An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide, and used for the determination of single-stranded binding protein （SSB） by surface plasmon resonance microscopy （SPR...An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide, and used for the determination of single-stranded binding protein （SSB） by surface plasmon resonance microscopy （SPR）. The experiment results showed that SSB binds ss-DNA with high specificity, and relative signal of SPR response is proportional to the concentration of SSB in the range of 0.1-100 ng/mL with a detection limit （S/N = 3） of 0.07 ng/mL.展开更多
Using a molecular theory, we investigate the temperature-dependent self-assembly of single-stranded DNA（ss DNA）tethered to a charged nanoparticle surface. Here the size, conformations, and charge properties of ss DN...Using a molecular theory, we investigate the temperature-dependent self-assembly of single-stranded DNA（ss DNA）tethered to a charged nanoparticle surface. Here the size, conformations, and charge properties of ss DNA are taken into account. The main results are as follows： i） when the temperature is lower than the critical switching temperature, the ss DNA will collapse due to the existence of electrostatic interaction between ss DNA and charged nanoparticle surface; ii）for the short ss DNA chains with the number of bases less than 10, the switching of ss DNA cannot happen, and the critical temperature does not exist; iii） when the temperature increases, the electrostatic attractive interaction between ss DNA and charged nanoparticle surface becomes weak dramatically, and ss DNA chains will stretch if the electrostatic attractive interaction is insufficient to overcome the elastic energy of ss DNA and the electrostatic repulsion energy. These findings accord well with the experimental observations. It is predicted that the switching of ss DNA will not happen if the grafting densities are too high.展开更多
This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons constituting the sequence of single-stranded DNA of the...This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons constituting the sequence of single-stranded DNA of the entire human genome. Beyond the evolution and erratic mutations like transposons within the genome, it’s as if the memory of a fossil genome with multiple symmetries persists. This recalls the “intermingling” of information characterizing the fractal universe of chaos theory. The result leads to a balanced and perfect tuning between the masses of the two strands of the huge DNA molecule that constitute our genome. We show here how codon populations forming the single-stranded DNA sequences can constitute a critical approach to the understanding of junk DNA function. Then, we suggest revisiting certain methods published in our 2009 book “Codex Biogenesis”. In fact, we demonstrate here how the universal genetic code table is a powerful analytical filter to characterize single-stranded DNA sequences constituting chromosomes and genomes. We can then show that any genomic DNA sequence is featured by three numbers, which characterize it and its 64 codon populations with correlations greater than 99%. The number “1” is common to all sequences, expressing the second law of Chargaff. The other 2 numbers are related to each specific DNA sequence case characterizing life species. For example, the entire human genome is characterized by three remarkable numbers 1, 2, and Phi = 1.618 the golden ratio. Associated with each of these three numbers, we can match three axes of symmetry, then “imagine” a kind of hyperspace formed by these codon populations. Then we revisit the value (3-Phi)/2 which is probably universal and common to both the scale of quarks and atomic levels, balancing and tuning the whole human genome codon population. Finally, we demonstrate a new kind of duality between “form and substance” overlapping the whole human genome: we will show that—simultaneously with the duality between genes and junk DNA—there is a second layer of embedded hidden structure overlapping all the DNA of the whole human genome, dividing it into a second type of duality information/redundancy involving golden ratio proportions.展开更多
