DNA-based hydrogels are exceptional materials for biological applications because of their numerous advantages such as biodegradability,biocompatibility,hydrophilicity,super absorbency,porosity,and swelling.Among thes...DNA-based hydrogels are exceptional materials for biological applications because of their numerous advantages such as biodegradability,biocompatibility,hydrophilicity,super absorbency,porosity,and swelling.Among these advantages,the ability of DNA-based hydrogels to respond to specific physical and chemical triggers and undergo reversible phase transitions has garnered significant attention in the fields of disease diagnosis(biosensors)and treatment(drug delivery).This article focuses on the recent advancements in the research of DNA-based hydrogels and discusses the different types of these hydrogels,the synthetic methods,their unique properties,and their applications in biosensors and drug delivery.The types of DNA hydrogels are categorized based on their building blocks,and the process of synthesis as well as the unique characteristics of DNA-based hydrogels are described.Then,DNA-based responsive hydrogels utilized as intelligent materials for the development of biosensors are reviewed.Furthermore,this article also presents the current status of DNA-based responsive hydrogels in drug delivery for cancer treatment,wound healing,and other therapeutic applications.Ultimately,this paper discusses the current challenges in expanding the practical application of DNA-based hydrogels.展开更多
Multiple endocrine neoplasia type 2A （MEN2A）, a subtype of MEN2, is characterized by medullary thyroid cancer, pheochromocytoma, and primary hyperparathyroidism. A Han Chinese pedigree with MEN2A was investigated fo...Multiple endocrine neoplasia type 2A （MEN2A）, a subtype of MEN2, is characterized by medullary thyroid cancer, pheochromocytoma, and primary hyperparathyroidism. A Han Chinese pedigree with MEN2A was investigated following confirmation of the proband＇s diagnosis by pathological findings and DNA/biochemical screening. DNA samples from 4 other family members were collected and exon 5, 8, 10, 11, 13, 16 and 18 of the RET proto-oncogene were sequenced and then analyzed. A missense mutation of TGG （Trp） to TGC （Cys） at codon 634 （the classic MEN2A mutation） in exon 11 of the RET gene was detected in 3 family members, including the proband. Sequencing data were compared with the human gene mutation database. Elevated serum calcitonin level was detected initially; medullary thyroid carcinoma was revealed in the 3 cases and adrenal pheochromocytoma was also found in the proband. Elective operations were successfully performed on the adrenal and thyroid glands because of pheochromocytoma and medullary thyroid carcinoma. Our case study confirms that integrated DNA-based/biochemical screening is crucial for early diagnosis of MEN2A and is helpful in the screening of their relatives. In addition, DNA-based screening may occasionally uncover a previously unknown RET sequence.展开更多
An electrochemical sensor incorporating a signal enhancement for the determination of lead （II） ions （Pb2＋） was designed on the basis of the thrombin-binding aptamer （TBA） as a molecular recog- nition element a...An electrochemical sensor incorporating a signal enhancement for the determination of lead （II） ions （Pb2＋） was designed on the basis of the thrombin-binding aptamer （TBA） as a molecular recog- nition element and ionic liquid supported cerium oxide （CeO2） nanoparticles-carbon nanotubes compo- site modification. The composite comprises nanoparticles CeO2, multi-waU carbon nanotubes （MWNTs） and hydrophobic room temperature ionic liquid （RTIL） 1-ethyl-3-methylimidazolium tetrafluoroborate （EMIMBF4）. The electrochemical sensors were fabricated by immersing the CeOa-MWNTs-EMIMBF4 modified glassy carbon electrode （GCE） into the solution of TBA probe. In the presence of Pb2＋, the TBA probe could form stable G-quartet structure by the specific binding interactions between Pb2＋ and TBA. The TBA-bound Pb2＋ can be electrochemically reduced, which provides a readout signal for quantitative detection of Pb2＋. The reduction peak current is linearly related to the concentration of Pb2＋ from 1.0 ＊ 10-8 M to 1.0 ＊ 105 M with a detection limit of 5 ＊ 109 M. This work demonstrates that the CeOz-MWNTs-EMIMBF4 nanocomposite modified GCE provides a promising platform for immobi- lizing the TBA probe and enhancing the sensitivity of the DNA-based sensors.展开更多
This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA ...This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.展开更多
Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction and guide precision medicine but suffers from high cost and being time-consuming.Here,we cons...Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction and guide precision medicine but suffers from high cost and being time-consuming.Here,we construct a fast molecular classifier based on freeze-thaw cycling that implements an in silico support vector machine(SVM)classifier model at the molecular level with a panel of disease-related biomarkers expression patterns for rapid disease diagnosis.The molecular classifier employs DNA reaction networks as the computing module and repeated dehydration and concentration process as the driving force to implement a set of simplified mathematical operations(such as multiplication,summation and subtraction)for efficient classification of complex input patterns.We demonstrate that the fast DNA-based molecular classifier enables precise cancer diagnosis within a short turnaround time in synthetic samples compared to those of free diffusion classifiers.We envision that this all-in-one molecular classifier will create more opportunities for inexpensive,accurate,and rapid disease diagnosis,prognosis and therapy,particularly in emergency departments or the point of care.展开更多
RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases,including cancer,genetic disorders,and infectious diseases.However,the delivery of RNA molecules into target cells has ...RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases,including cancer,genetic disorders,and infectious diseases.However,the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake.To overcome these hurdles,DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics.Due to its excellent characteristics such as programmability and biocompatibility,these DNA-based nanostructures,composed of DNA molecules assembled into precise and programmable structures,have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations.In this review,we highlight the current progress in the design and application of three DNA-based nanostructures:DNA origami,lipid-nanoparticle(LNP)technology related to frame guided assembly(FGA),and DNA hydrogel for the delivery of RNA molecules.Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.展开更多
Three plasmid expression vectors containing modified hepatitis B surface antigen (HBsAg) carrying pres epitopes were constructed. Transient expression after in vitro transfection in COS-M6 cells showed that under the ...Three plasmid expression vectors containing modified hepatitis B surface antigen (HBsAg) carrying pres epitopes were constructed. Transient expression after in vitro transfection in COS-M6 cells showed that under the transcriptional control of the human cytomegalovirus (CMV) immediate early promoter, fusion genes expressed the modified HBV envelope proteins which were efficiently secreted into culture medium and presented HBsAg, preS1 and preS2 antigenicity. DNA-based immunization with these plasmids carrying pres sequences induced anti-HBs antibody in BALB/c mice. The titers of anti-HBs antibody were higher than those appeared in mice immunized with plasmid carrying S gene only. DNA injection with plasmids containing preS1 sequences elicited also high titers of anti-preS1 antibody. Moreover, the antipreS1 antibodies were found to appear earlier than anti-HBs antibodies.展开更多
Diabetes mellitus considerably affects bone marrow mesenchymal stem cells(BMSCs),for example,by inhibiting their proliferation and differentiation potential,which enhances the difficulty in endogenous bone regeneratio...Diabetes mellitus considerably affects bone marrow mesenchymal stem cells(BMSCs),for example,by inhibiting their proliferation and differentiation potential,which enhances the difficulty in endogenous bone regeneration.Hence,effective strategies for enhancing the functions of BMSCs in diabetes have farreaching consequences for bone healing and regeneration in diabetes patients.Tetrahedral framework nucleic acids(tFNAs)are nucleic acid nanomaterials that can autonomously enter cells and regulate their behaviors.In this study,we evaluated the effects of tFNAs on BMSCs from diabetic rats.We found that tFNAs could promote the proliferation,migration,and osteogenic differentiation of BMSCs from rats with type 2 diabetes mellitus,and inhibited cell senescence and apoptosis.Furthermore,tFNAs effectively scavenged the accumulated reactive oxygen species and activated the suppressed protein kinase B(Akt)signaling pathway.Overall,we show that tFNAs can recover the proliferation and osteogenic potential of diabetic BMSCs by alleviating oxidative stress and activating Akt signaling.The study provides a strategy for endogenous bone regeneration in diabetes and also paves the way for exploiting DNA-based nanomaterials in regenerative medicine.展开更多
Toll-like receptors (TLRs) recognize specific motifs which are frequently present in bacteria, fungi, prokaryotes and viruses. Amongst TLRs, TLR9 can be activated by such bacterial or viral DNA fragments, immunoglobul...Toll-like receptors (TLRs) recognize specific motifs which are frequently present in bacteria, fungi, prokaryotes and viruses. Amongst TLRs, TLR9 can be activated by such bacterial or viral DNA fragments, immunoglobulin-DNA complexes or synthetic oligonucleotides, which all contain unmethylated cytosineguanine nucleotide sequences (CpGs). Emerging data indicate that TLR9 signaling has a role in, and may influence, colorectal carcinogenesis and colonic inflammation. CpGs are classified into three groups according to their influence on both the antigen-specific humoraland cellular immunity, and the production of type 1 interferons and proinflammatory cytokines. TLR9 activation via CpGs may serve as a new therapeutic target for several cancerous and various inflammatory conditions. Due to its probable anti-cancer effects, the application possibilities of TLR9-signaling modulation may be extremely diverse even in colorectal tumors. In this review we aimed to summarize the current knowledge about TLR-signaling in the pathogenesis and therapy of inflammatory bowel diseases and colorectal cancer. Due to the species-specific differences in TLR9 expression, however, one must be careful in translating the animal model data into the human system, because of the differences between CpG-oligodeoxynucleotide-responsive cells. TLR9 agonist DNA-based immunomodulatory sequences could also represent a promising therapeutic alternative in systemic inflammatory conditions and chronic colonic inflammations as their side effects are not significant.展开更多
Since the advent of sequencing technologies,the determination of microbial diversity to predict microbial functions,which are the major determinants of soil functions,has become a major topic of interest,as evidenced ...Since the advent of sequencing technologies,the determination of microbial diversity to predict microbial functions,which are the major determinants of soil functions,has become a major topic of interest,as evidenced by the 900 publications dealing with soil metagenome published up to 2017.However,the detection of a gene in soil does not mean that the relative function is expressed,and the presence of a particular taxon does not mean that the relative functions determined in pure culture also occur in the studied soil.Another critical step is to link microbial community composition or function to the product analyzed to determine flux rates.Indeed,flux rates might not only be highly dynamic,but several metabolites can depend on different reactions,which makes the link to one process of interest difficult or even impossible.This review also discusses biases caused by sampling,storage of samples,DNA extraction and purification,sequencing(amplicon-vs.metagenome sequencing),and bioinformatic data analysis.Insights and the limits of predicting microbial interactions by network inference methods are critically discussed,and finally,future directions for a better understanding of soil functions by using measurements of microbial diversity are presented.展开更多
