Phaeocystis globosa Scherffel is one of the common harmful algae species in coastal waters of the southeastern China.In this study,sandwich hybridization integrated with nuclease protection assay(NPA-SH)was used to qu...Phaeocystis globosa Scherffel is one of the common harmful algae species in coastal waters of the southeastern China.In this study,sandwich hybridization integrated with nuclease protection assay(NPA-SH)was used to qualitatively and quantitatively detect P. globosa.Results showed that this method had good applicability and validity in analyzing the samples from laboratory cultures and from fields.The linear regression equation for P.globosa was obtained,and the lowest detection number of cells was 1.8×104 c...展开更多
Animal studies have shown that amphoteric detergent and nuclease(DNase I and ribonuclease A) is the most reliable decellularization method of the peripheral nerve. However, the optimal combination of chemical reagents...Animal studies have shown that amphoteric detergent and nuclease(DNase I and ribonuclease A) is the most reliable decellularization method of the peripheral nerve. However, the optimal combination of chemical reagents for decellularization of human nerve allograft needs further investigation. To find the optimal protocol to remove the immunogenic cellular components of the nerve tissue and preserve the basal lamina and extracellular matrix and whether the optimal protocol can be applied to larger-diameter human peripheral nerves, in this study, we decellularized the median and sural nerves from the cadavers with two different methods: nonionic and anionic detergents(Triton X-100 and sodium deoxycholate) and amphoteric detergent and nuclease(3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate(CHAPS), deoxyribonuclease I, and ribonuclease A). All cellular components were successfully removed from the median and sural nerves by amphoteric detergent and nuclease. Not all cellular components were removed from the median nerve by nonionic and anionic detergent. Both median and sural nerves treated with amphoteric detergent and nuclease maintained a completely intact extracellular matrix. Treatment with nonionic and anionic detergent decreased collagen content in both median and sural nerves, while the amphoteric detergent and nuclease treatment did not reduce collagen content. In addition, a contact cytotoxicity assay revealed that the nerves decellularized by amphoteric detergent and nuclease was biocompatible. Strength failure testing demonstrated that the biomechanical properties of nerves decellularized with amphoteric detergent and nuclease were comparable to those of fresh controls. Decellularization with amphoteric detergent and nuclease better remove cellular components and better preserve extracellular matrix than decellularization with nonionic and anionic detergents, even in large-diameter human peripheral nerves. In Korea, cadaveric studies are not yet legally subject to Institutional Review Board review.展开更多
Prorocentrum donghaiense is an important harmful algae bloom （HAB） causing creature in China＇s seas, and the conventional visual detection can not cope with long-term monitoring and highthroughput sampling projects...Prorocentrum donghaiense is an important harmful algae bloom （HAB） causing creature in China＇s seas, and the conventional visual detection can not cope with long-term monitoring and highthroughput sampling projects. An assay for P. donghaiense with sandwich hybridization integrated with nuclease protection assay （NPA-SH） was established. Tests with mixed samples and spiked field ones confirmed its good specificity and sensitivity. The cell number of P. donghaiense correlated well with the optical density, and the regression equation is y=4× 10^- 6x＋ 0.694 9, in which x is the cell number, and y is the optical density, with r2=0.953 5. These results show that the NPA-SH method has good feasibility in the detection of P. donghaiense. Results of NPA-SH and microscopy are excellent for each sample. The NPA-SH method was a simple way in quantitative detection of P. donghaiense, and the whole process could be finished in about six hours, which provided a new approach in high-throughput sampling and long-term monitoring of P. donghaiense.展开更多
Targeted genome editing is a continually evolving technology employing programmable nucleases to specifically change,insert,or remove a genomic sequence of interest.These advanced molecular tools include meganucleases...Targeted genome editing is a continually evolving technology employing programmable nucleases to specifically change,insert,or remove a genomic sequence of interest.These advanced molecular tools include meganucleases,zinc finger nucleases,transcription activator-like effector nucleases and RNA-guided engineered nucleases(RGENs),which create double-strand breaks at specific target sites in the genome,and repair DNA either by homologous recombination in the presence of donor DNA or via the error-prone non-homologous end-joining mechanism.A recently discovered group of RGENs known as CRISPR/Cas9 gene-editing systems allowed precise genome manipulation revealing a causal association between disease genotype and phenotype,without the need for the reengineering of the specific enzyme when targeting different sequences.CRISPR/Cas9 has been successfully employed as an ex vivo gene-editing tool in embryonic stem cells and patient-derived stem cells to understand pancreatic beta-cell development and function.RNA-guided nucleases also open the way for the generation of novel animal models for diabetes and allow testing the efficiency of various therapeutic approaches in diabetes,as summarized and exemplified in this manuscript.展开更多
