AIM: To discuss the possible effect of PTEN gene mutations on occurrence and development of gastric cancer. METHODS: Fifty-three gastric cancer specimens were selected to probe PTEN gene mutations in genome of gastric...AIM: To discuss the possible effect of PTEN gene mutations on occurrence and development of gastric cancer. METHODS: Fifty-three gastric cancer specimens were selected to probe PTEN gene mutations in genome of gastric cancer and paracancerous tissues using PCR-SSCP-DNA sequencing method based on microdissection and to observe the protein expression by immunohistochemistry technique. RESULTS: PCR-SSCP-DNA sequencing indicated that 4 kinds of mutation sites were found in 5 of 53 gastric cancer specimens. One kind of mutation was found in exons. AA-TCC mutation was located at 40bp upstream of 3’ lateral exon 7 (115946 AA-TCC). Such mutations led to terminator formation in the 297th codon of the PTEN gene. The other 3 kinds of mutation were found in introns,including a G-C point mutation at 91 bp upstream of 5’ lateral exon 5(90896 G-C),a T-G point mutation at 24 bp upstream of 5’ lateral exon 5 (90963 T-G),and a single base A mutation at 7 bp upstream of 5’ lateral exon 5 (90980 A del). The PTEN protein expression in gastric cancer and paracancerous tissues detected using immunohistochemistry technique indicated that the total positive rate of PTEN protein expression was 66% in gastric cancer tissue,which was significantly lower than that (100%) in paracancerous tissues (P < 0.005). CONCLUSION: PTEN gene mutation and expression may play an important role in the occurrence and development of gastric cancer.展开更多
The degenerate primer-based sequencing was developed by a synthesis method （DP-SBS） for high-throughput DNA sequencing, in which a set of degenerate primers are hybridized on the arrayed DNA templates and extended b...The degenerate primer-based sequencing was developed by a synthesis method （DP-SBS） for high-throughput DNA sequencing, in which a set of degenerate primers are hybridized on the arrayed DNA templates and extended by DNA polymerase on microarrays. In this method, a different set of degenerate primers containing a given number （n） of degenerate nucleotides at the 3＇-ends were annealed to the sequenced templates that were immobilized on the solid surface. The nucleotides （n＋1） on the template sequences were determined by detecting the incorporation of fluorescent labeled nucleotides. The fluorescent labeled nucleotide was incorporated into the primer in a base-specific manner after the enzymatic primer extension reactions and nine-base length were read out accurately. The main advantage of the DP-SBS is that the method only uses very conventional biochemical reagents and avoids the complicated special chemical reagents for removing the labeled nucleotides and reactivating the primer for further extension. From the present study, it is found that the DP-SBS method is reliable, simple, and cost-effective for laboratory-sequencing a large amount of short DNA fragments.展开更多
Quasi-interpenetrating network formed by polyacrylamide and poly （N-hydroxymethylacrylamide） was designed, synthesized, and tested for DNA sequencing by capillary electrophoresis. The performance of quasi-IPN on DNA...Quasi-interpenetrating network formed by polyacrylamide and poly （N-hydroxymethylacrylamide） was designed, synthesized, and tested for DNA sequencing by capillary electrophoresis. The performance of quasi-IPN on DNA sequencing was determined by the acrylamide to N-hydroxymethylacrylamide molar ratio and sequencing temperature.展开更多
The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has ne...The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.展开更多
To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical flu...To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical fluorescent bases(A_(y),tC,G_(b),T_(p))are proposed for four-color DNA sequencing.These quasi-intrinsic probes are derived from the fluorophore replacement and ring expansion on natural bases,which still keep the pyrimidine or purine underlying skeleton and Watson–Crick hydrogen bonding face to allow minimal perturbation to the native DNA duplex.More importantly,these nucleobase analogues possess red-shifted absorption and efficient photoluminescence due to the enhancedπ-conjugation in character.Meanwhile,the four analogues could generate distinct emission wavelength(Δλ~50 nm)for real-time sequencing.To assess the biological employment of the proposed biosensors,the effects of base pairing and linking deoxyribose are also considered.展开更多
Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale pore.It is still really tough to attain the single base discrimination on a DNA ...Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale pore.It is still really tough to attain the single base discrimination on a DNA strand by merely analyzing the ionic current due to speedy DNA translocation and low spatial resolution.More integrated configurations are pursued to present versatile comparative dissimilarities of the four bases by enhancing the spatial resolution within a DNA molecule translocation event,such as transverse tunneling current,local potential change,and capacitance oriented voltage resonance.In this mini review,the insight is provided into the status quo on several functionalized techniques and methodologies for DNA sequencing and furthermore concluding remark and outlook are presented.展开更多
Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The...Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein.Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale.In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.展开更多
This review briefly summarizes recent progress in nanopore DNA sequencing from the beginning of 2012 to July 2014. Although partial successes have been achieved in different types of nanopores, biological pores such ...This review briefly summarizes recent progress in nanopore DNA sequencing from the beginning of 2012 to July 2014. Although partial successes have been achieved in different types of nanopores, biological pores such as α- hemolysin and MspA afford most promising results.展开更多
Nanopores have been studied as a unique DNA sequencing technology that can quickly read long stretched DNA sequences. A DNA molecule could pass through a nanopore in a speed of microsecond per base and even faster. Wi...Nanopores have been studied as a unique DNA sequencing technology that can quickly read long stretched DNA sequences. A DNA molecule could pass through a nanopore in a speed of microsecond per base and even faster. With this speed, a human genome can potentially be sequenced by one nanopore in 〈1 h. In contrast to next- generation DNA sequencing （NGS）, the nanopore sequencing is enzyme free without need of sample amplification due to its single-molecule nature. The nanopore sequencing has been envisioned as a new generation of DNA sequencing technology in the post-NGS era. This progress focuses on status quo of the nanopore DNA sequencing and discusses the opportunities and challenges in this rapidly growing field.展开更多
We discuss the feasibility of using a nanopore sandwich device to implement the principle of kinetic proofreading to discriminate incorrect hybridizing oligonucleotides on a target DNA or RNA.We propose a method of se...We discuss the feasibility of using a nanopore sandwich device to implement the principle of kinetic proofreading to discriminate incorrect hybridizing oligonucleotides on a target DNA or RNA.We propose a method of sequencing DNA or RNA using this approach.The design parameters for such a DNA sequencer are estimated from the Hopfield・Ninio theory of kinetic proofreading and Schrodinger's first-passage-time distribution function.展开更多
[ Objective ] The study aimed to identify Lycium Linn. at molecular level. [ Method ] The nrDNA ITS sequence of 5 edible Lycium Linn. germplasm resources were investigated. [ Result ] The nrDNA ITS regions of five edi...[ Objective ] The study aimed to identify Lycium Linn. at molecular level. [ Method ] The nrDNA ITS sequence of 5 edible Lycium Linn. germplasm resources were investigated. [ Result ] The nrDNA ITS regions of five edible Lycium Liun. germplasm resources were sequenced. The whole sequences varied from 628 bp to 632 bp, with the average length of 630 bp. Total 79 variation sites were observed in the sequences, which accounts for 12. 5%. [ Conclusion] Sequence analysis based on nrDNA sequencing provides a new approach to identify edible Lycium Linn. germplasm resources.展开更多
[Objective] The study aimed to identify woltberry （Lycium Linn.） germplasm resources at molecular level by analyzing the nrDNA ITS sequence. [Method] Genomic DNA from woltberry leaves extracted by modified CTAB meth...[Objective] The study aimed to identify woltberry （Lycium Linn.） germplasm resources at molecular level by analyzing the nrDNA ITS sequence. [Method] Genomic DNA from woltberry leaves extracted by modified CTAB method were regarded as templates for PCR amplification by specific primer, clone and sequencing. [Result] The nrDNA ITS sequences were obtained and then differentiated among three tested materials. [Conclusion] PCR amplification and sequencing on nrDNA ITS is a feasible approach to identify different woltberry germplasm resources.展开更多