Most of the current analytical methods depend largely on laboratory-based analytical techniques that require expensive and bullky equipment,potentially incur costly testing,and involve lengthy detection processes.With...Most of the current analytical methods depend largely on laboratory-based analytical techniques that require expensive and bullky equipment,potentially incur costly testing,and involve lengthy detection processes.With increasing requirements for point-of-care testing(POCT),more attention has been paid to miniaturized analytical devices.Miniaturized electrochemical(MEC)sensors,including different material-based MEC sensors(such as DNA-,paper-,and screen electrode-based),have been in strong demand in analytical science due to their easy operation,portability,high sensitivity,as well as their short analysis time.They have been applied for the detection of trace amounts of target through measuring changes in electrochemical signal,such as current,voltage,potential,or impedance,due to the oxidation/reduction of chemical/biological molecules with the help of electrodes and electrochemical units.MEC sensors present great potential for the detection of targets including small organic molecules,metal ions,and biomolecules.In recent years,MEC sensors have been broadly applied to POCT in various fields,including health care,food safety,and environmental monitoring,owing to the excellent advantages of electrochemical(EC)technologies.This review summarized the state-of-the-art advancements on various types of MEC sensors and their applications in POCT.Furthermore,the future perspectives,opportunities,and challenges in this field are also discussed.展开更多
Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere.However,soil organic carbon accumulation associate...Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere.However,soil organic carbon accumulation associated with microbial methane oxidation is poorly understood.Therefore,to investigate methane-derived carbon incorporation into soil organic matter,paddy soils originated from different parent materials(Inceptisol,Entisol,and Alfisol) were collected after rice harvesting from four major rice-producing regions in Bangladesh.Following microcosm incubation with 5%(volume/volume)^(13) CH_(4),soil^(13) C-atom abundances significantly increased from background level of 1.08% to 1.88%–2.78%,leading to a net methane-derived accumulation of soil organic carbon ranging from 120 to 307 mg kg^(-1).Approximately 23.6%–60.0% of the methane consumed was converted to soil organic carbon during microbial methane oxidation.The phylogeny of^(13) C-labeled pmoA(enconding the alpha subunit of the particulate methane monooxygenase) and 16 S rRNA genes further revealed that canonical α(type II) and γ(type I) Proteobacteria were active methane oxidizers.Members within the Methylobacter-and Methylosarcina-affiliated type Ia lineages dominated active methane-oxidizing communities that were responsible for the majority of methane-derived carbon accumulation in all three paddy soils,while Methylocystis-affiliated type IIa lineage was the key contributor in one paddy soil of Inceptisol origin.These results suggest that methanotroph-mediated synthesis of biomass plays an important role in soil organic matter accumulation.This study thus supports the concept that methanotrophs not only consume the greenhouse gas methane but also serve as a key biotic factor in maintaining soil fertility.展开更多
The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community.The idea of using intracellular DNA("...The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community.The idea of using intracellular DNA("mgDNA")from environmental samples as holotypes seems at face value,to be a good idea,considering the expansion of knowledge among these‘dark taxa’or‘dark matter fungi’that it could provide(i.e.sequence based taxa without physical specimens and formal nomenclature).However,the limitations of using mgDNA as holotypes needs careful thought,i.e.can we use a short mgDNA fragment,which may contain a small amount of genetic information,to allow discrimination between species?What is the point and are the potential problems of giving valid scientific names to mgDNA?Numerous mycologists and taxonomists,who have many years of experience working on the taxonomy and phylogeny of different groups of fungi,are concerned about the consequences of providing valid names to mgDNA.There has been much debate,through several publications on the considerable problems of using mgDNA as holotypes.The proponents have tried to debate the virtues of using mgDNA as holotypes.Those against have shown that identification to species using mgDNA does not work in many fungal groups,while those for have shown cases where species can be identified with mgDNA.Different disciplines have different reasons and opinions for using mgDNA as holotypes,however even groups of the same disciplines have dissimilar ideas.In this paper we explore the use of mgDNA as holotypes.We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences.In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa,but relate the issues to fungal taxonomy.In fact we show the value of using sequence data from these approaches,in dealing with the discovery of already named taxa,taxa numbers and ecological roles.We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes.The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed.We provide evidence from case studies on Botryosphaeria,Colletotrichum,Penicillium and Xylaria.The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing.We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species.If this approach adopted,it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes.We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.展开更多