Accurate DNA quantitation is a prerequisite in many biomedical and pharmaceutical studies.Here we established a new DNA quantitation method by nuclease P1 digestion and UPLC-MS/MS analysis.DNA fragments can be efficie...Accurate DNA quantitation is a prerequisite in many biomedical and pharmaceutical studies.Here we established a new DNA quantitation method by nuclease P1 digestion and UPLC-MS/MS analysis.DNA fragments can be efficiently hydrolyzed to single deoxyribonucleotides by nuclease P1 in a short time.The decent stabilities of all the four deoxyribonucleotides were confirmed under different conditions.Deoxyadenosine monophosphate(dAMP)was selected as the surrogate for DNA quantitation because dAMP showed the highest sensitivity among the four deoxyribonucleotides in the UPLC-MS/MS analysis.The linear range in DNA quantitation by this method is 1.2-5000 ng/mL.In the validation,the inter-day and intra-day accuracies were within 90%-110%,and the inter-day and intra-day precision were acceptable(RSD<10%).The validated method was successfully applied to quantitate DNA isolated from tumors and organs of a mouse xenograft model.Compared to the quantitation methods using UV absorbance,the reported method provides an enhanced sensitivity,and it allows for the accurate quantitation of isolated DNA with contamination of RNA and ribonucleotide.展开更多
Internal solvation of protein was studied by site-directed mutagenesis, with which an intrinsically fluorescent probe,tryptophan, is inserted into the desired position inside a protein molecule for ultrafast spectrosc...Internal solvation of protein was studied by site-directed mutagenesis, with which an intrinsically fluorescent probe,tryptophan, is inserted into the desired position inside a protein molecule for ultrafast spectroscopic study. Here we review this unique method for protein dynamics research. We first introduce the frontiers of protein solvation, site-directed mutagenesis, protein stability and characteristics, and the spectroscopic methods. Then we present time-resolved spectroscopic dynamics of solvation dynamics inside cavities of active sites. The studies are carried out on a globular protein, staphylococcal nuclease. The solvation at sites inside the protein molecule＇s cavities clearly reveals characteristics of the local environment. These solvation behaviors are directly correlated to enzyme activity.展开更多
Tryptophan （Trp） is an intrinsic fluorescent probe for detecting the site-specified dynamics inside/outside protein. It is found that the Trp can easily be inserted in desired sites of protein, which affects the int...Tryptophan （Trp） is an intrinsic fluorescent probe for detecting the site-specified dynamics inside/outside protein. It is found that the Trp can easily be inserted in desired sites of protein, which affects the integrity of the overall structure. To evaluate this effect, we design thirteen double point mutants of staphylococcal nuclease, each of which has a single Trp residue planted at an internal site. The studies on Trp fluorescence, ANS-binding fluorescence, far- and near-UV CD spectra, and enzymatic activity are carried out. It is found that the mutation at the hydrophobic core of protein generates molten globular state conformation, which is a loose structure compared to their original compactness in wild type （WT）. Its enzyme activity and surface hydrophobicity are also affected. The studies show that by proper site designing and external binding, Trp mutagenesis is a suitable method for carrying out the study on site specified dynamics of proteins.展开更多
Objective: To establish a novel approach for quick and highly efficient verification of human gene imprinting. Methods: A pair of dye-labelled probes, 5' nuclease assay was combined with RT-PCR to determine the ge...Objective: To establish a novel approach for quick and highly efficient verification of human gene imprinting. Methods: A pair of dye-labelled probes, 5' nuclease assay was combined with RT-PCR to determine the genotype of a transcribed single nucleotide polymorphism (SNP) rs705(C>T) of a known imprinted gene, small nuclear ribonucleotide protein N (SNRPN), on both genomic DNA and cDNA of human lym-phoblast cell lines. Results: Allele discrimination showed a clear monoallelic expression pattern of SNRPN, which was confirmed by RT-PCR based restriction fragment length polymorphism (RFLPs). Pedigree analysis verified the paternal origin of expressed allele, which was in consistency with previous report. Conclusion: Transcribed SNP is an ideal marker for detecting gene imprinting by 5' nuclease assay. This approach also may be used to discover differential allele expression of non-imprinted genes, finding out gene cis-acting functional polymorphism.展开更多
The distribution and specificity of extracellular nucleases produced by marine fungi belonging to eleven genera, namely: Alternaria, Aspergillus, Aureobasidium, Chaetomium, Fusarium, Gliomastix, Humicola, Penicillium,...The distribution and specificity of extracellular nucleases produced by marine fungi belonging to eleven genera, namely: Alternaria, Aspergillus, Aureobasidium, Chaetomium, Fusarium, Gliomastix, Humicola, Penicillium, Scopulariopsis, Wardomyces, Periconia, have implied its important function in the organic phosphorus and nitrogen circle in the Ocean. The fungal nucleases of 64 isolates tested were more or less specific for single-stranded DNA with a high preferential specificity towards poly-U substrate with forming of 5’-phosphate mononucleotides. A couple of the nucleases were capable of RNA digesting. The highest level of extracellular nucleolytic ability was observed in Penicillium spp. isolates. The tight correlation found between extracellular nuclease activity and the rate of thymidine uptake by actively growing and sporulating marine fungus Penicillium melinii suggests that this nuclease is required for fulfilling the nucleotide pool of precursors of DNA biosynthesis during transformation of hyphae into the aerial mycelium and conidia in stressful environmental conditions.展开更多
Microalgae are photosynthetic microorganisms that function as primary producers in aquatic ecosystems. Some species of microalgae undergo rapid growth and cause harmful blooms in marine ecosystems. Heterocapsa triquet...Microalgae are photosynthetic microorganisms that function as primary producers in aquatic ecosystems. Some species of microalgae undergo rapid growth and cause harmful blooms in marine ecosystems. Heterocapsa triquetra is one of the most common bloom-forming species in estuarine and coastal waters worldwide. Although this species does not produce toxins, unlike some other Heterocapsa species, the high density of its blooms can cause significant ecological damage. We developed a H. triquetra species-specific nuclease protection assay sandwich hybridization（NPA-SH） probe that targets the large subunit of ribosomal RNA（LSU r RNA）. We tested probe specificity and sensitivity with five other dinoflagellates that also cause red tides. Our assay detected H.triquetra at a concentration of 1.5×10^4 cells/m L, more sensitive than required for a red-tide guidance warning by the Korea Ministry of Oceans and Fisheries in 2015（3.0×10^4 cells/m L）. We also used the NPA-SH assay to monitor H. triquetra in the Tongyeong region of the southern sea area of Korea during 2014. This method could detect H.triquetra cells within 3 h. Our assay is useful for monitoring H. triquetra under field conditions.展开更多
