Strand displacement reaction is a crucial component in the assembly of diverse DNA-based nanodevices,with the toehold-mediated strand displacement reaction representing the prevailing strategy.However,the single-stran...Strand displacement reaction is a crucial component in the assembly of diverse DNA-based nanodevices,with the toehold-mediated strand displacement reaction representing the prevailing strategy.However,the single-stranded Watson-Crick sticky region that serves as the trigger for strand displacement can also cause leakage reactions by introducing crosstalk in complex DNA circuits.Here,we proposed the toeless and reversible DNA strand displacement reaction based on the Hoogsteen-bond triplex,which is compatible with most of the existing DNA circuits.We demonstrated that our proposed reaction can occur at pH 5 and can be reversed at pH 9.We also observed an approximately linear relationship between the degree of reaction and pH within the range of pH 5-6,providing the potential for precise regulation of the reaction.Meanwhile,by altering the sequence orientation,we have demonstrated that our proposed reaction can be initiated or regulated through the same toeless mechanism without the requirement for protonation in low pH conditions.Based on the proposed reaction principle,we further constructed a variety of DNA nanodevices,including two types of DNA logic gates that rely on pH 5/pH 9 changes for initiating and reversing:the AND gate and the OR gate.We also successfully constructed a DNA Walker based on our proposed reaction modes,which can move along a given track after the introduction of a programmable DNA sequence and complete a cycle after 4 steps.Our findings suggest that this innovative approach will have broad utility in the development of DNA circuits,molecular sensors,and other complex biological systems.展开更多
The clustered regularly interspersed short palindromic repeats/CRISPR-associated protein 9(CRISPR/Cas9)system is an RNA-guided platform for highly efficient and specific genome targeting in diverse organisms,which has...The clustered regularly interspersed short palindromic repeats/CRISPR-associated protein 9(CRISPR/Cas9)system is an RNA-guided platform for highly efficient and specific genome targeting in diverse organisms,which has been exploited for various applications in gene manipulation.Compared with the constantly active CRISPR/Cas9 function,conditional control of its activity can improve the performance of the system with reduced side effects and high spatiotemporal precision.The pH-responsive triplex RNA was successful used in CRISPR-derived RNA/trans-activating crRNA(crRNA/tracrRNA)of CRISPR/Cas9,thus affecting RNA/dead Cas9(dCas9)complex to target DNA in vitro and in vivo.This design of triplex RNA opens a new window towards the broad involvement of eukaryotic cells for conditional control of CRISPR/Cas9function.?2024 Published by Elsevier B.V.on behalf of Chinese Chemical Society and Institute of Materia Medica,Chinese Academy of Medical Sciences.展开更多
DNA circuits are powerful tools in various applications such as logical computation,molecular diagnosis and synthetic biology.Leakage is a major problem in constructing complex DNA circuits.It directly affects the out...DNA circuits are powerful tools in various applications such as logical computation,molecular diagnosis and synthetic biology.Leakage is a major problem in constructing complex DNA circuits.It directly affects the output signal and harms the circuit’s performance significantly.In the traditional DNA circuits,the gate complex is a duplex structure.There are insufficient energy barriers to prevent spontaneous detachment of strands,resulting in a leak prone.Herein,we have developed triplex-structure based DNA circuit with ultra-low leakage and high signal-to-noise ratio(SNR).The triplex structure improves the stability in the absence of input.At the same time,the driving force of the strand displacement cascades reduces the influence of the triplex structure on the desired reaction.The SNR of the DNA circuit was increased to 695,while the desired reaction rate remained 90%of the conventional translator circuit.The triplex-structure mediated leakage prevention strategy was further tested at different temperatures and in DNA translator and seesaw circuits.We also constructed modular basic logic gates with a high efficiency and low leakage.On this basis,we further constructed triplex-structure based tertiary DNA logic circuits,and the SNR reached 295,which,to the best of our knowledge,was among the highest of the field.We believe that our scheme provides a novel,valid,and general tool for reducing leakages,and we anticipate that it will be widely adopted in DNA nanotechnology.展开更多