The self-assembly monolayer (SAM) was prepared with 2-aminoethanethiol (AET) on the gold electrode. A new approach based on potential was first used to control DNA self-assembly covalently onto the SAM with the activa...The self-assembly monolayer (SAM) was prepared with 2-aminoethanethiol (AET) on the gold electrode. A new approach based on potential was first used to control DNA self-assembly covalently onto the SAM with the activation of l-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDC) and N-hydroxysulfosuccinimide (NHS). The influence of potential on DNA self-assembly was investigated by means of cyclic voltammetry (CV), AC impedance, Auger electron spectrometry (AES) and atomic force microscopy (AFM). The result proves that controlled potential can affect the course of DNA self-assembly. More negative potential can restrain the DNA self-assembly, while more positive potential can accelerate the DNA self-assembly, which is of great significance for the control of DNA self-assembly and will find wide application in the field of DNA-based devices.展开更多
Theranostic nanoprobes can potentially integrate imaging and therapeutic capabilities into a single platform,offering a new personalized cancer diagnostic tool.However,there is a growing concern that their clinical ap...Theranostic nanoprobes can potentially integrate imaging and therapeutic capabilities into a single platform,offering a new personalized cancer diagnostic tool.However,there is a growing concern that their clinical application is not safe,particularly due to metal-containing elements,such as the gadolinium used in magnetic resonance imaging(MRI).We demonstrate for the first time that the photothermal melting of the DNA duplex helix was a reliable and versatile strategy that enables the on-demand degradation of the gadolinium-containing MRI reporter gene from polydopamine(PDA)-based theranostic nanoprobes.The combination of chemotherapy(doxorubicin)and photothermal therapy,which leads to the enhanced anti-tumor effect.In vivo MRI tracking reveals that renal filtration was able to rapidly clear the free gadolinium-containing MRI reporter from the mice body.This results in a decrease in the long-term toxic effect of theranostic MRI nanoprobes.Our findings may pave the way to address toxicity issues of the theranostic nanoprobes.展开更多
Endogenous biomolecules in cells are the basis of all life activities.Directly visualizing the structural characteristics and dynamic behaviors of cellular biomolecules is signiffcant for understanding the molecular m...Endogenous biomolecules in cells are the basis of all life activities.Directly visualizing the structural characteristics and dynamic behaviors of cellular biomolecules is signiffcant for understanding the molecular mechanisms in various biological processes.Singlemolecule localization microscopy(SMLM)can circumvent the optical diffraction limit,achieving analysis of the ffne structures and biological processes in living cells with nanoscale resolution.However,the large size of traditional imaging probes prevents SMLM from accurately locating ffne structures and densely distributed biomolecules within cells.In recent years,nucleic acid probes have emerged as potential tools to replace conventional SMLM probes by virtue of their small size and high speciffcity.In addition,due to their programmability,nucleic acid probes with different conformations can be constructed via sequence design,further extending the application of SMLM in bioanalysis.Here,we discuss the design concepts of different conformational nucleic acid probes for SMLM and summarize the application of SMLM based on nucleic acid probes in the ffeld of biomolecules.Furthermore,we provide a summary and future perspectives of the nucleic acid probe-based SMLM technology,aiming to provide guidance for the acquisition of nanoscale information about cellular biological processes.展开更多
基金financially supported by the National Natural Science Foundation of China(No.21804014)the Natural Science Foundation of Chongqing Science&Technology Commission(No.2023jcyjA3529)+1 种基金the Science and Technology Research Program of Chongqing Municipal Education Commission(No.KJQN202200832)Construction of Graduate Joint Training Base of Chongqing Municipal Education Commission(No.yjd223005)。
文摘DNA-based hydrogels are exceptional materials for biological applications because of their numerous advantages such as biodegradability,biocompatibility,hydrophilicity,super absorbency,porosity,and swelling.Among these advantages,the ability of DNA-based hydrogels to respond to specific physical and chemical triggers and undergo reversible phase transitions has garnered significant attention in the fields of disease diagnosis(biosensors)and treatment(drug delivery).This article focuses on the recent advancements in the research of DNA-based hydrogels and discusses the different types of these hydrogels,the synthetic methods,their unique properties,and their applications in biosensors and drug delivery.The types of DNA hydrogels are categorized based on their building blocks,and the process of synthesis as well as the unique characteristics of DNA-based hydrogels are described.Then,DNA-based responsive hydrogels utilized as intelligent materials for the development of biosensors are reviewed.Furthermore,this article also presents the current status of DNA-based responsive hydrogels in drug delivery for cancer treatment,wound healing,and other therapeutic applications.Ultimately,this paper discusses the current challenges in expanding the practical application of DNA-based hydrogels.