Background:The analysis of chromatin integrity has become an important determinant of sperm quality.In frozenthawed bovine sperm,neither the sequence of post-thaw injury events nor the dynamics of different types of s...Background:The analysis of chromatin integrity has become an important determinant of sperm quality.In frozenthawed bovine sperm,neither the sequence of post-thaw injury events nor the dynamics of different types of sperm DNA breaks are well understood.The aim of the present work was to describe such sperm degradation aftermath focusing on DNA damage dynamics,and to assess if this parameter can predict pregnancy rates in cattle.Results:A total of 75 cryopreserved ejaculates from 25 Holstein bulls were evaluated at two post-thawing periods(0-2 h and 2-4 h),analyzing global and double-stranded DNA damage through alkaline and neutral Comet assays,chromatin deprotamination and decondensation,sperm motility,viability,acrosomal status,and intracellular levels of total ROS,superoxides and calcium.Insemination of 59,605 females was conducted using sperm from the same bulls,thus obtaining the non-return to estrus rates after 90 d(NRR).Results showed an increased rate of double-stranded breaks in the first period(0-2 h:1.29±1.01%/h vs.2-4 h:0.13±1.37%/h;P<0.01),whereas the rate of sperm with moderate+high single-stranded breaks was higher in the second period(0-2 h:3.52±7.77%/h vs.2-4h:21.06±11.69%/h;P<0.0001).Regarding sperm physiology,viability decrease rate was different between the two periods(0-2 h:-4.49±1.79%/h vs.2-4 h:-2.50±3.39%/h;P=0.032),but the progressive motility decrease rate was constant throughout post-thawing incubation(0-2 h:-4.70±3.42%/h vs.2-4 h:-1.89±2.97%/h;P>0.05).Finally,whereas no correlations between bull fertility and any dynamic parameter were found,there were correlations between the NRR and the basal percentage of highly-damaged sperm assessed with the alkaline Comet(Rs=-0.563,P=0.003),between NRR and basal progressive motility(Rs=0.511,P=0.009),and between NRR and sperm with high ROS at 4 h post-thaw(Rs=0.564,P=0.003).Conclusion:The statistically significant correlations found between intracellular ROS,sperm viability,sperm motility,DNA damage and chromatin deprotamination suggested a sequence of events all driven by oxidative stress,where viability and motility would be affected first and sperm chromatin would be altered at a later stage,thus suggesting that bovine sperm should be used for fertilization within 2 h post-thaw.Fertility correlations supported that the assessment of global DNA damage through the Comet assay may help predict bull fertility.展开更多
Previous investigation on the mutagenic effects of 3,N4-Ethenocytosine (εC), a nonpairing DNA lesion,revealed the existence of a novel SOS-independent inducible mutagenic mechanism in E. coli termed UVM for UV modula...Previous investigation on the mutagenic effects of 3,N4-Ethenocytosine (εC), a nonpairing DNA lesion,revealed the existence of a novel SOS-independent inducible mutagenic mechanism in E. coli termed UVM for UV modulation of mutagenesis. To investigate whether UVM is mediated by an alteration of DNA replication, we have set up an in vitro replication system ill which phage M13 viral single-stranded DNA bearing a single site-specific (εC) residue is replicated by soluble protein extracts from E. coli cells. Replication products were analyzed by agarose gel electrophoresis and the frequency of translesion synthesis was determined by restriction endonuclease analyses. Our data indicate that DNA replication is strongly inhibited by εC, but that translesion DNA synthesis does occur in about 14% of the replicated DNA molecules. These results are very similar to those observed previously in vivo, and suggest that this experimental system may be suitable for evaluating alterations in DNA replication in UVM-induced cells.展开更多
Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear.In this study,a novel...Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear.In this study,a novel circular ssDNA virus,tentatively named Diaporthe sojae circular DNA virus 1(DsCDV1),was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear trees.DsCDV1 has a monopartite genome(3185 nt in size)encapsidated in isometric virions(21-26 nm in diameter).The genome comprises seven putative open reading frames encoding a discrete replicase(Rep)split by an intergenic region,a putative capsid protein(CP),several proteins of unknown function(P1-P4),and a long intergenic region.Notably,the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae,respectively,indicating an evolutionary linkage with both families.Phylogenetic analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster,supporting the establishment of a new family,tentatively named Gegemycoviridae,intermediate