Triplexers are designed based on SOl flattop arrayed waveguide gratings （AWGs）. Three wavelengths （1310, 1490,and 1550nm） operate at three diffraction orders of AWGs. Simulation shows that the 3dB bandwidth,crosst...Triplexers are designed based on SOl flattop arrayed waveguide gratings （AWGs）. Three wavelengths （1310, 1490,and 1550nm） operate at three diffraction orders of AWGs. Simulation shows that the 3dB bandwidth,crosstalk, and loss are 6nm,less than -40dB, and 5dB, respectively. The output optical fields of the device fabricated in our laboratory are clear and show a good triplexing function.展开更多
In this paper, we report the influence of cooling processes on the yielding behavior of a medium Mn steel(MMS) with triplex microstructure, i.e. austenite(γ), ferrite(α) and as-quenched martensite(α’). After the i...In this paper, we report the influence of cooling processes on the yielding behavior of a medium Mn steel(MMS) with triplex microstructure, i.e. austenite(γ), ferrite(α) and as-quenched martensite(α’). After the intercritical annealing(IA) at both 725℃ and 750℃, the steel was subjected to the two cooling processes, i.e. air cooling(AC) and water quenching(WQ). It exhibits the discontinuous yielding after the AC following the IA at 750℃ while the continuous yielding after the WQ. Compared with WQ process,both the dilatometry and the microstructural examinations show that the AC process leads to lower Ms temperature, larger retained austenite(RA) fraction and less martensite, the latter is always companied with geometry necessary dislocations(GNDs) generated near the α/α’ interfaces. Considering the complexity of nanosized tri-phases in this steel, the presence of martensite with key features in the resultant specimens was systematically examined by atom probe tomography(APT) on the samples prepared by the specific target lift-out method. The APT results directly revealed the C/Mn co-segregation at the α’/αinterfaces in the AC samples but not in WQ samples. The numerical simulation results further suggest that the segregation of C and Mn at the α’/α interfaces may be due to different mechanisms. We conclude that the yielding of triplex MMS is determined by both the quantity of GNDs generated near theα/α’ interfaces, which increases with martensite fraction, and the extent of their immobilization resulting from the interfacial segregation of solute atoms when the presence of martensite is sufficient. WQ tends to suppress the discontinuous yielding of MMS since the rapid cooling may promote more martensite formed with the increasing quantity of GNDs and prevent the interfacial segregation of both C and Mn.展开更多
Saxitoxin(STX),one of the most toxic paralytic shellfish poisons discovered to date,is listed as a required item of aquatic product safety inspection worldwide.However,conventional detection methods for STX are limite...Saxitoxin(STX),one of the most toxic paralytic shellfish poisons discovered to date,is listed as a required item of aquatic product safety inspection worldwide.However,conventional detection methods for STX are limited by various issues,such as low sensitivity,complicated operations,and ethical considerations.In this study,an aptamer-triplex molecular switch(APT-TMS)and gold nanoparticle(AuNP)nanozyme were combined to develop a label-free colorimetric aptasensor for the rapid and highly sensitive de-tection of STX.An anti-STX aptamer designed with pyrimidine arms and a purine chain was fabricated to form an APT-TMS.Specific binding between the aptamer and STX triggered the opening of the switch,which causes the purine chains to adsorb onto the surface of the AuNPs and enhances the peroxidase-like activity of the AuNP nanozyme toward 3,3’,5,5’-tetramethylbenzidine.Under optimized conditions,the proposed aptasensor showed high sensitivity and selectivity for STX,with a limit of detection of 335.6 pmol L^(−1) and a linear range of 0.59-150 nmol L^(−1).Moreover,good recoveries of 82.70%-92.66%for shellfish and 88.97%-106.5%for seawater were obtained.The analysis could be completed within 1 h.The proposed design also offers a robust strategy to achieve detection of other marine toxin targets by altering the corresponding aptamers.展开更多
We investigate an optical compact triplexer based on two photonic crystal waveguides and resonant cavities. For performing wavelength selection, we use three core-shell rods as the resonant cavities. The core rods are...We investigate an optical compact triplexer based on two photonic crystal waveguides and resonant cavities. For performing wavelength selection, we use three core-shell rods as the resonant cavities. The core rods are created by introducing air holes in the center of the silicon rods. By varying the radii of the air holes, three specific wavelengths 1.31, 1.49 and 1.55μm can be obtained. This structure is designed and its performance is verified by the finite-difference time-domain method, which is highly suitable for photonic integrated circuits （PICs）. The average output transmission efficiency and quality factor are more than 98.85% and 560, respectively. The mean value of the crosstalk between output channels is about -36.49 dB. The present device is extremely compact with total size 96.24μm2, which is suitable for PICs and can be utilized in the fiber-to-the-home system.展开更多