基金supported by grant 81170747 from the National Natural Sciences Foundation of Chinagrant H201106 from Health Promotion Foundation of Jiangsu Provincegrant from the Office of Human Resources and Social Security of Jiangsu Province (Peak of the Six Personnel in Jiangsu Province) to Hongwen Zhou
文摘Multiple endocrine neoplasia type 2A （MEN2A）, a subtype of MEN2, is characterized by medullary thyroid cancer, pheochromocytoma, and primary hyperparathyroidism. A Han Chinese pedigree with MEN2A was investigated following confirmation of the proband＇s diagnosis by pathological findings and DNA/biochemical screening. DNA samples from 4 other family members were collected and exon 5, 8, 10, 11, 13, 16 and 18 of the RET proto-oncogene were sequenced and then analyzed. A missense mutation of TGG （Trp） to TGC （Cys） at codon 634 （the classic MEN2A mutation） in exon 11 of the RET gene was detected in 3 family members, including the proband. Sequencing data were compared with the human gene mutation database. Elevated serum calcitonin level was detected initially; medullary thyroid carcinoma was revealed in the 3 cases and adrenal pheochromocytoma was also found in the proband. Elective operations were successfully performed on the adrenal and thyroid glands because of pheochromocytoma and medullary thyroid carcinoma. Our case study confirms that integrated DNA-based/biochemical screening is crucial for early diagnosis of MEN2A and is helpful in the screening of their relatives. In addition, DNA-based screening may occasionally uncover a previously unknown RET sequence.
基金supports from the National Science Foundations of China (Nos. 20875076 and 21005061)the Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20096101120011)+2 种基金the Natural Science Basic Research Plan in Shaanxi Province of China (No.2010JQ2013)the Education Department of Shaanxi Province,China (No. 09JK759)the NWU Graduate Innovation and Creativity Funds (No. 09YSY04)
文摘An electrochemical sensor incorporating a signal enhancement for the determination of lead （II） ions （Pb2＋） was designed on the basis of the thrombin-binding aptamer （TBA） as a molecular recog- nition element and ionic liquid supported cerium oxide （CeO2） nanoparticles-carbon nanotubes compo- site modification. The composite comprises nanoparticles CeO2, multi-waU carbon nanotubes （MWNTs） and hydrophobic room temperature ionic liquid （RTIL） 1-ethyl-3-methylimidazolium tetrafluoroborate （EMIMBF4）. The electrochemical sensors were fabricated by immersing the CeOa-MWNTs-EMIMBF4 modified glassy carbon electrode （GCE） into the solution of TBA probe. In the presence of Pb2＋, the TBA probe could form stable G-quartet structure by the specific binding interactions between Pb2＋ and TBA. The TBA-bound Pb2＋ can be electrochemically reduced, which provides a readout signal for quantitative detection of Pb2＋. The reduction peak current is linearly related to the concentration of Pb2＋ from 1.0 ＊ 10-8 M to 1.0 ＊ 105 M with a detection limit of 5 ＊ 109 M. This work demonstrates that the CeOz-MWNTs-EMIMBF4 nanocomposite modified GCE provides a promising platform for immobi- lizing the TBA probe and enhancing the sensitivity of the DNA-based sensors.
基金This work was supportedin part by the National Nature Science Foundation of China (No.60474037and60004006) Programfor NewCentury Excellent Talents in University (NCET04 415) +1 种基金Specialized Research Fund for the Doctoral Programof Higher Educationfrom Educational Committee of China (No.20030255009) the Youth Foundation fromEducational Committee of Anhui Province(No.2005jql043) .
文摘This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.
基金supported by the National Science Foundation of China(Grant Nos.21991134,22074041)the Shanghai Science and Technology Committee(STCSM)(23ZR1479600).
