.展开更多
Solid bubbles have expanded the SERS assay toolbox,but their detection performance in biofluids is still hampered by the irrational design of the plasmonic sensing interface.A plasmonic bubble aggregate-driven DNA-enc...Solid bubbles have expanded the SERS assay toolbox,but their detection performance in biofluids is still hampered by the irrational design of the plasmonic sensing interface.A plasmonic bubble aggregate-driven DNA-encoded SERS assay is reported here that enables simultaneous,ultrasensitive,and specific detection of multiple miRNAs in blood samples for accurate cancer diagnosis.In this assay,the buoyancy of plasmonic bubbles allows them to self-aggregate at a droplet apex for SERS reconfiguration,form single-layer bubble aggregates with plasmonic nanogaps,and prevent the coffee ring effect during evaporation assembly.Furthermore,DNA-encoded plasmonic bubbles seamlessly couple with dual-color catalytic hybridization assembly to amplify the specific miRNA-responsive Raman signal,and function as both an analyte concentrator and a Raman signal aggregator without external forces.Using these merits,this magnet-free,portable assay achieves femtomolar dual-miRNA quantitation with single-base resolution,simultaneous miRNA detection across four cell lines,and accurate cancer diagnosis(AUC=1)via analyzing 40 blood samples with machine learning,thus providing a promising tool for clinical diagnosis.展开更多
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 crossli...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.展开更多
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...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展开更多
Plasmid mutagenesis is an essential step to engineer protein variants with desired properties.Direct generation of mutations on plasmids is a promising method compared to PCR-based methods and subcloning,yet it suffer...Plasmid mutagenesis is an essential step to engineer protein variants with desired properties.Direct generation of mutations on plasmids is a promising method compared to PCR-based methods and subcloning,yet it suffers from the sequence restriction in the generation of single-stranded circular plasmids.Here we demonstrate the CRISPR/Cas system-guided plasmid mutagenesis,a method using gRNA/Cas9 nickase complex to generate single-stranded circular plasmids as polymerization templates for mutagenesis.This method can directly create user-defined mutation libraries on the plasmid.It offers broad sequence programmability and even covers methylated plasmids.We further combine this method with rational design to engineer genome-editing protein FnCpf1.The FnCpf1 variants with mutations in the PAM-binding groove were generated.Several variants expanded the PAM range and exhibited lower off-target effect,which can loosen PAM constraint and enhance target specificity for genome editing.This work presents an effective tool for plasmid mutagenesis and protein engineering studies.展开更多
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 coll...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.展开更多
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,whi...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.展开更多
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...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,展开更多
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 g...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.展开更多
基金supported by the 973 program,Grant No.2012CB721102
文摘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.
基金supported by the National Natural Science Foundation of China (Nos. 81972799, 82202834, and 81871449)。
文摘Lung cancer-derived exosomes are a kind of valuable and clinically-predictable biomarkers for lung cancer, but they have the limitations in individual differences when being applied in liquid biopsy. To improve their application value and accuracy in clinical diagnosis, a dual-labelled electrochemical method is herein reported for precise assessment of lung cancer-derived exosomes. To do so, two probes are prepared for the dual labeling of exosome membrane to run DNA assembly reactions: One is modified with cholesterol and can insert into exosome membrane through hydrophobic interaction;another one is linked with programmed death ligand-1(PD-L1) antibody and can bind to exosome surface-expressing PD-L1 via specific immunoreaction. Quantum dots-tagged signal strands are used to collect respective DNA products, and produce stripping signals corresponding to the amounts of total exosome and surfaceexpressing PD-L1, respectively. A wide linear relationship is established for the quantitative determination of lung cancer-derived exosomes in the range from 103to 1010particles/m L, whereas the ratiometric value of the two stripping signals is proven to have a better diagnostic use in screening and staging of lung cancer when being applied to clinical samples. Therefore, our method might provide a new insight into precise diagnosis of lung cancer, and offer sufficient information to refiect the biomarker level and guide the personalized treatment level even at an early stage in clinic.
基金supported in part by National Key R&D Program of China(Grant No.2018YFA0902300)。
文摘DNA synthesis and assembly technology is the fundamental enabling technology of synthetic biology,providing methods for humans to understand and modify organisms.Oligonucleotide chains and long DNA fragments synthesized through DNA synthesis and assembly technology are becoming increasingly widely used in fields such as biomedicine,energy,new materials,and information storage,with strong application prospects.This review provides a comprehensive and systematic introduction and exposition of current DNA synthesis and assembly technologies,discussing current challenges and future research prospects.
文摘Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology.In this study,we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate assembly technique,utilizing Escherichia coli as the model organism.Through polymerase chain reaction(PCR)amplification,restriction enzyme digestion,ligation,transformation,and Sanger sequencing,we assessed the operational efficiency and cloning fidelity of both strategies.Our results demonstrated that Golden Gate assembly,leveraging type IIS restriction enzymes and simultaneous ligation,significantly enhanced cloning efficiency and precision,particularly for seamless multi-fragment assembly.In contrast,the classical cloning approach maintained certain advantages in simplicity and robustness for specific experimental conditions.Challenges encountered during transformation and sequencing highlighted the critical impact of technical accuracy on experimental outcomes.This study underscores the importance of selecting appropriate cloning methodologies tailored to experimental objectives and laboratory capabilities,providing a foundation for optimized molecular cloning workflows in future synthetic biology and biotechnology applications.
