DNA double-stranded break(DSB)is one of the most catastrophic damages of genotoxic insult.Inappropriate repair of DNA DSBs results in the loss of genetic information,mutation,and the generation of harmful genomic rear...DNA double-stranded break(DSB)is one of the most catastrophic damages of genotoxic insult.Inappropriate repair of DNA DSBs results in the loss of genetic information,mutation,and the generation of harmful genomic rearrangements,which predisposes an organism to immunodeficiency,neurological damage,and cancer.The tumor repressor p53 plays a key role in DNA damage response,and has been found to be mutated in 50%of human cancer.p53,p63,and p73 are three members of the p53 gene family.Recent discoveries have shown that human p53 gene encodes at least 12 isoforms.Different p53 members and isoforms play various roles in orchestrating DNA damage response to maintain genomic integrity.This review briefly explores the functions of p53 and its isoforms in DNA DSB repair.展开更多
In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondri...In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.展开更多
Meiotic prophase I is a long and complex phase. Homologous recombination is an important process that occurs between homologous chromosomes during meiotic prophase I. Formation of chiasmata, which hold homologous chro...Meiotic prophase I is a long and complex phase. Homologous recombination is an important process that occurs between homologous chromosomes during meiotic prophase I. Formation of chiasmata, which hold homologous chromosomes together until the metaphase I to anaphase I transition, is critical for proper chromosome segregation. Recent studies have suggested that the SPO 11 proteins have conserved functions in a number of organisms in generating sites of double-stranded DNA breaks （DSBs） that are thought to be the starting points of homologous recombination. Processing of these sites of DSBs requires the function of RecA homologs, such as RAD5 1, DMC 1, and others, as suggested by mutant studies; thus the failure to repair these meiotic DSBs results in abnormal chromosomal alternations, leading to disrupted meiosis. Recent discoveries on the functions of these RecA homologs have improved the understanding of the mechanisms underlying meiotic homologous recombination.展开更多
In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal a...In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal and electrical properties of DNA biofilm. In this paper, the elastic properties of dsDNA biofilm are studied. First, the Parsegian＇s empirical potential based on a mesoscopic liq- uid crystal theory is employed to describe the interaction energy among coarse-grained DNA cylinders. Then, con- sidering a Gaussian distribution of DNA interaxial distance, the thought experiment method is used to derive an analyti- cal expression for Young＇s modulus of DNA biofilm with a stochastic packing pattern for the first time. Results show that Young＇s modulus of DNA biofilm is on the order of 10 MPa. These findings could provide a simple and effective method to evaluate the mechanical properties of soft biofilm on snbstrate.展开更多
The adsorption dynamics of double-stranded DNA(dsDNA)molecules on a graphene oxide(GO)surface are important for applications of DNA/GO functional structures in biosensors,biomedicine and materials science.In this work...The adsorption dynamics of double-stranded DNA(dsDNA)molecules on a graphene oxide(GO)surface are important for applications of DNA/GO functional structures in biosensors,biomedicine and materials science.In this work,molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules(from 4 bp to24 bp)on the GO surface.The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface.For short dsDNA(4 bp)molecules,the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface.For long dsDNA molecules(from 8 bp to 24 bp)adsorption is stable.By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface,we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp.We attributed this behavior to the flexibility of dsDNA molecules.With increasing length,the flexibility of dsDNA molecules also increases,and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal.This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.展开更多