文摘Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction and guide precision medicine but suffers from high cost and being time-consuming.Here,we construct a fast molecular classifier based on freeze-thaw cycling that implements an in silico support vector machine(SVM)classifier model at the molecular level with a panel of disease-related biomarkers expression patterns for rapid disease diagnosis.The molecular classifier employs DNA reaction networks as the computing module and repeated dehydration and concentration process as the driving force to implement a set of simplified mathematical operations(such as multiplication,summation and subtraction)for efficient classification of complex input patterns.We demonstrate that the fast DNA-based molecular classifier enables precise cancer diagnosis within a short turnaround time in synthetic samples compared to those of free diffusion classifiers.We envision that this all-in-one molecular classifier will create more opportunities for inexpensive,accurate,and rapid disease diagnosis,prognosis and therapy,particularly in emergency departments or the point of care.
基金National Basic Research Plan of China(2023YFA0915201)Beijing Municipal Science&Technology Commission(Z231100007223003)National Natural Science Foundation of China(21890731,21821001,21890730,and 32270627)。
文摘RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases,including cancer,genetic disorders,and infectious diseases.However,the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake.To overcome these hurdles,DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics.Due to its excellent characteristics such as programmability and biocompatibility,these DNA-based nanostructures,composed of DNA molecules assembled into precise and programmable structures,have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations.In this review,we highlight the current progress in the design and application of three DNA-based nanostructures:DNA origami,lipid-nanoparticle(LNP)technology related to frame guided assembly(FGA),and DNA hydrogel for the delivery of RNA molecules.Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.
文摘Three plasmid expression vectors containing modified hepatitis B surface antigen (HBsAg) carrying pres epitopes were constructed. Transient expression after in vitro transfection in COS-M6 cells showed that under the transcriptional control of the human cytomegalovirus (CMV) immediate early promoter, fusion genes expressed the modified HBV envelope proteins which were efficiently secreted into culture medium and presented HBsAg, preS1 and preS2 antigenicity. DNA-based immunization with these plasmids carrying pres sequences induced anti-HBs antibody in BALB/c mice. The titers of anti-HBs antibody were higher than those appeared in mice immunized with plasmid carrying S gene only. DNA injection with plasmids containing preS1 sequences elicited also high titers of anti-preS1 antibody. Moreover, the antipreS1 antibodies were found to appear earlier than anti-HBs antibodies.
基金supported by National Natural Science Foundation of China(No.82301030)China Postdoctoral Science Foundation(No.2022M712384)+2 种基金Tianjin Education Commission Research Project(No.2021KJ244)Tianjin Health Science and Technology Project(No.TJWJ2021QN038)Tianjin Key Medical Discipline(Specialty)Construction Project(No.TJYXZDXK-038A).
文摘Diabetes mellitus considerably affects bone marrow mesenchymal stem cells(BMSCs),for example,by inhibiting their proliferation and differentiation potential,which enhances the difficulty in endogenous bone regeneration.Hence,effective strategies for enhancing the functions of BMSCs in diabetes have farreaching consequences for bone healing and regeneration in diabetes patients.Tetrahedral framework nucleic acids(tFNAs)are nucleic acid nanomaterials that can autonomously enter cells and regulate their behaviors.In this study,we evaluated the effects of tFNAs on BMSCs from diabetic rats.We found that tFNAs could promote the proliferation,migration,and osteogenic differentiation of BMSCs from rats with type 2 diabetes mellitus,and inhibited cell senescence and apoptosis.Furthermore,tFNAs effectively scavenged the accumulated reactive oxygen species and activated the suppressed protein kinase B(Akt)signaling pathway.Overall,we show that tFNAs can recover the proliferation and osteogenic potential of diabetic BMSCs by alleviating oxidative stress and activating Akt signaling.The study provides a strategy for endogenous bone regeneration in diabetes and also paves the way for exploiting DNA-based nanomaterials in regenerative medicine.
文摘Toll-like receptors (TLRs) recognize specific motifs which are frequently present in bacteria, fungi, prokaryotes and viruses. Amongst TLRs, TLR9 can be activated by such bacterial or viral DNA fragments, immunoglobulin-DNA complexes or synthetic oligonucleotides, which all contain unmethylated cytosineguanine nucleotide sequences (CpGs). Emerging data indicate that TLR9 signaling has a role in, and may influence, colorectal carcinogenesis and colonic inflammation. CpGs are classified into three groups according to their influence on both the antigen-specific humoraland cellular immunity, and the production of type 1 interferons and proinflammatory cytokines. TLR9 activation via CpGs may serve as a new therapeutic target for several cancerous and various inflammatory conditions. Due to its probable anti-cancer effects, the application possibilities of TLR9-signaling modulation may be extremely diverse even in colorectal tumors. In this review we aimed to summarize the current knowledge about TLR-signaling in the pathogenesis and therapy of inflammatory bowel diseases and colorectal cancer. Due to the species-specific differences in TLR9 expression, however, one must be careful in translating the animal model data into the human system, because of the differences between CpG-oligodeoxynucleotide-responsive cells. TLR9 agonist DNA-based immunomodulatory sequences could also represent a promising therapeutic alternative in systemic inflammatory conditions and chronic colonic inflammations as their side effects are not significant.