Objective To investigate the vertical transmission rate of Chlamy dia trachomatis (CT) in Chongqing, China. Methods Specimens taken from 278 women and from their 79 infants were e xamined b y cell culture, polymeras...Objective To investigate the vertical transmission rate of Chlamy dia trachomatis (CT) in Chongqing, China. Methods Specimens taken from 278 women and from their 79 infants were e xamined b y cell culture, polymerase chain reaction (PCR) and DNA sequence analysis. Chlam ydia trachomatis was isolated in McCoy cell culture. CT DNA was extracted with a modified NaI method. After cloning, recombinant plasmids were used for sequence analysis with the dideoxy chain termination method.Results 10.8% (30/278) of the cervical cultures of pregnant women were positive for Chlamydia trachomatis, while the positive rate tested by PCR was 14.0% (39/2 78). The vertical transmission rate of Chlamydia trachomatis was 55. 0% (11/20). The incidences of conjunctivitis and pneumonia in infants with Chlamydia t rachom atis positive mothers were 27.3% and 18.2%, respectively. DNA sequence s of Chlam ydia trachomatis isolated from the cervix of a mother and the nasopharynx of her baby were identical.Conclusion Chlamydia trachomatis infection is quite common in Cho ngqing , China. Our report is the first report of CT vertical transmission proved by DN A sequence analysis.展开更多
Nanopores for DNA sequencing have drawn much attention due to their potentials to achieve amplification-free, low-cost, and high-throughput analysis of nuclei acids. The material configuration and fabrication of the n...Nanopores for DNA sequencing have drawn much attention due to their potentials to achieve amplification-free, low-cost, and high-throughput analysis of nuclei acids. The material configuration and fabrication of the nanopore has become one important consideration in the nanopore based DNA sequencing research. Among various materials, the newly emerged graphene has brought more opportunities to the development of sequencing technology because of its unique structures and properties. This review mainly focuses on the experimental aspects of graphene nanopore research including the nanopore fabrication methods and processes. Meanwhile, the challenges in the present graphene nanopore research including hydrophobicity, translocation velocity and noise are also addressed and discussed.展开更多
Background Mutation and expression change of p21 WAF1/CIP1 may play a role in the growth of osteosarcoma. This study was to investigate the expression of the p21 WAF1/CIP1 gene in human osteosarcoma,p21 WAF1/...Background Mutation and expression change of p21 WAF1/CIP1 may play a role in the growth of osteosarcoma. This study was to investigate the expression of the p21 WAF1/CIP1 gene in human osteosarcoma,p21 WAF1/CIP1 gene DNA sequence change and their relationships with the phenotype and clinical prognosis.Methods p21 WAF1/CIP1 gene in 10 normal people and the tumours of 45 osteosarcoma patients were examined using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) with silver staining. The PCR product with an abnormal strand was sequenced directly. The p21 WAF1/CIP1 gene mRNA and P21 protein of 45 cases of osteosarcoma were investigated by using in situ hybridization and immunohistochemistry,respectively. Results The occurrence of P21 protein in osteosarcoma was 17.78% (8/45),and p21 WAF1/CIP1 mRNA expression in osteosarcoma was 42.22% (19/45). The p21 WAF1/CIP1 gene DNA sequencing of amplified production showed that in p21 WAF1/CIP1 gene exon 3 of 36 cases of human osteosarcoma,there were 17 cases (47.22%) with C→T at position 609; 10 normal blood samples’ DNA sequence analysis yielded 8 cases (80.00%) with C→T at the same position. Conclusions Along with the increase of malignancy,the expression of p21 WAF1/CIP1 mRNA and P21 protein in osteosarcoma tends to decrease. It is uncommon for the p21 WAF1/CIP1 gene mutation to occur in human osteosarcoma. As a result, the possible existence of tumour subtypes of p21 WAF1/CIP1 gene mutation should be investigated. Our research leads to the location of p21 WAF1/CIP1 gene polymorphism of Chinese osteosarcoma patients,which can provide a basis for further research.展开更多