to both families.DsCDV1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host fungus.Remarkably,DsCDV1 can systematically infect tobacco and pear seedlings,providing broad-spectrum resistance to fungal diseases.Subcellular localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata,while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus,suggesting that P3 is a movement protein.DsCDV1 exhibits unique molecular and biological traits not observed in other ssDNA viruses,serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and fungi.These findings contribute to expanding our understanding of ssDNA virus diversity and evolution,offering potential biocontrol applications for managing crucial plant diseases.展开更多
Terminal deoxynucleotidyl transferase(Td T) has been characterized as template-independent polymerase using single-stranded DNA(ss DNA) as primers to generate random oligonucleotides. However, the extension performanc...Terminal deoxynucleotidyl transferase(Td T) has been characterized as template-independent polymerase using single-stranded DNA(ss DNA) as primers to generate random oligonucleotides. However, the extension performance of Td T to single-stranded RNA(ss RNA) is vague. By systematically comparing and contrasting the performance of Td T-catalyzed ss DNA and ss RNA extension, it is indicated that the catalytic efficiency of ss RNA as primers was about 3 times lower than ss DNA as primers. Collectively, it is believed that understanding the catalytic performance of Td T will help to design the strategy to synthesize chimeric DNA on 3-OH of ss RNA, which becomes invaluable.展开更多
[Objective] This study aimed to optimize the PCR amplification conditions for random ssDNA pool in SELEX technology. [Method] L16（45） orthogonal experimental design was adopted for optimization of five important fac...[Objective] This study aimed to optimize the PCR amplification conditions for random ssDNA pool in SELEX technology. [Method] L16（45） orthogonal experimental design was adopted for optimization of five important factors affecting PCR reaction system for random single-stranded DNA pool including Mg2＋ concentration, dNTP concentration, amount of Taq DNA polymerase, primer concentration and amount of random single-stranded DNA pool at four levels. Meanwhile, the annealing temperature and number of PCR reaction cycles were optimized to establish the optimal reaction system and PCR procedure. [Result] The optimal combination of PCR reaction system for random ssDNA pool was obtained, with a total system volume of 20 μl containing 2.0 μl of 10 × Buffer, 0.5 ng of random ssDNA pool, 2.5 mmol/L Mg2＋, 0.25 mmol/L dNTP Mixture, 0.6 μmol/L upstream and downstream primers and 1.5 U of Taq DNA polymerase; the optimal annealing temperature was 68 ℃ and the optimal number of cycles was 12. Under the above conditions, clear and stable bands with high specificity for random ssDNA pool were amplified. [Conclusion] This study laid the foundation for selection of parameters with higher specificity in SELEX technology.展开更多
Atomically precise gold nanoclusters(Au NCs) are an emerging class of quantum-sized nanomaterials with discrete electronic energy levels, which has led to a range of attractive electronic and optical applications. Nev...Atomically precise gold nanoclusters(Au NCs) are an emerging class of quantum-sized nanomaterials with discrete electronic energy levels, which has led to a range of attractive electronic and optical applications. Nevertheless, the lack of general methods to transfer Au NCs protected with hydrophobic ligands to an aqueous solution hampers their use in physiological settings. Here,we developed a single-stranded DNA-based approach that could transfer ~90% hydrophobic Au NCs into an aqueous solution.We experimentally and theoretically established that multivalent electrostatic and hydrophobic interactions between DNA strands and the hydrophobic ligand layer on Au NCs resulted in monodispersed DNA-coated Au NCs with high physical integrity in an aqueous solution. The fluorescence quantum yield of Au NCs was increased by ~13 fold, and surface-constrained DNA retained the specific recognition ability for biosensing. We further demonstrated the versatility of this phase-transfer approach, which thus holds great potential to advance biological and medical applications of Au NCs.展开更多
基金the Science Foundation of the National Education Ministry （No, 206096） the Education Department of Hubei Province （No. Z200522002）.