文摘Since the advent of sequencing technologies,the determination of microbial diversity to predict microbial functions,which are the major determinants of soil functions,has become a major topic of interest,as evidenced by the 900 publications dealing with soil metagenome published up to 2017.However,the detection of a gene in soil does not mean that the relative function is expressed,and the presence of a particular taxon does not mean that the relative functions determined in pure culture also occur in the studied soil.Another critical step is to link microbial community composition or function to the product analyzed to determine flux rates.Indeed,flux rates might not only be highly dynamic,but several metabolites can depend on different reactions,which makes the link to one process of interest difficult or even impossible.This review also discusses biases caused by sampling,storage of samples,DNA extraction and purification,sequencing(amplicon-vs.metagenome sequencing),and bioinformatic data analysis.Insights and the limits of predicting microbial interactions by network inference methods are critically discussed,and finally,future directions for a better understanding of soil functions by using measurements of microbial diversity are presented.
基金the China National Key R&D Program(No.2017YFC1601604)National Natural Science Foundation of China(NSFC)(No.21777189)for financially supporting this research。
文摘Most of the current analytical methods depend largely on laboratory-based analytical techniques that require expensive and bullky equipment,potentially incur costly testing,and involve lengthy detection processes.With increasing requirements for point-of-care testing(POCT),more attention has been paid to miniaturized analytical devices.Miniaturized electrochemical(MEC)sensors,including different material-based MEC sensors(such as DNA-,paper-,and screen electrode-based),have been in strong demand in analytical science due to their easy operation,portability,high sensitivity,as well as their short analysis time.They have been applied for the detection of trace amounts of target through measuring changes in electrochemical signal,such as current,voltage,potential,or impedance,due to the oxidation/reduction of chemical/biological molecules with the help of electrodes and electrochemical units.MEC sensors present great potential for the detection of targets including small organic molecules,metal ions,and biomolecules.In recent years,MEC sensors have been broadly applied to POCT in various fields,including health care,food safety,and environmental monitoring,owing to the excellent advantages of electrochemical(EC)technologies.This review summarized the state-of-the-art advancements on various types of MEC sensors and their applications in POCT.Furthermore,the future perspectives,opportunities,and challenges in this field are also discussed.
基金financially supported by the National Natural Science Foundation of China (Nos. 91751204, 41630862, 41701302, 41530857, and 41877062)The first author, Ms. Nasrin Sultana, gratefully acknowledges the Organization for Women in Science for the Developing World (OWSD) Ph.D. Fellowship。
文摘Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere.However,soil organic carbon accumulation associated with microbial methane oxidation is poorly understood.Therefore,to investigate methane-derived carbon incorporation into soil organic matter,paddy soils originated from different parent materials(Inceptisol,Entisol,and Alfisol) were collected after rice harvesting from four major rice-producing regions in Bangladesh.Following microcosm incubation with 5%(volume/volume)^(13) CH_(4),soil^(13) C-atom abundances significantly increased from background level of 1.08% to 1.88%–2.78%,leading to a net methane-derived accumulation of soil organic carbon ranging from 120 to 307 mg kg^(-1).Approximately 23.6%–60.0% of the methane consumed was converted to soil organic carbon during microbial methane oxidation.The phylogeny of^(13) C-labeled pmoA(enconding the alpha subunit of the particulate methane monooxygenase) and 16 S rRNA genes further revealed that canonical α(type II) and γ(type I) Proteobacteria were active methane oxidizers.Members within the Methylobacter-and Methylosarcina-affiliated type Ia lineages dominated active methane-oxidizing communities that were responsible for the majority of methane-derived carbon accumulation in all three paddy soils,while Methylocystis-affiliated type IIa lineage was the key contributor in one paddy soil of Inceptisol origin.These results suggest that methanotroph-mediated synthesis of biomass plays an important role in soil organic matter accumulation.This study thus supports the concept that methanotrophs not only consume the greenhouse gas methane but also serve as a key biotic factor in maintaining soil fertility.
基金supported by the development special funds of Shenzhen strategic emerging industries and future industries(201708021308)the Shenzhen science and technology key project(JSGG20171013091238230).