An effective procedure for constructing a DNA biosensor is developed based on covalent immobilization of NH2 labeled,single strand DNA（NH2-ssDNA） onto a self-assembled diazo-thiourea and gold nanoparticles modified ...An effective procedure for constructing a DNA biosensor is developed based on covalent immobilization of NH2 labeled,single strand DNA（NH2-ssDNA） onto a self-assembled diazo-thiourea and gold nanoparticles modified Au electrode（diazo-thiourea/GNM/Au）.Gold nano-particles expand the electrode surface area and increase the amount of immobilized thiourea and single stranded DNA（ssDNA） onto the electrode surface.Diazo-thiourea film provides a surface with high conductibility for electron transfer and a bed for the covalent coupling of NH2-ssDNA onto the electrode surface.The immobilization and hybridization of the probe DNA on the modified electrode is studied by differential pulse voltammetry（DPV） using methylene blue（MB） as a well-known electrochemical hybridization indicator.The linear range for the determination of complementary target ssDNA is from 9.5（±0.1） × 10^-13 mol/L to1.2（±0.2） x 10^-9 mol/L with a detection limit of 1.2（±0.1） 〉 10^-13 mol/L.展开更多
An E. coli SOS-EGFP biosensor which expresses enhanced green fluorescent protein as a reporter protein under the control of recA gene promoter in SOS response was constructed for detection of DNA damage and evaluation...An E. coli SOS-EGFP biosensor which expresses enhanced green fluorescent protein as a reporter protein under the control of recA gene promoter in SOS response was constructed for detection of DNA damage and evaluation of DNA damaging chemicals. The chemicals that may cause substantial DNA damage will trigger SOS response in the constructed bacterial biosensor, and then the reporter egfp gene under the control of recA promoter is stimulated to express as a fluorescent protein, allowing fast and sensitive fluorescence detection. Interestingly, this biosensor can be simultaneously applied for evaluation of genotoxicity and cytotoxicity. The SOS-EGFP bacterial biosensor provides a sensitive, specific and simple method for detecting known and potential DNA damaging chemicals.展开更多
A DNA biosensor with [Ru（DA-bpy）3]Cl2（DA-bpy：4,4＇-diamino-2,2＇-bipyridine） （RuL） as the electrochemical probe was prepared on pyrolytic graphite electrode （PGE） through the supramolecular interaction betwee...A DNA biosensor with [Ru（DA-bpy）3]Cl2（DA-bpy：4,4＇-diamino-2,2＇-bipyridine） （RuL） as the electrochemical probe was prepared on pyrolytic graphite electrode （PGE） through the supramolecular interaction between RuL complex and DNA template. Cyclic voltammetry of RuL-DNA film showed a pair of stable and reversible peaks corresponding to the Ru（Ⅲ）/Ru（Ⅲ） redox potential of-0.165 V versus AglAgCl in pa 7.4 0.1 mol·L^-1Tris-HCl. The electron transfer was expected across the double-strand DNA by an ＂electron tunneling＂ mechanism. When the DNA biosensor was immerged in gold （Ⅲ） buffer solution, the current peak signal （I） of the RuL-DNA supramolecular depressed and △I was linear in the concentration range of Au ion from 1×10^-7 to 2×10^-5 mol·L^-1 with a regression coefficient of 0.9879. The detection limit was 5×10^-8 mol·L^-1. The developed procedures were applied to the analysis of synthetic samples of real materials with good sensitivity and selectivity.展开更多
DNA is the hereditary material in humans and almost all other organisms. It is essential for maintaining accurate transmission of genetic information. In the life cycle, DNA replication, cell division, or genome damag...DNA is the hereditary material in humans and almost all other organisms. It is essential for maintaining accurate transmission of genetic information. In the life cycle, DNA replication, cell division, or genome damage, including that caused by endogenous and exogenous agents, may cause DNA aberrations. Of all forms of DNA damage, DNA double-strand breaks(DSBs) are the most serious. If the repair function is defective, DNA damage may cause gene mutation, genome instability, and cell chromosome loss, which in turn can even lead to tumorigenesis. DNA damage can be repaired through multiple mechanisms. Homologous recombination(HR) and non-homologous end joining(NHEJ) are the two main repair mechanisms for DNA DSBs. Increasing amounts of evidence reveal that protein modifications play an essential role in DNA damage repair.Protein deubiquitination is a vital post-translational modification which removes ubiquitin molecules or polyubiquitinated chains from substrates in order to reverse the ubiquitination reaction. This review discusses the role of deubiquitinating enzymes(DUBs) in repairing DNA DSBs. Exploring the molecular mechanisms of DUB regulation in DSB repair will provide new insights to combat human diseases and develop novel therapeutic approaches.展开更多