文摘An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide, and used for the determination of single-stranded binding protein （SSB） by surface plasmon resonance microscopy （SPR）. The experiment results showed that SSB binds ss-DNA with high specificity, and relative signal of SPR response is proportional to the concentration of SSB in the range of 0.1-100 ng/mL with a detection limit （S/N = 3） of 0.07 ng/mL.
基金Project supported by the Joint Funds of Xinjiang Natural Science Foundation,China(Grant No.2015211C298)
文摘Using a molecular theory, we investigate the temperature-dependent self-assembly of single-stranded DNA（ss DNA）tethered to a charged nanoparticle surface. Here the size, conformations, and charge properties of ss DNA are taken into account. The main results are as follows： i） when the temperature is lower than the critical switching temperature, the ss DNA will collapse due to the existence of electrostatic interaction between ss DNA and charged nanoparticle surface; ii）for the short ss DNA chains with the number of bases less than 10, the switching of ss DNA cannot happen, and the critical temperature does not exist; iii） when the temperature increases, the electrostatic attractive interaction between ss DNA and charged nanoparticle surface becomes weak dramatically, and ss DNA chains will stretch if the electrostatic attractive interaction is insufficient to overcome the elastic energy of ss DNA and the electrostatic repulsion energy. These findings accord well with the experimental observations. It is predicted that the switching of ss DNA will not happen if the grafting densities are too high.
文摘This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons constituting the sequence of single-stranded DNA of the entire human genome. Beyond the evolution and erratic mutations like transposons within the genome, it’s as if the memory of a fossil genome with multiple symmetries persists. This recalls the “intermingling” of information characterizing the fractal universe of chaos theory. The result leads to a balanced and perfect tuning between the masses of the two strands of the huge DNA molecule that constitute our genome. We show here how codon populations forming the single-stranded DNA sequences can constitute a critical approach to the understanding of junk DNA function. Then, we suggest revisiting certain methods published in our 2009 book “Codex Biogenesis”. In fact, we demonstrate here how the universal genetic code table is a powerful analytical filter to characterize single-stranded DNA sequences constituting chromosomes and genomes. We can then show that any genomic DNA sequence is featured by three numbers, which characterize it and its 64 codon populations with correlations greater than 99%. The number “1” is common to all sequences, expressing the second law of Chargaff. The other 2 numbers are related to each specific DNA sequence case characterizing life species. For example, the entire human genome is characterized by three remarkable numbers 1, 2, and Phi = 1.618 the golden ratio. Associated with each of these three numbers, we can match three axes of symmetry, then “imagine” a kind of hyperspace formed by these codon populations. Then we revisit the value (3-Phi)/2 which is probably universal and common to both the scale of quarks and atomic levels, balancing and tuning the whole human genome codon population. Finally, we demonstrate a new kind of duality between “form and substance” overlapping the whole human genome: we will show that—simultaneously with the duality between genes and junk DNA—there is a second layer of embedded hidden structure overlapping all the DNA of the whole human genome, dividing it into a second type of duality information/redundancy involving golden ratio proportions.