文摘The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community.The idea of using intracellular DNA("mgDNA")from environmental samples as holotypes seems at face value,to be a good idea,considering the expansion of knowledge among these‘dark taxa’or‘dark matter fungi’that it could provide(i.e.sequence based taxa without physical specimens and formal nomenclature).However,the limitations of using mgDNA as holotypes needs careful thought,i.e.can we use a short mgDNA fragment,which may contain a small amount of genetic information,to allow discrimination between species?What is the point and are the potential problems of giving valid scientific names to mgDNA?Numerous mycologists and taxonomists,who have many years of experience working on the taxonomy and phylogeny of different groups of fungi,are concerned about the consequences of providing valid names to mgDNA.There has been much debate,through several publications on the considerable problems of using mgDNA as holotypes.The proponents have tried to debate the virtues of using mgDNA as holotypes.Those against have shown that identification to species using mgDNA does not work in many fungal groups,while those for have shown cases where species can be identified with mgDNA.Different disciplines have different reasons and opinions for using mgDNA as holotypes,however even groups of the same disciplines have dissimilar ideas.In this paper we explore the use of mgDNA as holotypes.We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences.In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa,but relate the issues to fungal taxonomy.In fact we show the value of using sequence data from these approaches,in dealing with the discovery of already named taxa,taxa numbers and ecological roles.We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes.The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed.We provide evidence from case studies on Botryosphaeria,Colletotrichum,Penicillium and Xylaria.The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing.We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species.If this approach adopted,it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes.We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.
基金This work was supported by the National Natural Science Foundation of China (Grant Nos. 69890220 and 60171005) the Natural Science Foundation of Jiangsu Province (China) (Grant Nos. BK99006 and BK2001131)the Promotional Foundation of the Ministry of
文摘The self-assembly monolayer (SAM) was prepared with 2-aminoethanethiol (AET) on the gold electrode. A new approach based on potential was first used to control DNA self-assembly covalently onto the SAM with the activation of l-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDC) and N-hydroxysulfosuccinimide (NHS). The influence of potential on DNA self-assembly was investigated by means of cyclic voltammetry (CV), AC impedance, Auger electron spectrometry (AES) and atomic force microscopy (AFM). The result proves that controlled potential can affect the course of DNA self-assembly. More negative potential can restrain the DNA self-assembly, while more positive potential can accelerate the DNA self-assembly, which is of great significance for the control of DNA self-assembly and will find wide application in the field of DNA-based devices.
基金supported by the National Natural Science Foundation of China(21635007 and 21605137)the National Key Research and Development Program of China(2016YFA0203200)+2 种基金Natural Science Foundation of Shandong Province(2018GGX102030)Taishan Scholar Program of Shandong Province(ts201511027)K.C.Wong Education Foundation。
文摘Theranostic nanoprobes can potentially integrate imaging and therapeutic capabilities into a single platform,offering a new personalized cancer diagnostic tool.However,there is a growing concern that their clinical application is not safe,particularly due to metal-containing elements,such as the gadolinium used in magnetic resonance imaging(MRI).We demonstrate for the first time that the photothermal melting of the DNA duplex helix was a reliable and versatile strategy that enables the on-demand degradation of the gadolinium-containing MRI reporter gene from polydopamine(PDA)-based theranostic nanoprobes.The combination of chemotherapy(doxorubicin)and photothermal therapy,which leads to the enhanced anti-tumor effect.In vivo MRI tracking reveals that renal filtration was able to rapidly clear the free gadolinium-containing MRI reporter from the mice body.This results in a decrease in the long-term toxic effect of theranostic MRI nanoprobes.Our findings may pave the way to address toxicity issues of the theranostic nanoprobes.
基金supported by the Natural Science Foundation of Hunan Province(2022JJ20005)National Natural Science Foundation of China(22174038,21925401,and 52221001),and Tencent Foundation.
文摘Endogenous biomolecules in cells are the basis of all life activities.Directly visualizing the structural characteristics and dynamic behaviors of cellular biomolecules is signiffcant for understanding the molecular mechanisms in various biological processes.Singlemolecule localization microscopy(SMLM)can circumvent the optical diffraction limit,achieving analysis of the ffne structures and biological processes in living cells with nanoscale resolution.However,the large size of traditional imaging probes prevents SMLM from accurately locating ffne structures and densely distributed biomolecules within cells.In recent years,nucleic acid probes have emerged as potential tools to replace conventional SMLM probes by virtue of their small size and high speciffcity.In addition,due to their programmability,nucleic acid probes with different conformations can be constructed via sequence design,further extending the application of SMLM in bioanalysis.Here,we discuss the design concepts of different conformational nucleic acid probes for SMLM and summarize the application of SMLM based on nucleic acid probes in the ffeld of biomolecules.Furthermore,we provide a summary and future perspectives of the nucleic acid probe-based SMLM technology,aiming to provide guidance for the acquisition of nanoscale information about cellular biological processes.