Nanopore-based devices have provided exciting opportunities to develop affordable label-free DNA sequencing platforms.Over a decade ago,graphene has been proposed as a two-dimensional(2D)nanopore membrane in order to ...Nanopore-based devices have provided exciting opportunities to develop affordable label-free DNA sequencing platforms.Over a decade ago,graphene has been proposed as a two-dimensional(2D)nanopore membrane in order to achieve single-base resolution.However,it was experimentally revealed that clogging of the graphene nanopore can occur due to the hydrophobic nature of graphene,thus hindering the translocation of DNA.To overcome this problem,the exploration of alternative 2D materials has gained considerable interest over the last decade.Here we show that a Ti_(2)C-based MXene nanopore functionalized by hydroxyl groups(–OH)exhibits transverse conductance properties that allow for the distinction between all four naturally occurring DNA bases.We have used a combination of density functional theory and non-equilibrium Green’s function method to sample over multiple orientations of the nucleotides in the nanopore,as generated from molecular dynamics simulations.The conductance variation resulting from sweeping an applied gate voltage demonstrates that the Ti_(2)C-based MXene nanopore possesses high potential to rapidly and reliably sequence DNA.Our findings open the door to further theoretical and experimental explorations of MXene nanopores as a promising 2D material for nanopore-based DNA sensing.展开更多
The authors regret that there was an incorrect citation in the Table 1 of the article ＂Nanopore-based Fourth-generation DNA Sequencing Technology＂, which was published in the journal Genomics, Proteomics ＆ Bioinfor...The authors regret that there was an incorrect citation in the Table 1 of the article ＂Nanopore-based Fourth-generation DNA Sequencing Technology＂, which was published in the journal Genomics, Proteomics ＆ Bioinformatics, Issue 1, 2015. In the table, the image in the 4th row originally appeared in the article ＂Nanopore-based sequence-specific detection of duplex DNA for geno- mic profiling＂ published by Nano Letters in 2010. Therefore, Ref. [8], which was associated with the image in the current Table l, should be replaced by the reference： Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M, Meller A. Nanopore- based sequence specific detection of duplex DNA for genomic profiling. Nano Lett 2010; 10：738-42.＂ The copy right permission of this article has been obtained. The authors would like to apologize for any inconvenience caused.展开更多
The authors regret that there were typos in the online version of Figure 4 published in Issue 1,2015.In the figure legend boxes of panels F and G,‘‘Ni’’should be corrected to‘‘N’’for the labeling of the green ...The authors regret that there were typos in the online version of Figure 4 published in Issue 1,2015.In the figure legend boxes of panels F and G,‘‘Ni’’should be corrected to‘‘N’’for the labeling of the green curves.The figure in the printed version has been corrected.The correct Figure 4 is shown below.The authors would like to apologize for any inconvenience caused.展开更多
With the support from the National Natural Science Foundation of China,Prof.Huang Yanyi(黄岩谊)led a team at Peking University to demonstrate a novel approach,which combined fluorogenic sequencingby-synthesis(SBS)chem...With the support from the National Natural Science Foundation of China,Prof.Huang Yanyi(黄岩谊)led a team at Peking University to demonstrate a novel approach,which combined fluorogenic sequencingby-synthesis(SBS)chemistry with an information theory-based error-correction coding scheme to展开更多
Objective: To investigate the p21WAF1 /CIP1gene DNA sequence change and their relationship with the phenotype of human osteosarcoma. Methods: p21WAF1 /CIP1gene DNA of 36 osteosarcoma spec- ...Objective: To investigate the p21WAF1 /CIP1gene DNA sequence change and their relationship with the phenotype of human osteosarcoma. Methods: p21WAF1 /CIP1gene DNA of 36 osteosarcoma spec- imens was examined by using polymerase chain reaction-single strand conformation polymorphism (PCR- SSCP) method. The PCR products were sequenced directly. Results: In p21WAF1 /CIP1 gene exon3 of 36 cases of human osteosarcoma, the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 17 cases with the incidence being 44.4%. In 10 normal blood samples, DNA sequence analysis showed the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 8 cases with the incidence being 80%. Conclusion: The novel location of p21WAF1 /CIP1gene polymorphism of osteosarcoma, but not mutation was de?ned, and this location might provide the meaningful reference for the further research of p21WAF1/CIP1 gene.p2lWAF1/CIP1基因DNA序列分析及其与骨肉瘤表型的关系展开更多