基金the European Union’s Horizon 2020 Research and Innovation scheme under the Marie Sklodowska-Curie grant agreement No.801342(Tecniospring INDUSTRY,TECSPR-19-1-0003)the Ministry of Science and Innovation,Spain(AGL2017-88329-R and PID2020-113320RBI00)+2 种基金the Catalan Agency for Management of University and Research Grants,Regional Government of Catalonia,Spain(2017-SGR-1229)the Catalan Institution for Research and Advanced Studies(ICREA)La Maratóde TV3 Foundation(214/857-202039)。
文摘Background:The analysis of chromatin integrity has become an important determinant of sperm quality.In frozenthawed bovine sperm,neither the sequence of post-thaw injury events nor the dynamics of different types of sperm DNA breaks are well understood.The aim of the present work was to describe such sperm degradation aftermath focusing on DNA damage dynamics,and to assess if this parameter can predict pregnancy rates in cattle.Results:A total of 75 cryopreserved ejaculates from 25 Holstein bulls were evaluated at two post-thawing periods(0-2 h and 2-4 h),analyzing global and double-stranded DNA damage through alkaline and neutral Comet assays,chromatin deprotamination and decondensation,sperm motility,viability,acrosomal status,and intracellular levels of total ROS,superoxides and calcium.Insemination of 59,605 females was conducted using sperm from the same bulls,thus obtaining the non-return to estrus rates after 90 d(NRR).Results showed an increased rate of double-stranded breaks in the first period(0-2 h:1.29±1.01%/h vs.2-4 h:0.13±1.37%/h;P<0.01),whereas the rate of sperm with moderate+high single-stranded breaks was higher in the second period(0-2 h:3.52±7.77%/h vs.2-4h:21.06±11.69%/h;P<0.0001).Regarding sperm physiology,viability decrease rate was different between the two periods(0-2 h:-4.49±1.79%/h vs.2-4 h:-2.50±3.39%/h;P=0.032),but the progressive motility decrease rate was constant throughout post-thawing incubation(0-2 h:-4.70±3.42%/h vs.2-4 h:-1.89±2.97%/h;P>0.05).Finally,whereas no correlations between bull fertility and any dynamic parameter were found,there were correlations between the NRR and the basal percentage of highly-damaged sperm assessed with the alkaline Comet(Rs=-0.563,P=0.003),between NRR and basal progressive motility(Rs=0.511,P=0.009),and between NRR and sperm with high ROS at 4 h post-thaw(Rs=0.564,P=0.003).Conclusion:The statistically significant correlations found between intracellular ROS,sperm viability,sperm motility,DNA damage and chromatin deprotamination suggested a sequence of events all driven by oxidative stress,where viability and motility would be affected first and sperm chromatin would be altered at a later stage,thus suggesting that bovine sperm should be used for fertilization within 2 h post-thaw.Fertility correlations supported that the assessment of global DNA damage through the Comet assay may help predict bull fertility.
文摘Previous investigation on the mutagenic effects of 3,N4-Ethenocytosine (εC), a nonpairing DNA lesion,revealed the existence of a novel SOS-independent inducible mutagenic mechanism in E. coli termed UVM for UV modulation of mutagenesis. To investigate whether UVM is mediated by an alteration of DNA replication, we have set up an in vitro replication system ill which phage M13 viral single-stranded DNA bearing a single site-specific (εC) residue is replicated by soluble protein extracts from E. coli cells. Replication products were analyzed by agarose gel electrophoresis and the frequency of translesion synthesis was determined by restriction endonuclease analyses. Our data indicate that DNA replication is strongly inhibited by εC, but that translesion DNA synthesis does occur in about 14% of the replicated DNA molecules. These results are very similar to those observed previously in vivo, and suggest that this experimental system may be suitable for evaluating alterations in DNA replication in UVM-induced cells.
基金supported by Earmarked Fund for China Agricultural Research System(grant number CARS-28)to G.W.and W.X.the National Natural Science Foundation of China(grant number 32172475)to W.X.
文摘Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear.In this study,a novel circular ssDNA virus,tentatively named Diaporthe sojae circular DNA virus 1(DsCDV1),was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear trees.DsCDV1 has a monopartite genome(3185 nt in size)encapsidated in isometric virions(21-26 nm in diameter).The genome comprises seven putative open reading frames encoding a discrete replicase(Rep)split by an intergenic region,a putative capsid protein(CP),several proteins of unknown function(P1-P4),and a long intergenic region.Notably,the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae,respectively,indicating an evolutionary linkage with both families.Phylogenetic analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster,supporting the establishment of a new family,tentatively named Gegemycoviridae,intermediate to both families.DsCDV1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host fungus.Remarkably,DsCDV1 can systematically infect tobacco and pear seedlings,providing broad-spectrum resistance to fungal diseases.Subcellular localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata,while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus,suggesting that P3 is a movement protein.DsCDV1 exhibits unique molecular and biological traits not observed in other ssDNA viruses,serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and fungi.These findings contribute to expanding our understanding of ssDNA virus diversity and evolution,offering potential biocontrol applications for managing crucial plant diseases.