Dear Editor,This study reports a nuclease-mediated tiling deletion(NTD)method that uses LbCas12a nuclease with a tiling CRISPRderived RNA(crRNA)library to efficiently induce numerous nucleotide deletions in non-coding...Dear Editor,This study reports a nuclease-mediated tiling deletion(NTD)method that uses LbCas12a nuclease with a tiling CRISPRderived RNA(crRNA)library to efficiently induce numerous nucleotide deletions in non-coding regulatory regions of endogenous rice genes.This method was applied to non-coding regions of the Green Revolution gene SD1,generating 6 mutants with quantitative variations in plant height,which were then used to investigate associations between genotype and phenotype.NTD is thus a promising tool for molecular rice breeding.展开更多
Zinc-finger nucleases and transcription activator-like effector nucleases are novel gene-editing platformscontributing to redefine the boundaries of modern biological research. They are composed of a non-specificcleav...Zinc-finger nucleases and transcription activator-like effector nucleases are novel gene-editing platformscontributing to redefine the boundaries of modern biological research. They are composed of a non-specificcleavage domain and a tailor made DNA-binding module, which enables a broad range of genetic modifications byinducing efficient DNA double-strand breaks at desired loci. Among other remarkable uses, these nucleases havebeen employed to produce gene knockouts in mid-size and large animals, such as rabbits and pigs, respectively.This approach is cost effective, relatively quick, and can produce invaluable models for human disease studies,biotechnology or agricultural purposes. Here we describe a protocol for the efficient generation of knockout rabbitsusing transcription activator-like effector nucleases, and a perspective of the field.展开更多
Nuclease effects on the cell internalization of single-walled carbon nanotubes(SWNTs)functionalized with fluorescent-labeled DNA in serum containing cell growth media were examined.When Cy3-labeled DNA-functionalized ...Nuclease effects on the cell internalization of single-walled carbon nanotubes(SWNTs)functionalized with fluorescent-labeled DNA in serum containing cell growth media were examined.When Cy3-labeled DNA-functionalized SWNT conjugates(Cy3DNA-SWNTs)were incubated with HeLa cells in a fatal bovine serum(FBS)medium,a high fl uorescence intensity was obtained from the cells,indicative for the high level inclusion of Cy3DNA-SWNTs.However,the fluorescence intensity was remarkably reduced if Cy3DNA-SWNTs were incubated with cells in the FBS-free medium.Further systematic control experiments revealed that Cy3 dye molecules were released from Cy3DNA-SWNT conjugates by nuclease,and the free Cy3 dyes penetrate into HeLa cell with high efficiency.Although the actual amounts of SWNTs internalized in the cells were almost identical for both cells incubated in the FBS-present and FBS-absent media according to the Raman measurements,one should be cautious to determine the degree of SWNT internalization based on the fl uorescence intensities especially when the coloring dye molecules were linked to oligonucleotides in nuclease containing media.展开更多
Plant senescence- or PCD-associated nucleases share significant homology with nucleases from different organisms. However, knowledge of their function is limited. Intracellular localization of the Arabidopsis senescen...Plant senescence- or PCD-associated nucleases share significant homology with nucleases from different organisms. However, knowledge of their function is limited. Intracellular localization of the Arabidopsis senescence- and PCD-associated nuclease BFN1 was investigated. Analysis of BFN1-GFP localization in transiently transformed tobacco protoplasts revealed initial localization in filamentous structures spread throughout the cytoplasm, which then clustered around the nuclei as the protoplasts senesced. These filamentous structures were identified as being of ER origin. In BFN1- GFP-transgenicArabidopsis plants, similar localization of BFN1-GFP was observed in young leaves, that is, in filamentous structures that reorganized around the nuclei only in senescing cells. In late senescence, BFN1-GFP was localized with fragmented nuclei in membrane-wrapped vesicles. BFNI＇s postulated function as a nucleic acid-degrading enzyme in senescence and PCD is supported by its localization pattern. Our results suggest the existence of a dedicated compartment mediating nucleic acid degradation in senescence and PCD processes.展开更多
Developing nanomaterial-based enzyme mimics for DNA cleavage is an interesting challenge and it has many potential applications.Single-layered graphene oxide(GO)is an excellent platform for DNA adsorption.In addition,...Developing nanomaterial-based enzyme mimics for DNA cleavage is an interesting challenge and it has many potential applications.Single-layered graphene oxide(GO)is an excellent platform for DNA adsorption.In addition,GO has been employed for photosensitized generation of reactive oxygen species(ROS).Herein,we demonstrate that GO sheets could cleave DNA as anuclease mimicking nanozyme in the presence of UV or blue light.For various DNA sequences and lengths,well-defined product bands were observed along with photobleaching of the fluorophore label on the DNA.Different from previously reported GO cleavage of DNA,our method did not require metal ions such as Cu^2+.Fluorescence spectroscopy suggested a high adsorption affinity between GO and DNA.For comparison,although zero-dimensional fluorescent carbon dots(C-dots)had higher photosensitivity ir terms of producing ROS,their cleavage activity was much lower and only smeared cleavage products were observed,indicatingthat the ROS acted on the DNA in solution.Based on the results,GO behaved like a classic heterogeneous catalyst following substrate adsorption,reaction,and product desorption steps.This simple strategy may help in the design of new nanozymes by introducing light.展开更多