The core-shell structured Au@Bi2S3 nanorods have been prepared through direct in-situ growth of Bi2S3 at the surface of pre-synthesized gold nanorods.The product was characterized by X-ray diffraction,transmission ele...The core-shell structured Au@Bi2S3 nanorods have been prepared through direct in-situ growth of Bi2S3 at the surface of pre-synthesized gold nanorods.The product was characterized by X-ray diffraction,transmission electron microscopy and energy-dispersive X-ray spectroscopy.Then the obtained Au@Bi2S3 nanorods were coated onto glassy carbon electrode to act as a scaffold for fabrication of electrochemical DNA biosensor on the basis of the coordination of-NH2 modified on 5’-end of probe DNA and Au@Bi2S3.Electrochemical characterization assays demonstrate that the Au@Bi2S3 nanorods behave as an excellent electronic transport channel to promote the electron transfer kinetics and increase the effective surface area by their nanosize effect.The hybridization experiments reveal that the Au@Bi2S3 matrix-based DNA biosensor is capable of recognizing complementary DNA over a wide concentration ranging from 10 fmol/L to 1 nmol/L.The limit of detection was estimated to be 2 fmol/L(S/N=3).The biosensor also presents remarkable selectivity to distinguish fully complementa ry sequences from basemismatched and non-complementary ones,showing great promising in practical application.展开更多
In the present study, a disposable electrochemical DNA nano-biosensor is proposed for the rapid detection of genotoxic compounds and bio-analysis of water pollution. The DNA nano-biosensor is prepared by immobilizing ...In the present study, a disposable electrochemical DNA nano-biosensor is proposed for the rapid detection of genotoxic compounds and bio-analysis of water pollution. The DNA nano-biosensor is prepared by immobilizing DNA on Au nanoparticles and a self-assembled monolayer of cysteamine modified Au electrode. The assembly processes of cysteamine, Au nanoparticles and DNA were characterized by cyclic voltammetry （CV）. The Au nanoparticles enhanced DNA immobilization resulting in an increased guanine signal. The interaction of the analyte with the immobilized DNA was measured through the variation of the electrochemical signal of guanine by square wave voltammetry （SWV）. The biosensor was able to detect the known genotoxic compounds： 2-anthramine, acridine orange and 2- naphthylamine with detection limits of 2, 3 and 50 nmol/L, respectively. The biosensor was also used to test actual water samples to evaluate the contamination level. Additionally, the comparison of results from the classical genotoxiciw bioassay has confirmed the applicability of the method for real samoles.展开更多
Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently occurring cancers.Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the he...Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently occurring cancers.Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the hepatocarcinogenesis.More and more researches were designed to find the relationship of the two.In this study,we investigated whether HBV DNA integration occurred at sites of DNA double-strand breaks(DSBs),one of the most detrimental DNA damage.An 18-bp I-SceI homing endonuclease recognition site was introduced into the DNA of HepG2 cell line by stable DNA transfection,then cells were incubated in patients’ serum with high HBV DNA copies and at the same time,DSBs were induced by transient expression of I-SceI after transfection of an I-SceI expression vector.By using nest PCR,the viral DNA was detected at the sites of the break.It appeared that integra-tion occurred between part of HBV x gene and the I-SceI induced breaks.The results suggested that DSBs,as the DNA damages,may serve as potential targets for hepadnaviral DNA insertion and the integrants would lead to widespread host genome changes necessarily.It provided a new site to investi-gate the integration.展开更多
DNA damage in oocytes can cause infertility and birth defects. DNA double-strand breaks （DSBs） are highly deleterious and can substantially impair genome integrity. Homologous recombination （HR）-mediated DNA DSB r...DNA damage in oocytes can cause infertility and birth defects. DNA double-strand breaks （DSBs） are highly deleterious and can substantially impair genome integrity. Homologous recombination （HR）-mediated DNA DSB repair plays dominant roles in safeguarding oocyte quantity and quality. However, little is known regarding the key players of the HR repair pathway in oocytes. Here, we identified oocyte-specific gene Ooep as a novel key component of the HR repair pathway in mouse oocytes. OOEP was required for efficient ataxia telangiectasia mutated （ATM） kinase activation and Rad51 recombinase （RAD51） focal accumulation at DNA DSBs. Ooep null oocytes were defective in DNA DSB repair and prone to apoptosis upon exogenous DNA damage insults. Moreover, Ooep null oocytes exhibited delayed meiotic maturation. Therefore, OOEP played roles in preserving oocyte quantity and quality by maintaining genome stability. Ooep expression decreased with the advance of maternal age, suggesting its involvement in maternal aging.展开更多