基金Zabei Medical Science and Technology Foundation of Shanghai,No.grant 200701
文摘AIM: To discuss the possible effect of PTEN gene mutations on occurrence and development of gastric cancer. METHODS: Fifty-three gastric cancer specimens were selected to probe PTEN gene mutations in genome of gastric cancer and paracancerous tissues using PCR-SSCP-DNA sequencing method based on microdissection and to observe the protein expression by immunohistochemistry technique. RESULTS: PCR-SSCP-DNA sequencing indicated that 4 kinds of mutation sites were found in 5 of 53 gastric cancer specimens. One kind of mutation was found in exons. AA-TCC mutation was located at 40bp upstream of 3’ lateral exon 7 (115946 AA-TCC). Such mutations led to terminator formation in the 297th codon of the PTEN gene. The other 3 kinds of mutation were found in introns,including a G-C point mutation at 91 bp upstream of 5’ lateral exon 5(90896 G-C),a T-G point mutation at 24 bp upstream of 5’ lateral exon 5 (90963 T-G),and a single base A mutation at 7 bp upstream of 5’ lateral exon 5 (90980 A del). The PTEN protein expression in gastric cancer and paracancerous tissues detected using immunohistochemistry technique indicated that the total positive rate of PTEN protein expression was 66% in gastric cancer tissue,which was significantly lower than that (100%) in paracancerous tissues (P < 0.005). CONCLUSION: PTEN gene mutation and expression may play an important role in the occurrence and development of gastric cancer.
基金the National Natural Sci-ence Foundation of China (No. 60121101)the Hi-Tech Research and Development Program of China (No. 2006AA020702).
文摘The degenerate primer-based sequencing was developed by a synthesis method （DP-SBS） for high-throughput DNA sequencing, in which a set of degenerate primers are hybridized on the arrayed DNA templates and extended by DNA polymerase on microarrays. In this method, a different set of degenerate primers containing a given number （n） of degenerate nucleotides at the 3＇-ends were annealed to the sequenced templates that were immobilized on the solid surface. The nucleotides （n＋1） on the template sequences were determined by detecting the incorporation of fluorescent labeled nucleotides. The fluorescent labeled nucleotide was incorporated into the primer in a base-specific manner after the enzymatic primer extension reactions and nine-base length were read out accurately. The main advantage of the DP-SBS is that the method only uses very conventional biochemical reagents and avoids the complicated special chemical reagents for removing the labeled nucleotides and reactivating the primer for further extension. From the present study, it is found that the DP-SBS method is reliable, simple, and cost-effective for laboratory-sequencing a large amount of short DNA fragments.
基金support of this work by the National Natural Science Foundation of China(No.50373040)the Scientific Research Foundation for the Returned 0verseas Chinese Scholars,State Education Ministrythe Foundation for Development of Talent of Anhui Province(No.2005Z026).
文摘Quasi-interpenetrating network formed by polyacrylamide and poly （N-hydroxymethylacrylamide） was designed, synthesized, and tested for DNA sequencing by capillary electrophoresis. The performance of quasi-IPN on DNA sequencing was determined by the acrylamide to N-hydroxymethylacrylamide molar ratio and sequencing temperature.
基金Supported by the National Natural Science Foundation of China(Nos.41876171,41506167,41476144)。
文摘The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11804195,11847224,11674198,and 12274265)the Natural Science Foundation of Shandong Province,China(Grant Nos.ZR2018BA034 and ZR2022MA006)。
文摘To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical fluorescent bases(A_(y),tC,G_(b),T_(p))are proposed for four-color DNA sequencing.These quasi-intrinsic probes are derived from the fluorophore replacement and ring expansion on natural bases,which still keep the pyrimidine or purine underlying skeleton and Watson–Crick hydrogen bonding face to allow minimal perturbation to the native DNA duplex.More importantly,these nucleobase analogues possess red-shifted absorption and efficient photoluminescence due to the enhancedπ-conjugation in character.Meanwhile,the four analogues could generate distinct emission wavelength(Δλ~50 nm)for real-time sequencing.To assess the biological employment of the proposed biosensors,the effects of base pairing and linking deoxyribose are also considered.