Large scale genomic aberrations including duplication,deletion,translocation,and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer.The cu...Large scale genomic aberrations including duplication,deletion,translocation,and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer.The current prime editor,PE2,consisting of Cas9-nickase and reverse transcriptase enables efficient editing of genomic deletion and insertion,however,at small scale.Here,we designed a novel prime editor by fusing reverse transcriptase(RT)to nuclease wild-type Cas9(WT-PE)to edit large genomic fragment.展开更多
MAD7 is an engineered nuclease of the Class 2 type V-A CRISPR-Cas(Cas12 a/Cpf1)family with a low level of homology to canonical Cas12 a nucleases.It has been publicly released as a royalty-free nuclease for both acade...MAD7 is an engineered nuclease of the Class 2 type V-A CRISPR-Cas(Cas12 a/Cpf1)family with a low level of homology to canonical Cas12 a nucleases.It has been publicly released as a royalty-free nuclease for both academic and commercial use.Here,we demonstrate that the CRISPR-MAD7 system can be used for genome editing and recognizes T-rich PAM sequences(YTTN)in plants.Its editing efficiency in rice and wheat is comparable to that of the widely used CRISPR-Lb Cas12 a system.We develop two variants,MAD7-RR and MAD7-RVR that increase the target range of MAD7,as well as an M-AFID(a MAD7-APOBEC fusion-induced deletion)system that creates predictable deletions from 50-deaminated Cs to the MAD7-cleavage site.Moreover,we show that MAD7 can be used for multiplex gene editing and that it is effective in generating indels when combined with other CRISPR RNA orthologs.Using the CRISPR-MAD7 system,we have obtained regenerated mutant rice and wheat plants with up to 65.6%efficiency.展开更多
The design of artificial nucleases and nuclease mimics has attracted extensive attention and made great progress due to their significant scientific meanings and potential application in the field of gene medicine and...The design of artificial nucleases and nuclease mimics has attracted extensive attention and made great progress due to their significant scientific meanings and potential application in the field of gene medicine and molecular biology. This paper reviews recent progress in the investigation of artificial nuclease,including "bifunctional cooperative catalysis","dinuclear synergistic catalysis","metal-free catalysis" ,and especially,the studies of aza-crown ethers as artificial nucleases and their interaction with DNA.展开更多
The staphylococcal nuclease, encoded by the nucl gene, is an important virulence factor of Staphylococcus aureus. However, the physiological role of the nuclease has not been fully characterized. The current study obs...The staphylococcal nuclease, encoded by the nucl gene, is an important virulence factor of Staphylococcus aureus. However, the physiological role of the nuclease has not been fully characterized. The current study observed that biofilm development could be prevented in staphylococcal nuclease-producing strains of S. aureus; however, when the nucl gene was knocked out, the ability to form a biofilm significantly increased. Scanning electron and confocal scanning laser microscopy were used to evaluate the role of the nucl gene in biofilm formation. Moreover, the nucl gene product, staphylococcal nuclease, and re- combinant NUC1 protein were found to have a visible effect on other biofilm-forming bacteria, such as Pseudomonas aeru- ginosa, Actinobacillus pleuropneurnoniae, and Haernophilus parasuis. The current study showed a direct relationship between staphylococcal nuclease production and the prevention of biofilm development. The findings from this study underscore the important role of staphylococcal nuclease activity to prevent biofilm formation in S. aureus. They also provided evidence for the biological role of staphylococcal nucleases in other organisms.展开更多
Site-specific recognition modules with DNA nuclease have tremendous potential as molecular tools for genome targeting. The type III transcription activator-like effectors （TALEs） contain a DNA binding domain consist...Site-specific recognition modules with DNA nuclease have tremendous potential as molecular tools for genome targeting. The type III transcription activator-like effectors （TALEs） contain a DNA binding domain consisting of tandem repeats that can be engineered to bind user-defined specific DNA sequences. We demonstrated that customized TALE-based nucleases （TALENs）, constructed using a method called ＂unit assembly＂, specifically target the endogenous FRIGIDA gene in Brassica oleracea L. var. capitata L. The results indicate that the TALENs bound to the target site and cleaved double-strand DNA in vitro and in vivo, whereas the effector binding elements have a 23 bp spacer. The T7 endonuclease I assay and sequencing data show that TALENs made double-strand breaks, which were repaired by a non- homologous end-joining pathway within the target sequence. These data show the feasibility of applying customized TALENs to target and modify the genome with deletions in those organisms that are still in lacking gene target methods to provide germplasms in breeding improvement.展开更多
基金supported by the National Hi-Tech Research and Development Program(863)of China(No.2006AA09Z178,2001AA635090)the National Nat-ural Science Foundation of China(No.40706044)
文摘Phaeocystis globosa Scherffel is one of the common harmful algae species in coastal waters of the southeastern China.In this study,sandwich hybridization integrated with nuclease protection assay(NPA-SH)was used to qualitatively and quantitatively detect P. globosa.Results showed that this method had good applicability and validity in analyzing the samples from laboratory cultures and from fields.The linear regression equation for P.globosa was obtained,and the lowest detection number of cells was 1.8×104 c...