Gene targeting technology is an important means to investigate gene functions, but its efficiency of gene targeting is very low, especially for somatic cell targeting. Artificially induced double-strand breaks （DSB）...Gene targeting technology is an important means to investigate gene functions, but its efficiency of gene targeting is very low, especially for somatic cell targeting. Artificially induced double-strand breaks （DSB） and triplex forming oligonucleotide （TFO） are currently developed methods to improve the targeting efficiency. This paper summarized the basic principles, design ideas and application in gene targeting efficiency improvement of these two methods, analyzed and com- pared their characteristics, and finally proposed prospects for their future development.展开更多
This study is used to investigate the feasibility of employing the Iodogen method to label triplex-forming oligonucleotide (TFO) targeted to the initiator of the S gene of HBV with 125I. A 17-mer oligonucleotides sequ...This study is used to investigate the feasibility of employing the Iodogen method to label triplex-forming oligonucleotide (TFO) targeted to the initiator of the S gene of HBV with 125I. A 17-mer oligonucleotides sequence was synthesized and grafted at the 5′ terminal with a tyramine group. Radioiodination of the tyramine-TFO with 125I was then performed using the Iodogen method. After TFO was labeled with 125I using the Iodogen method, the label- ing rate, the radiochemical purity, stability and bioactivity were determined, respectively. The results show that the radiolabeling rate and the radiochemical purity were 93% and 99%, respectively; and the radiochemical purity is more than 90% in vitro at -20°C on the 5th day after labeling; and the rate of 125I-tyramine-TFO binding to HepG2.2.15 cells was (37.2 ± 1.4)% and statistically different from the rate of HepG2 (p < 0.5). Hence, it is concluded that the labeling of oligonucleotides conjugated with tyramine using the Iodogen method is successful and is characterized with a high labeling rate, high stability, and a low loss of bioactivity of the labeled agent.展开更多
基金financially supported by the National Key Research and Development Program of China(No.2021YFC2701402)the Open Research Fund of State Key Laboratory of Bioelectronics,Southeast University(No.Sklb2021-k06)+1 种基金the Open Foundation of NHC Key Laboratory of Birth Defect for Research and Prevention(Hunan Provincial Maternal and Child Health Care Hospital)(No.KF2020007)the Open Foundation of Translational Medicine National Science and Technology Infrastructure(Shanghai)(No.TMSK-2021-141)。
文摘Strand displacement reaction is a crucial component in the assembly of diverse DNA-based nanodevices,with the toehold-mediated strand displacement reaction representing the prevailing strategy.However,the single-stranded Watson-Crick sticky region that serves as the trigger for strand displacement can also cause leakage reactions by introducing crosstalk in complex DNA circuits.Here,we proposed the toeless and reversible DNA strand displacement reaction based on the Hoogsteen-bond triplex,which is compatible with most of the existing DNA circuits.We demonstrated that our proposed reaction can occur at pH 5 and can be reversed at pH 9.We also observed an approximately linear relationship between the degree of reaction and pH within the range of pH 5-6,providing the potential for precise regulation of the reaction.Meanwhile,by altering the sequence orientation,we have demonstrated that our proposed reaction can be initiated or regulated through the same toeless mechanism without the requirement for protonation in low pH conditions.Based on the proposed reaction principle,we further constructed a variety of DNA nanodevices,including two types of DNA logic gates that rely on pH 5/pH 9 changes for initiating and reversing:the AND gate and the OR gate.We also successfully constructed a DNA Walker based on our proposed reaction modes,which can move along a given track after the introduction of a programmable DNA sequence and complete a cycle after 4 steps.Our findings suggest that this innovative approach will have broad utility in the development of DNA circuits,molecular sensors,and other complex biological systems.