基金supported by the National Basic Research Program of China(Grant No.2011CB707605)National Natural Science Foundation of China(Grant Nos.50925519 and 51375092)G.S.Wu was supported by the Scientific Research Foundation of Graduate School of Southeast University
文摘Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale pore.It is still really tough to attain the single base discrimination on a DNA strand by merely analyzing the ionic current due to speedy DNA translocation and low spatial resolution.More integrated configurations are pursued to present versatile comparative dissimilarities of the four bases by enhancing the spatial resolution within a DNA molecule translocation event,such as transverse tunneling current,local potential change,and capacitance oriented voltage resonance.In this mini review,the insight is provided into the status quo on several functionalized techniques and methodologies for DNA sequencing and furthermore concluding remark and outlook are presented.
基金supported by the National Natural Science Foundation of China–China(Grant No.61471336)the Joint-Scholar of West Light Foundation of the Chinese Academy of Sciences awarded to DW and Shanghai Synchrotron Radiation FacilityCY was supported by China Postdoctoral Science Foundation–China(Grant No.2014M551011)
文摘Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein.Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale.In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.
基金supported by the National Natural Science Foundation of China (21175135, 21375130, 21205119)the National Basic Research Program of China (2010CB933600)the 100 Talents Program of the Chinese Academy of Sciences
文摘This review briefly summarizes recent progress in nanopore DNA sequencing from the beginning of 2012 to July 2014. Although partial successes have been achieved in different types of nanopores, biological pores such as α- hemolysin and MspA afford most promising results.
基金supported by the National Natural Science Foundation of China (21372183)the Hubei Province Natural Science Foundation (2013CFB328)+1 种基金the Key Laboratory of Analytical Chemistry for Biology and Medicine (Wuhan University), Ministry of Education (ACBM2014001)the Start-Up-Fund grant provided by Wuhan University of Science and Technology
文摘Nanopores have been studied as a unique DNA sequencing technology that can quickly read long stretched DNA sequences. A DNA molecule could pass through a nanopore in a speed of microsecond per base and even faster. With this speed, a human genome can potentially be sequenced by one nanopore in 〈1 h. In contrast to next- generation DNA sequencing （NGS）, the nanopore sequencing is enzyme free without need of sample amplification due to its single-molecule nature. The nanopore sequencing has been envisioned as a new generation of DNA sequencing technology in the post-NGS era. This progress focuses on status quo of the nanopore DNA sequencing and discusses the opportunities and challenges in this rapidly growing field.
文摘We discuss the feasibility of using a nanopore sandwich device to implement the principle of kinetic proofreading to discriminate incorrect hybridizing oligonucleotides on a target DNA or RNA.We propose a method of sequencing DNA or RNA using this approach.The design parameters for such a DNA sequencer are estimated from the Hopfield・Ninio theory of kinetic proofreading and Schrodinger's first-passage-time distribution function.
基金Natural Science Foundation of Ningxia Hui Autonomous Region(NZ0769)~~
文摘[ Objective ] The study aimed to identify Lycium Linn. at molecular level. [ Method ] The nrDNA ITS sequence of 5 edible Lycium Linn. germplasm resources were investigated. [ Result ] The nrDNA ITS regions of five edible Lycium Liun. germplasm resources were sequenced. The whole sequences varied from 628 bp to 632 bp, with the average length of 630 bp. Total 79 variation sites were observed in the sequences, which accounts for 12. 5%. [ Conclusion] Sequence analysis based on nrDNA sequencing provides a new approach to identify edible Lycium Linn. germplasm resources.