基金supported by the Korea Health Industry Development Institute,No.HI17C1221(to JKK)National Research Foundation of Korea,Nos.NRF-2017R1A2B4003692,NRF-2020R1A2C1006656(both to JKK)the Asan Institute for Life Sciences,Asan Medical Center,Nos.2018-766,2019IP0766(both to JKK)。
文摘Animal studies have shown that amphoteric detergent and nuclease(DNase I and ribonuclease A) is the most reliable decellularization method of the peripheral nerve. However, the optimal combination of chemical reagents for decellularization of human nerve allograft needs further investigation. To find the optimal protocol to remove the immunogenic cellular components of the nerve tissue and preserve the basal lamina and extracellular matrix and whether the optimal protocol can be applied to larger-diameter human peripheral nerves, in this study, we decellularized the median and sural nerves from the cadavers with two different methods: nonionic and anionic detergents(Triton X-100 and sodium deoxycholate) and amphoteric detergent and nuclease(3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate(CHAPS), deoxyribonuclease I, and ribonuclease A). All cellular components were successfully removed from the median and sural nerves by amphoteric detergent and nuclease. Not all cellular components were removed from the median nerve by nonionic and anionic detergent. Both median and sural nerves treated with amphoteric detergent and nuclease maintained a completely intact extracellular matrix. Treatment with nonionic and anionic detergent decreased collagen content in both median and sural nerves, while the amphoteric detergent and nuclease treatment did not reduce collagen content. In addition, a contact cytotoxicity assay revealed that the nerves decellularized by amphoteric detergent and nuclease was biocompatible. Strength failure testing demonstrated that the biomechanical properties of nerves decellularized with amphoteric detergent and nuclease were comparable to those of fresh controls. Decellularization with amphoteric detergent and nuclease better remove cellular components and better preserve extracellular matrix than decellularization with nonionic and anionic detergents, even in large-diameter human peripheral nerves. In Korea, cadaveric studies are not yet legally subject to Institutional Review Board review.
基金The National High Technology Research and Development Program ("863" Program) of China under contract No 2006AA09Z178 the National Natural Science Foundation of China under contract No 40706044
文摘Prorocentrum donghaiense is an important harmful algae bloom （HAB） causing creature in China＇s seas, and the conventional visual detection can not cope with long-term monitoring and highthroughput sampling projects. An assay for P. donghaiense with sandwich hybridization integrated with nuclease protection assay （NPA-SH） was established. Tests with mixed samples and spiked field ones confirmed its good specificity and sensitivity. The cell number of P. donghaiense correlated well with the optical density, and the regression equation is y=4× 10^- 6x＋ 0.694 9, in which x is the cell number, and y is the optical density, with r2=0.953 5. These results show that the NPA-SH method has good feasibility in the detection of P. donghaiense. Results of NPA-SH and microscopy are excellent for each sample. The NPA-SH method was a simple way in quantitative detection of P. donghaiense, and the whole process could be finished in about six hours, which provided a new approach in high-throughput sampling and long-term monitoring of P. donghaiense.
基金the Akdeniz University Scientific Research Commission and the Scientific and Technological Research Council of Turkey,No.TUBITAK-215S820.
文摘Targeted genome editing is a continually evolving technology employing programmable nucleases to specifically change,insert,or remove a genomic sequence of interest.These advanced molecular tools include meganucleases,zinc finger nucleases,transcription activator-like effector nucleases and RNA-guided engineered nucleases(RGENs),which create double-strand breaks at specific target sites in the genome,and repair DNA either by homologous recombination in the presence of donor DNA or via the error-prone non-homologous end-joining mechanism.A recently discovered group of RGENs known as CRISPR/Cas9 gene-editing systems allowed precise genome manipulation revealing a causal association between disease genotype and phenotype,without the need for the reengineering of the specific enzyme when targeting different sequences.CRISPR/Cas9 has been successfully employed as an ex vivo gene-editing tool in embryonic stem cells and patient-derived stem cells to understand pancreatic beta-cell development and function.RNA-guided nucleases also open the way for the generation of novel animal models for diabetes and allow testing the efficiency of various therapeutic approaches in diabetes,as summarized and exemplified in this manuscript.
文摘Accurate DNA quantitation is a prerequisite in many biomedical and pharmaceutical studies.Here we established a new DNA quantitation method by nuclease P1 digestion and UPLC-MS/MS analysis.DNA fragments can be efficiently hydrolyzed to single deoxyribonucleotides by nuclease P1 in a short time.The decent stabilities of all the four deoxyribonucleotides were confirmed under different conditions.Deoxyadenosine monophosphate(dAMP)was selected as the surrogate for DNA quantitation because dAMP showed the highest sensitivity among the four deoxyribonucleotides in the UPLC-MS/MS analysis.The linear range in DNA quantitation by this method is 1.2-5000 ng/mL.In the validation,the inter-day and intra-day accuracies were within 90%-110%,and the inter-day and intra-day precision were acceptable(RSD<10%).The validated method was successfully applied to quantitate DNA isolated from tumors and organs of a mouse xenograft model.Compared to the quantitation methods using UV absorbance,the reported method provides an enhanced sensitivity,and it allows for the accurate quantitation of isolated DNA with contamination of RNA and ribonucleotide.