基金supported by NNSFC(Nos.21273214,21425521,21521001)Hefei Center for Physical Science and Technology(No2014FXCX010)Collaborative Innovation Center of Suzhou Nano Science and Technology
文摘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.
基金supported by the National Natural Science Foundation of China(NSFC, No. 21174029)the Industry Academia Cooperation Innovation Fund of Jiangsu Province(No.BY201412707)+1 种基金the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)the Fundamental Research Funds for the Central Universities (No. 2242016K41020)
文摘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.
基金supported by the National Key Research and Development Program of China(2018YFA0900100 and 2019YFA0903800)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB18)+3 种基金the National Natural Science Foundation of China(31800069,32030004,31725002 and 32001065)Shenzhen Science and Technology Program(KQTD20180413181837372)Guangdong Provincial Key Laboratory of Synthetic Genomics(2019B030301006)Shenzhen Outstanding Talents Training Fund and the CAS President’s International Fellowship Initiative(2021VBB0002)。
文摘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.
基金supported by the National Key Research and Development Program of China[2020YFA0906900,2018YFA0900700]Natural Science Foundation of China[31500069]+1 种基金the Chinese Academy of Sciences[No.QYZDB-SSW-SMC050,No.XDB0480000 of the Strategic Priority Research Program]CAS Youth Interdisciplinary Team and the Shenzhen Science and Technology Innovation Committee[No.JCYJ20180507182241844,JCHZ20200005,DWKF20190009].
文摘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.
基金National Natural Science Foundation of China,Grant/Award Numbers:21974037,22264007,22104020Natural Science Foundation of Guangxi,Grant/Award Numbers:2021GXNSFFA220003,2022GXNSFDA035072,Guike-AD23026133+2 种基金Guangxi Science and Technology Major Program,Grant/Award Number:Guike-AA24011005Innovation Project of Guangxi Graduate Education,Grant/Award Numbers:YCBZ2023105,YCBZ2024135Guangxi Medical University Training Program for Distinguished Young Scholars。
文摘Solid bubbles have expanded the SERS assay toolbox,but their detection performance in biofluids is still hampered by the irrational design of the plasmonic sensing interface.A plasmonic bubble aggregate-driven DNA-encoded SERS assay is reported here that enables simultaneous,ultrasensitive,and specific detection of multiple miRNAs in blood samples for accurate cancer diagnosis.In this assay,the buoyancy of plasmonic bubbles allows them to self-aggregate at a droplet apex for SERS reconfiguration,form single-layer bubble aggregates with plasmonic nanogaps,and prevent the coffee ring effect during evaporation assembly.Furthermore,DNA-encoded plasmonic bubbles seamlessly couple with dual-color catalytic hybridization assembly to amplify the specific miRNA-responsive Raman signal,and function as both an analyte concentrator and a Raman signal aggregator without external forces.Using these merits,this magnet-free,portable assay achieves femtomolar dual-miRNA quantitation with single-base resolution,simultaneous miRNA detection across four cell lines,and accurate cancer diagnosis(AUC=1)via analyzing 40 blood samples with machine learning,thus providing a promising tool for clinical diagnosis.
基金financially supported by the National Natural Science Foundation of China(Nos.51573060 and 21427805)the Pearl River S&T Nova Program of Guangzhou(No.201710010146)
文摘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.
文摘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
基金supported by the National Natural Science Foundation of China(32101013,92068118 and 22125404)the China Postdoctoral Science Foundation(2018M643614)+1 种基金the Natural Science Basic Research Program of Shaanxi(2021JQ-016)the Fundamental Research Funds for the Central Universities.
文摘Plasmid mutagenesis is an essential step to engineer protein variants with desired properties.Direct generation of mutations on plasmids is a promising method compared to PCR-based methods and subcloning,yet it suffers from the sequence restriction in the generation of single-stranded circular plasmids.Here we demonstrate the CRISPR/Cas system-guided plasmid mutagenesis,a method using gRNA/Cas9 nickase complex to generate single-stranded circular plasmids as polymerization templates for mutagenesis.This method can directly create user-defined mutation libraries on the plasmid.It offers broad sequence programmability and even covers methylated plasmids.We further combine this method with rational design to engineer genome-editing protein FnCpf1.The FnCpf1 variants with mutations in the PAM-binding groove were generated.Several variants expanded the PAM range and exhibited lower off-target effect,which can loosen PAM constraint and enhance target specificity for genome editing.This work presents an effective tool for plasmid mutagenesis and protein engineering studies.
基金supported by the National Natural Science Foundation of China(21535006,21405123)
文摘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.
基金Cryo-EM images were collected at SKLB West China Cryo-EM Center in Sichuan UniversityThis work has been financially supported by the National Natural Science Foundation of China(No.22077089)Sichuan Province Science and Technology Support Program(No.2022YFSY0013).
文摘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.
文摘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,
基金the National Institutes of Health(GM077596)the National Academies Keck Futures Initiative on Synthetic Biology,Defense Advanced Research Program Agency,Roy J.Carver Charitable TrustInstitute for Genomic Biology at the University of Illinois at Urbana-Champaign for financial support in our development and application of DNA assembly technologies
文摘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.