基金Supported by Natural Science foundation of Ningxia Hui Antonomous Region(NZ0769)~~
文摘[Objective] The study aimed to identify woltberry （Lycium Linn.） germplasm resources at molecular level by analyzing the nrDNA ITS sequence. [Method] Genomic DNA from woltberry leaves extracted by modified CTAB method were regarded as templates for PCR amplification by specific primer, clone and sequencing. [Result] The nrDNA ITS sequences were obtained and then differentiated among three tested materials. [Conclusion] PCR amplification and sequencing on nrDNA ITS is a feasible approach to identify different woltberry germplasm resources.
文摘Objective To investigate the vertical transmission rate of Chlamy dia trachomatis (CT) in Chongqing, China. Methods Specimens taken from 278 women and from their 79 infants were e xamined b y cell culture, polymerase chain reaction (PCR) and DNA sequence analysis. Chlam ydia trachomatis was isolated in McCoy cell culture. CT DNA was extracted with a modified NaI method. After cloning, recombinant plasmids were used for sequence analysis with the dideoxy chain termination method.Results 10.8% (30/278) of the cervical cultures of pregnant women were positive for Chlamydia trachomatis, while the positive rate tested by PCR was 14.0% (39/2 78). The vertical transmission rate of Chlamydia trachomatis was 55. 0% (11/20). The incidences of conjunctivitis and pneumonia in infants with Chlamydia t rachom atis positive mothers were 27.3% and 18.2%, respectively. DNA sequence s of Chlam ydia trachomatis isolated from the cervix of a mother and the nasopharynx of her baby were identical.Conclusion Chlamydia trachomatis infection is quite common in Cho ngqing , China. Our report is the first report of CT vertical transmission proved by DN A sequence analysis.
基金supported by the National Natural Science Foundation of China (81471697)the Key Technology R&D Program of Hubei Province (2014BBB003)+1 种基金Yellow Crane Talent (Science & Technology) Program of Wuhan City and Applied Basic Research Program of Wuhan City (2016060101010044, 2016060101010048)the Fundamental Research Funds for the Central Universities (2016YXMS253)
文摘Nanopores for DNA sequencing have drawn much attention due to their potentials to achieve amplification-free, low-cost, and high-throughput analysis of nuclei acids. The material configuration and fabrication of the nanopore has become one important consideration in the nanopore based DNA sequencing research. Among various materials, the newly emerged graphene has brought more opportunities to the development of sequencing technology because of its unique structures and properties. This review mainly focuses on the experimental aspects of graphene nanopore research including the nanopore fabrication methods and processes. Meanwhile, the challenges in the present graphene nanopore research including hydrophobicity, translocation velocity and noise are also addressed and discussed.
基金ThisstudywassupportedbytheChineseNationalInstituteofHealthGrant (No 96 13 7)
文摘Background Mutation and expression change of p21 WAF1/CIP1 may play a role in the growth of osteosarcoma. This study was to investigate the expression of the p21 WAF1/CIP1 gene in human osteosarcoma,p21 WAF1/CIP1 gene DNA sequence change and their relationships with the phenotype and clinical prognosis.Methods p21 WAF1/CIP1 gene in 10 normal people and the tumours of 45 osteosarcoma patients were examined using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) with silver staining. The PCR product with an abnormal strand was sequenced directly. The p21 WAF1/CIP1 gene mRNA and P21 protein of 45 cases of osteosarcoma were investigated by using in situ hybridization and immunohistochemistry,respectively. Results The occurrence of P21 protein in osteosarcoma was 17.78% (8/45),and p21 WAF1/CIP1 mRNA expression in osteosarcoma was 42.22% (19/45). The p21 WAF1/CIP1 gene DNA sequencing of amplified production showed that in p21 WAF1/CIP1 gene exon 3 of 36 cases of human osteosarcoma,there were 17 cases (47.22%) with C→T at position 609; 10 normal blood samples’ DNA sequence analysis yielded 8 cases (80.00%) with C→T at the same position. Conclusions Along with the increase of malignancy,the expression of p21 WAF1/CIP1 mRNA and P21 protein in osteosarcoma tends to decrease. It is uncommon for the p21 WAF1/CIP1 gene mutation to occur in human osteosarcoma. As a result, the possible existence of tumour subtypes of p21 WAF1/CIP1 gene mutation should be investigated. Our research leads to the location of p21 WAF1/CIP1 gene polymorphism of Chinese osteosarcoma patients,which can provide a basis for further research.