基金Project supported by the National Basic Research Program of China(Grant Nos.2013CB921904,2009CB930504,and 2013CB328700)the National Natural Science Foundation of China(Grant Nos.11074016,11121091,10934001,61177020,11134001,and 10828407)
文摘Internal solvation of protein was studied by site-directed mutagenesis, with which an intrinsically fluorescent probe,tryptophan, is inserted into the desired position inside a protein molecule for ultrafast spectroscopic study. Here we review this unique method for protein dynamics research. We first introduce the frontiers of protein solvation, site-directed mutagenesis, protein stability and characteristics, and the spectroscopic methods. Then we present time-resolved spectroscopic dynamics of solvation dynamics inside cavities of active sites. The studies are carried out on a globular protein, staphylococcal nuclease. The solvation at sites inside the protein molecule＇s cavities clearly reveals characteristics of the local environment. These solvation behaviors are directly correlated to enzyme activity.
基金Supported by the National Key Basic Research Program of China under Grant Nos 2013CB921904,2013CB328701-2013CB328706the National Natural Science Foundation of China under Grant Nos 11074016,11121091,61177020,11134001and 10828407
文摘Tryptophan （Trp） is an intrinsic fluorescent probe for detecting the site-specified dynamics inside/outside protein. It is found that the Trp can easily be inserted in desired sites of protein, which affects the integrity of the overall structure. To evaluate this effect, we design thirteen double point mutants of staphylococcal nuclease, each of which has a single Trp residue planted at an internal site. The studies on Trp fluorescence, ANS-binding fluorescence, far- and near-UV CD spectra, and enzymatic activity are carried out. It is found that the mutation at the hydrophobic core of protein generates molten globular state conformation, which is a loose structure compared to their original compactness in wild type （WT）. Its enzyme activity and surface hydrophobicity are also affected. The studies show that by proper site designing and external binding, Trp mutagenesis is a suitable method for carrying out the study on site specified dynamics of proteins.
文摘Objective: To establish a novel approach for quick and highly efficient verification of human gene imprinting. Methods: A pair of dye-labelled probes, 5' nuclease assay was combined with RT-PCR to determine the genotype of a transcribed single nucleotide polymorphism (SNP) rs705(C>T) of a known imprinted gene, small nuclear ribonucleotide protein N (SNRPN), on both genomic DNA and cDNA of human lym-phoblast cell lines. Results: Allele discrimination showed a clear monoallelic expression pattern of SNRPN, which was confirmed by RT-PCR based restriction fragment length polymorphism (RFLPs). Pedigree analysis verified the paternal origin of expressed allele, which was in consistency with previous report. Conclusion: Transcribed SNP is an ideal marker for detecting gene imprinting by 5' nuclease assay. This approach also may be used to discover differential allele expression of non-imprinted genes, finding out gene cis-acting functional polymorphism.
文摘The distribution and specificity of extracellular nucleases produced by marine fungi belonging to eleven genera, namely: Alternaria, Aspergillus, Aureobasidium, Chaetomium, Fusarium, Gliomastix, Humicola, Penicillium, Scopulariopsis, Wardomyces, Periconia, have implied its important function in the organic phosphorus and nitrogen circle in the Ocean. The fungal nucleases of 64 isolates tested were more or less specific for single-stranded DNA with a high preferential specificity towards poly-U substrate with forming of 5’-phosphate mononucleotides. A couple of the nucleases were capable of RNA digesting. The highest level of extracellular nucleolytic ability was observed in Penicillium spp. isolates. The tight correlation found between extracellular nuclease activity and the rate of thymidine uptake by actively growing and sporulating marine fungus Penicillium melinii suggests that this nuclease is required for fulfilling the nucleotide pool of precursors of DNA biosynthesis during transformation of hyphae into the aerial mycelium and conidia in stressful environmental conditions.
基金The Public Welfare&Safety Research Program through the National Research Foundation of Korea(NRF)funded by the Ministry of Science,ICT&Future Planning under contract No.NRF-2013M3A2A1067529
文摘Microalgae are photosynthetic microorganisms that function as primary producers in aquatic ecosystems. Some species of microalgae undergo rapid growth and cause harmful blooms in marine ecosystems. Heterocapsa triquetra is one of the most common bloom-forming species in estuarine and coastal waters worldwide. Although this species does not produce toxins, unlike some other Heterocapsa species, the high density of its blooms can cause significant ecological damage. We developed a H. triquetra species-specific nuclease protection assay sandwich hybridization（NPA-SH） probe that targets the large subunit of ribosomal RNA（LSU r RNA）. We tested probe specificity and sensitivity with five other dinoflagellates that also cause red tides. Our assay detected H.triquetra at a concentration of 1.5×10^4 cells/m L, more sensitive than required for a red-tide guidance warning by the Korea Ministry of Oceans and Fisheries in 2015（3.0×10^4 cells/m L）. We also used the NPA-SH assay to monitor H. triquetra in the Tongyeong region of the southern sea area of Korea during 2014. This method could detect H.triquetra cells within 3 h. Our assay is useful for monitoring H. triquetra under field conditions.