基金supported by the National Key R&D Program of China(Nos.2022YFC2804101,2020YFA0211200)National Natural Science Foundation of China(Nos.22377056,22222706,21977122)。
文摘The clustered regularly interspersed short palindromic repeats/CRISPR-associated protein 9(CRISPR/Cas9)system is an RNA-guided platform for highly efficient and specific genome targeting in diverse organisms,which has been exploited for various applications in gene manipulation.Compared with the constantly active CRISPR/Cas9 function,conditional control of its activity can improve the performance of the system with reduced side effects and high spatiotemporal precision.The pH-responsive triplex RNA was successful used in CRISPR-derived RNA/trans-activating crRNA(crRNA/tracrRNA)of CRISPR/Cas9,thus affecting RNA/dead Cas9(dCas9)complex to target DNA in vitro and in vivo.This design of triplex RNA opens a new window towards the broad involvement of eukaryotic cells for conditional control of CRISPR/Cas9function.?2024 Published by Elsevier B.V.on behalf of Chinese Chemical Society and Institute of Materia Medica,Chinese Academy of Medical Sciences.
基金the National Natural Science Foundation of China(No.81871732)the National Key Research and Development Program of China(No.2021YFC2701402)+4 种基金the Open Research Fund of State Key Laboratory of Bioelectronics,southeast University(No.Sklb2021-k06)the Open Foundation of NHC Key Laboratory of Birth Defect for Research and Prevention(Hunan Provincial Maternal and Child Health Care Hospital)(No.KF2020007)the Open Foundation of Translational Medicine National Science and Technology Infrastructure(Shanghai)(No.TMSK-2021-141)the Open Fund from Key Laboratory of Cellular Physiology(Shanxi Medical University)Ministry of Education,China(No.CPOF202103).
文摘DNA circuits are powerful tools in various applications such as logical computation,molecular diagnosis and synthetic biology.Leakage is a major problem in constructing complex DNA circuits.It directly affects the output signal and harms the circuit’s performance significantly.In the traditional DNA circuits,the gate complex is a duplex structure.There are insufficient energy barriers to prevent spontaneous detachment of strands,resulting in a leak prone.Herein,we have developed triplex-structure based DNA circuit with ultra-low leakage and high signal-to-noise ratio(SNR).The triplex structure improves the stability in the absence of input.At the same time,the driving force of the strand displacement cascades reduces the influence of the triplex structure on the desired reaction.The SNR of the DNA circuit was increased to 695,while the desired reaction rate remained 90%of the conventional translator circuit.The triplex-structure mediated leakage prevention strategy was further tested at different temperatures and in DNA translator and seesaw circuits.We also constructed modular basic logic gates with a high efficiency and low leakage.On this basis,we further constructed triplex-structure based tertiary DNA logic circuits,and the SNR reached 295,which,to the best of our knowledge,was among the highest of the field.We believe that our scheme provides a novel,valid,and general tool for reducing leakages,and we anticipate that it will be widely adopted in DNA nanotechnology.
文摘Triplexers are designed based on SOl flattop arrayed waveguide gratings （AWGs）. Three wavelengths （1310, 1490,and 1550nm） operate at three diffraction orders of AWGs. Simulation shows that the 3dB bandwidth,crosstalk, and loss are 6nm,less than -40dB, and 5dB, respectively. The output optical fields of the device fabricated in our laboratory are clear and show a good triplexing function.
基金financial support from National Natural Science Foundation of China (Nos. 51861135302 and 51831002)the National Natural Science Foundation (No. 51904028)+2 种基金Fundamental Research Funds for the Central Universities (No. 06600019, 06500151)the Deutsche Forschungsgemeinschaft (DFG) for funding the research work (grant number BL 402/49–1, “Characterizing and modeling on microstructural evolution during intercritical annealing of high performance medium Mn steel”)the Powder Diffraction and Total Scattering Beamline P02.1 of PETRA III at DESY (Proposal No.: I-20191416)
文摘In this paper, we report the influence of cooling processes on the yielding behavior of a medium Mn steel(MMS) with triplex microstructure, i.e. austenite(γ), ferrite(α) and as-quenched martensite(α’). After the intercritical annealing(IA) at both 725℃ and 750℃, the steel was subjected to the two cooling processes, i.e. air cooling(AC) and water quenching(WQ). It exhibits the discontinuous yielding after the AC following the IA at 750℃ while the continuous yielding after the WQ. Compared with WQ process,both the dilatometry and the microstructural examinations show that the AC process leads to lower Ms temperature, larger retained austenite(RA) fraction and less martensite, the latter is always companied with geometry necessary dislocations(GNDs) generated near the α/α’ interfaces. Considering the complexity of nanosized tri-phases in this steel, the presence of martensite with key features in the resultant specimens was systematically examined by atom probe tomography(APT) on the samples prepared by the specific target lift-out method. The APT results directly revealed the C/Mn co-segregation at the α’/αinterfaces in the AC samples but not in WQ samples. The numerical simulation results further suggest that the segregation of C and Mn at the α’/α interfaces may be due to different mechanisms. We conclude that the yielding of triplex MMS is determined by both the quantity of GNDs generated near theα/α’ interfaces, which increases with martensite fraction, and the extent of their immobilization resulting from the interfacial segregation of solute atoms when the presence of martensite is sufficient. WQ tends to suppress the discontinuous yielding of MMS since the rapid cooling may promote more martensite formed with the increasing quantity of GNDs and prevent the interfacial segregation of both C and Mn.