基金support from the Thailand Research Fund(MRG6280150)S.J.is supported by Suranaree University of Technology(SUT)+3 种基金Thailand Science Research and Innovation(TSRI)National Science,Research and Innovation Fund(NSRF grant No.B05F640051)R.G.A.thanks for financial support from CNPq(Nos.437182/2018-5 and 313076/2020-0)also FAPERJ(Nos.E-26/010.101126/2018 and 26/202.699/2019).R.H.S.ackn。
文摘Nanopore-based devices have provided exciting opportunities to develop affordable label-free DNA sequencing platforms.Over a decade ago,graphene has been proposed as a two-dimensional(2D)nanopore membrane in order to achieve single-base resolution.However,it was experimentally revealed that clogging of the graphene nanopore can occur due to the hydrophobic nature of graphene,thus hindering the translocation of DNA.To overcome this problem,the exploration of alternative 2D materials has gained considerable interest over the last decade.Here we show that a Ti_(2)C-based MXene nanopore functionalized by hydroxyl groups(–OH)exhibits transverse conductance properties that allow for the distinction between all four naturally occurring DNA bases.We have used a combination of density functional theory and non-equilibrium Green’s function method to sample over multiple orientations of the nucleotides in the nanopore,as generated from molecular dynamics simulations.The conductance variation resulting from sweeping an applied gate voltage demonstrates that the Ti_(2)C-based MXene nanopore possesses high potential to rapidly and reliably sequence DNA.Our findings open the door to further theoretical and experimental explorations of MXene nanopores as a promising 2D material for nanopore-based DNA sensing.
文摘The authors regret that there was an incorrect citation in the Table 1 of the article ＂Nanopore-based Fourth-generation DNA Sequencing Technology＂, which was published in the journal Genomics, Proteomics ＆ Bioinformatics, Issue 1, 2015. In the table, the image in the 4th row originally appeared in the article ＂Nanopore-based sequence-specific detection of duplex DNA for geno- mic profiling＂ published by Nano Letters in 2010. Therefore, Ref. [8], which was associated with the image in the current Table l, should be replaced by the reference： Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M, Meller A. Nanopore- based sequence specific detection of duplex DNA for genomic profiling. Nano Lett 2010; 10：738-42.＂ The copy right permission of this article has been obtained. The authors would like to apologize for any inconvenience caused.
文摘The authors regret that there were typos in the online version of Figure 4 published in Issue 1,2015.In the figure legend boxes of panels F and G,‘‘Ni’’should be corrected to‘‘N’’for the labeling of the green curves.The figure in the printed version has been corrected.The correct Figure 4 is shown below.The authors would like to apologize for any inconvenience caused.
文摘With the support from the National Natural Science Foundation of China,Prof.Huang Yanyi(黄岩谊)led a team at Peking University to demonstrate a novel approach,which combined fluorogenic sequencingby-synthesis(SBS)chemistry with an information theory-based error-correction coding scheme to
文摘Objective: To investigate the p21WAF1 /CIP1gene DNA sequence change and their relationship with the phenotype of human osteosarcoma. Methods: p21WAF1 /CIP1gene DNA of 36 osteosarcoma spec- imens was examined by using polymerase chain reaction-single strand conformation polymorphism (PCR- SSCP) method. The PCR products were sequenced directly. Results: In p21WAF1 /CIP1 gene exon3 of 36 cases of human osteosarcoma, the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 17 cases with the incidence being 44.4%. In 10 normal blood samples, DNA sequence analysis showed the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 8 cases with the incidence being 80%. Conclusion: The novel location of p21WAF1 /CIP1gene polymorphism of osteosarcoma, but not mutation was de?ned, and this location might provide the meaningful reference for the further research of p21WAF1/CIP1 gene.p2lWAF1/CIP1基因DNA序列分析及其与骨肉瘤表型的关系