基金supported by grants from the National Natural Science Foundation of China,China (31871948)the STI 2030–Major Projects (2023ZD04074)+3 种基金the Hainan Yazhou Bay Seed Lab (B21HJ0215)the Central Public-interest Scientific Institution Basal Research Fund (Y2022QC03)the Key Research and Development Program of Shandong Province,China (Agricultural Seed Improvement Project,2022LZGC012)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences,China。
文摘Dear Editor,This study reports a nuclease-mediated tiling deletion(NTD)method that uses LbCas12a nuclease with a tiling CRISPRderived RNA(crRNA)library to efficiently induce numerous nucleotide deletions in non-coding regulatory regions of endogenous rice genes.This method was applied to non-coding regions of the Green Revolution gene SD1,generating 6 mutants with quantitative variations in plant height,which were then used to investigate associations between genotype and phenotype.NTD is thus a promising tool for molecular rice breeding.
基金Work on this topic in the authors’laboratories is supported by grants from:the Strategic Priority Research Program of the Chinese Academy of Sciences(number XDA01020106)the Ministry of Science and Technology of China 973 program(2011CB965200)+2 种基金the National Natural Science Foundation of China(81261130317)to MAEthe Bureau of Science,Technology and Information of Guangzhou Municipality(2012 J5100040)to MAE and JFgrants 2010U1-E00811-5 and ZNGI-2011-010 from the Guangzhou Municipality and the Chinese Academy of Sciences,respectively,to LL.
文摘Zinc-finger nucleases and transcription activator-like effector nucleases are novel gene-editing platformscontributing to redefine the boundaries of modern biological research. They are composed of a non-specificcleavage domain and a tailor made DNA-binding module, which enables a broad range of genetic modifications byinducing efficient DNA double-strand breaks at desired loci. Among other remarkable uses, these nucleases havebeen employed to produce gene knockouts in mid-size and large animals, such as rabbits and pigs, respectively.This approach is cost effective, relatively quick, and can produce invaluable models for human disease studies,biotechnology or agricultural purposes. Here we describe a protocol for the efficient generation of knockout rabbitsusing transcription activator-like effector nucleases, and a perspective of the field.
基金This work was supported by the Nano/Bio Science&Technology Program of MOST(2008-00759)Korean Research Foundation(MOEHRD,KRF-2005-005-J13103 and KRF-2007-313-C00386)KOSEF(2007-8-1158).
文摘Nuclease effects on the cell internalization of single-walled carbon nanotubes(SWNTs)functionalized with fluorescent-labeled DNA in serum containing cell growth media were examined.When Cy3-labeled DNA-functionalized SWNT conjugates(Cy3DNA-SWNTs)were incubated with HeLa cells in a fatal bovine serum(FBS)medium,a high fl uorescence intensity was obtained from the cells,indicative for the high level inclusion of Cy3DNA-SWNTs.However,the fluorescence intensity was remarkably reduced if Cy3DNA-SWNTs were incubated with cells in the FBS-free medium.Further systematic control experiments revealed that Cy3 dye molecules were released from Cy3DNA-SWNT conjugates by nuclease,and the free Cy3 dyes penetrate into HeLa cell with high efficiency.Although the actual amounts of SWNTs internalized in the cells were almost identical for both cells incubated in the FBS-present and FBS-absent media according to the Raman measurements,one should be cautious to determine the degree of SWNT internalization based on the fl uorescence intensities especially when the coloring dye molecules were linked to oligonucleotides in nuclease containing media.
文摘Plant senescence- or PCD-associated nucleases share significant homology with nucleases from different organisms. However, knowledge of their function is limited. Intracellular localization of the Arabidopsis senescence- and PCD-associated nuclease BFN1 was investigated. Analysis of BFN1-GFP localization in transiently transformed tobacco protoplasts revealed initial localization in filamentous structures spread throughout the cytoplasm, which then clustered around the nuclei as the protoplasts senesced. These filamentous structures were identified as being of ER origin. In BFN1- GFP-transgenicArabidopsis plants, similar localization of BFN1-GFP was observed in young leaves, that is, in filamentous structures that reorganized around the nuclei only in senescing cells. In late senescence, BFN1-GFP was localized with fragmented nuclei in membrane-wrapped vesicles. BFNI＇s postulated function as a nucleic acid-degrading enzyme in senescence and PCD is supported by its localization pattern. Our results suggest the existence of a dedicated compartment mediating nucleic acid degradation in senescence and PCD processes.
基金Funding for this work was from the Natural Sciences and Engineering Research Council of Canada(NSERC)the National Natural Science Foundation of China(No.U19A2005).