基金funded by the National Natural Science Foundation of China(No.31801620).
文摘Saxitoxin(STX),one of the most toxic paralytic shellfish poisons discovered to date,is listed as a required item of aquatic product safety inspection worldwide.However,conventional detection methods for STX are limited by various issues,such as low sensitivity,complicated operations,and ethical considerations.In this study,an aptamer-triplex molecular switch(APT-TMS)and gold nanoparticle(AuNP)nanozyme were combined to develop a label-free colorimetric aptasensor for the rapid and highly sensitive de-tection of STX.An anti-STX aptamer designed with pyrimidine arms and a purine chain was fabricated to form an APT-TMS.Specific binding between the aptamer and STX triggered the opening of the switch,which causes the purine chains to adsorb onto the surface of the AuNPs and enhances the peroxidase-like activity of the AuNP nanozyme toward 3,3’,5,5’-tetramethylbenzidine.Under optimized conditions,the proposed aptasensor showed high sensitivity and selectivity for STX,with a limit of detection of 335.6 pmol L^(−1) and a linear range of 0.59-150 nmol L^(−1).Moreover,good recoveries of 82.70%-92.66%for shellfish and 88.97%-106.5%for seawater were obtained.The analysis could be completed within 1 h.The proposed design also offers a robust strategy to achieve detection of other marine toxin targets by altering the corresponding aptamers.
文摘We investigate an optical compact triplexer based on two photonic crystal waveguides and resonant cavities. For performing wavelength selection, we use three core-shell rods as the resonant cavities. The core rods are created by introducing air holes in the center of the silicon rods. By varying the radii of the air holes, three specific wavelengths 1.31, 1.49 and 1.55μm can be obtained. This structure is designed and its performance is verified by the finite-difference time-domain method, which is highly suitable for photonic integrated circuits （PICs）. The average output transmission efficiency and quality factor are more than 98.85% and 560, respectively. The mean value of the crosstalk between output channels is about -36.49 dB. The present device is extremely compact with total size 96.24μm2, which is suitable for PICs and can be utilized in the fiber-to-the-home system.
基金Supported by Shandong Swine Industry Technology System and Science and Technology Planning Program for Basic Research in Qingdao City(12-1-4-14-jch)
文摘Gene targeting technology is an important means to investigate gene functions, but its efficiency of gene targeting is very low, especially for somatic cell targeting. Artificially induced double-strand breaks （DSB） and triplex forming oligonucleotide （TFO） are currently developed methods to improve the targeting efficiency. This paper summarized the basic principles, design ideas and application in gene targeting efficiency improvement of these two methods, analyzed and com- pared their characteristics, and finally proposed prospects for their future development.
文摘This study is used to investigate the feasibility of employing the Iodogen method to label triplex-forming oligonucleotide (TFO) targeted to the initiator of the S gene of HBV with 125I. A 17-mer oligonucleotides sequence was synthesized and grafted at the 5′ terminal with a tyramine group. Radioiodination of the tyramine-TFO with 125I was then performed using the Iodogen method. After TFO was labeled with 125I using the Iodogen method, the label- ing rate, the radiochemical purity, stability and bioactivity were determined, respectively. The results show that the radiolabeling rate and the radiochemical purity were 93% and 99%, respectively; and the radiochemical purity is more than 90% in vitro at -20°C on the 5th day after labeling; and the rate of 125I-tyramine-TFO binding to HepG2.2.15 cells was (37.2 ± 1.4)% and statistically different from the rate of HepG2 (p < 0.5). Hence, it is concluded that the labeling of oligonucleotides conjugated with tyramine using the Iodogen method is successful and is characterized with a high labeling rate, high stability, and a low loss of bioactivity of the labeled agent.