基金supported by the National Natural Science Foundation of China (NSFC, Nos. 21927814 and 21772143 to J.Y. Zhang)the National Science Foundation of Tianjin (Nos. 20YDTPJC00090, 19ZXDBSY00070 and 20YFZCSY00990 to X.Q. Gong)。
文摘Terminal deoxynucleotidyl transferase(Td T) has been characterized as template-independent polymerase using single-stranded DNA(ss DNA) as primers to generate random oligonucleotides. However, the extension performance of Td T to single-stranded RNA(ss RNA) is vague. By systematically comparing and contrasting the performance of Td T-catalyzed ss DNA and ss RNA extension, it is indicated that the catalytic efficiency of ss RNA as primers was about 3 times lower than ss DNA as primers. Collectively, it is believed that understanding the catalytic performance of Td T will help to design the strategy to synthesize chimeric DNA on 3-OH of ss RNA, which becomes invaluable.
基金Supported by Central University Basic Research Operating Expenses Special Fund(XDJK2011C026)Southwest University Doctoral Fund(09BSR04)~~
文摘[Objective] This study aimed to optimize the PCR amplification conditions for random ssDNA pool in SELEX technology. [Method] L16（45） orthogonal experimental design was adopted for optimization of five important factors affecting PCR reaction system for random single-stranded DNA pool including Mg2＋ concentration, dNTP concentration, amount of Taq DNA polymerase, primer concentration and amount of random single-stranded DNA pool at four levels. Meanwhile, the annealing temperature and number of PCR reaction cycles were optimized to establish the optimal reaction system and PCR procedure. [Result] The optimal combination of PCR reaction system for random ssDNA pool was obtained, with a total system volume of 20 μl containing 2.0 μl of 10 × Buffer, 0.5 ng of random ssDNA pool, 2.5 mmol/L Mg2＋, 0.25 mmol/L dNTP Mixture, 0.6 μmol/L upstream and downstream primers and 1.5 U of Taq DNA polymerase; the optimal annealing temperature was 68 ℃ and the optimal number of cycles was 12. Under the above conditions, clear and stable bands with high specificity for random ssDNA pool were amplified. [Conclusion] This study laid the foundation for selection of parameters with higher specificity in SELEX technology.
基金supported by the National Key R&D Program of China (2020YFA0908104)the National Natural Science Foundation of China (91953106, 92056117, 21904087, 21705159)+1 种基金the Shanghai Municipal Science and Technology Commission (19JC1410300,19ZR1474600, 20dz1101000, 21QA1404800)the Fundamental Research Funds for the Central Universities and Shanghai Jiao Tong University。
文摘Atomically precise gold nanoclusters(Au NCs) are an emerging class of quantum-sized nanomaterials with discrete electronic energy levels, which has led to a range of attractive electronic and optical applications. Nevertheless, the lack of general methods to transfer Au NCs protected with hydrophobic ligands to an aqueous solution hampers their use in physiological settings. Here,we developed a single-stranded DNA-based approach that could transfer ~90% hydrophobic Au NCs into an aqueous solution.We experimentally and theoretically established that multivalent electrostatic and hydrophobic interactions between DNA strands and the hydrophobic ligand layer on Au NCs resulted in monodispersed DNA-coated Au NCs with high physical integrity in an aqueous solution. The fluorescence quantum yield of Au NCs was increased by ~13 fold, and surface-constrained DNA retained the specific recognition ability for biosensing. We further demonstrated the versatility of this phase-transfer approach, which thus holds great potential to advance biological and medical applications of Au NCs.