文摘Developing nanomaterial-based enzyme mimics for DNA cleavage is an interesting challenge and it has many potential applications.Single-layered graphene oxide(GO)is an excellent platform for DNA adsorption.In addition,GO has been employed for photosensitized generation of reactive oxygen species(ROS).Herein,we demonstrate that GO sheets could cleave DNA as anuclease mimicking nanozyme in the presence of UV or blue light.For various DNA sequences and lengths,well-defined product bands were observed along with photobleaching of the fluorophore label on the DNA.Different from previously reported GO cleavage of DNA,our method did not require metal ions such as Cu^2+.Fluorescence spectroscopy suggested a high adsorption affinity between GO and DNA.For comparison,although zero-dimensional fluorescent carbon dots(C-dots)had higher photosensitivity ir terms of producing ROS,their cleavage activity was much lower and only smeared cleavage products were observed,indicatingthat the ROS acted on the DNA in solution.Based on the results,GO behaved like a classic heterogeneous catalyst following substrate adsorption,reaction,and product desorption steps.This simple strategy may help in the design of new nanozymes by introducing light.
基金We thank Yang Yang for providing python script for HTS data analysis.This work was supported by National Natural Science Foundation of China.No.U19A2002,No.81771220 and No.81974238.
文摘Large scale genomic aberrations including duplication,deletion,translocation,and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer.The current prime editor,PE2,consisting of Cas9-nickase and reverse transcriptase enables efficient editing of genomic deletion and insertion,however,at small scale.Here,we designed a novel prime editor by fusing reverse transcriptase(RT)to nuclease wild-type Cas9(WT-PE)to edit large genomic fragment.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(Precision Seed Design and Breeding,XDA24020101 and XDA24020310)the National Natural Science Foundation of China(31672015,31788103)the Youth Innovation Promotion Association of the Chinese Academy of Sciences(2020000003)。
文摘MAD7 is an engineered nuclease of the Class 2 type V-A CRISPR-Cas(Cas12 a/Cpf1)family with a low level of homology to canonical Cas12 a nucleases.It has been publicly released as a royalty-free nuclease for both academic and commercial use.Here,we demonstrate that the CRISPR-MAD7 system can be used for genome editing and recognizes T-rich PAM sequences(YTTN)in plants.Its editing efficiency in rice and wheat is comparable to that of the widely used CRISPR-Lb Cas12 a system.We develop two variants,MAD7-RR and MAD7-RVR that increase the target range of MAD7,as well as an M-AFID(a MAD7-APOBEC fusion-induced deletion)system that creates predictable deletions from 50-deaminated Cs to the MAD7-cleavage site.Moreover,we show that MAD7 can be used for multiplex gene editing and that it is effective in generating indels when combined with other CRISPR RNA orthologs.Using the CRISPR-MAD7 system,we have obtained regenerated mutant rice and wheat plants with up to 65.6%efficiency.
基金Supported by the National Natural Science Foundation of China (Grant Nos. 20872061 & 20372032)the National Basic Research of China (Grant No. 2007CB925103)
文摘The design of artificial nucleases and nuclease mimics has attracted extensive attention and made great progress due to their significant scientific meanings and potential application in the field of gene medicine and molecular biology. This paper reviews recent progress in the investigation of artificial nuclease,including "bifunctional cooperative catalysis","dinuclear synergistic catalysis","metal-free catalysis" ,and especially,the studies of aza-crown ethers as artificial nucleases and their interaction with DNA.
基金supported by the National Natural Science Foundation of China (Grant Nos. 31071515 and 31070113)the Special Foundation for Young Scientists of Sichuan Province,China (Grant No. 2011JQ0043)the Fundamental Research Funds for the Central Universities,Southwest University for Nationalities (Grant No. 09NZYZJ04)
文摘The staphylococcal nuclease, encoded by the nucl gene, is an important virulence factor of Staphylococcus aureus. However, the physiological role of the nuclease has not been fully characterized. The current study observed that biofilm development could be prevented in staphylococcal nuclease-producing strains of S. aureus; however, when the nucl gene was knocked out, the ability to form a biofilm significantly increased. Scanning electron and confocal scanning laser microscopy were used to evaluate the role of the nucl gene in biofilm formation. Moreover, the nucl gene product, staphylococcal nuclease, and re- combinant NUC1 protein were found to have a visible effect on other biofilm-forming bacteria, such as Pseudomonas aeru- ginosa, Actinobacillus pleuropneurnoniae, and Haernophilus parasuis. The current study showed a direct relationship between staphylococcal nuclease production and the prevention of biofilm development. The findings from this study underscore the important role of staphylococcal nuclease activity to prevent biofilm formation in S. aureus. They also provided evidence for the biological role of staphylococcal nucleases in other organisms.
基金supported by grants from the National Basic Research Program of China (973 program, 2012CB113900)the National Natural Science Foundation of China (31071802)the Chongqing Natural Science Foundation (2011BA1002)
文摘Site-specific recognition modules with DNA nuclease have tremendous potential as molecular tools for genome targeting. The type III transcription activator-like effectors （TALEs） contain a DNA binding domain consisting of tandem repeats that can be engineered to bind user-defined specific DNA sequences. We demonstrated that customized TALE-based nucleases （TALENs）, constructed using a method called ＂unit assembly＂, specifically target the endogenous FRIGIDA gene in Brassica oleracea L. var. capitata L. The results indicate that the TALENs bound to the target site and cleaved double-strand DNA in vitro and in vivo, whereas the effector binding elements have a 23 bp spacer. The T7 endonuclease I assay and sequencing data show that TALENs made double-strand breaks, which were repaired by a non- homologous end-joining pathway within the target sequence. These data show the feasibility of applying customized TALENs to target and modify the genome with deletions in those organisms that are still in lacking gene target methods to provide germplasms in breeding improvement.