Nowadays,due to excellent biological and polymeric characteristics,DNA has been widely noted as an emerging building block to construct diverse materials for biosensing,in vivo imaging,drug delivery,and disease therap...Nowadays,due to excellent biological and polymeric characteristics,DNA has been widely noted as an emerging building block to construct diverse materials for biosensing,in vivo imaging,drug delivery,and disease therapy.Particularly,relying on programmability,predictability,and stability of DNA,DNA walkers have opened new and exciting opportunities in modern life sciences for target detection and biological analysis,which are constructed by self-assembly of DNA or combining DNA with other nanomaterials(e.g.,quantum dots,gold nanoparticles,magnetic nanoparticles,polymers).Compared with conventional nanomaterials(lanthanide-doped upconversion nanoparticles,magnetic nanomaterials,carbon dots,silicon dots,and so on),DNA walkers showed convenient modification,lower biotoxicity,excellent biocompatibility and high biostability,improving the biological application.Meanwhile,with high-speed operating efficiency and sustainable operation,DNA walkers powered by strand displacement reaction or protein enzyme/DNAzyme reaction,have highly sensitive detection and signal amplification abilities,which are applied in biosensing,material assembly and synthesis,and early cancer diagnosis.Worthily,DNA walkers could be regarded as signal amplifiers,which enhanced the signal transduction and amplified biosensor sensing signals.Herein,we systematically and comprehensively summarized the operating principles of various DNA walkers,categorized rational design of the DNA walker,and outlined the application of DNA walker in biosensors.Furthermore,the challenges and future trends of DNA walkers were discussed.展开更多
Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break(DSB)signaling.P53-binding protein 1(53BP1)plays a critical role in coordinating the DSB repair pathway c...Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break(DSB)signaling.P53-binding protein 1(53BP1)plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining(NHEJ)-mediated DSB repair pathway that rejoins DSB ends.New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination(HR)signaling.This review focuses on the up-and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair,which in turn promotes the sensitivity of poly(ADP-ribose)polymerase inhibitor(PARPi)in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.展开更多
Titanium dioxide (TiO2) thin film was deposited on the surface of the light addressable potentiometric sensor (LAPS) to modify the sensor surface for the non-labeled detection of DNA molecules. To evaluate the effect ...Titanium dioxide (TiO2) thin film was deposited on the surface of the light addressable potentiometric sensor (LAPS) to modify the sensor surface for the non-labeled detection of DNA molecules. To evaluate the effect of ultraviolet (UV) treatment on the silanization level of TiO2 thin film by 3-aminopropyltriethoxysilane (APTS),fluorescein isothiocyanate (FITC) was used to label the amine group on the end of APTS immobilized onto the TiO2 thin film. We found that,with UV irradiation,the silanization level of the irradiated area of the TiO2 film was improved compared with the non-irradiated area under well-controlled conditions. This result indicates that TiO2 can act as a coating material on the biosensor surface to improve the effect and efficiency of the covalent immobilization of biomolecules on the sensor surface. The artificially synthesized probe DNA molecules were covalently linked onto the surface of TiO2 film. The hybridization of probe DNA and target DNA was monitored by the recording of I-V curves that shift along the voltage axis during the process of reaction. A significant LAPS signal can be detected at 10 μmol/L of target DNA sample.展开更多
Herein we report an electrochemical DNA biosensor for the rapid detection of sequence (5’ AAT GGA TTT ATC TGC TCT TCG 3’) specific for the breast cancer 1 (BRCA1) gene. The proposed electrochemical genosensor is bas...Herein we report an electrochemical DNA biosensor for the rapid detection of sequence (5’ AAT GGA TTT ATC TGC TCT TCG 3’) specific for the breast cancer 1 (BRCA1) gene. The proposed electrochemical genosensor is based on short oligonucleotide DNA probe immobilized onto zinc oxide nanowires (ZnONWs) chemically synthesized onto gold electrode via hydrothermal technique. The morphology studies of the ZnONWs, performed by field emission scanning electron microscopy (FESEM), showed that the ZnO nanowires are uniform, highly dense and oriented perpendicularly to the substrate. Recognition event between the DNA probe and the target was investigated by differential pulse voltammetry (DPV) in 0.1 M acetate buffer solution (ABS), pH 7.00;as a result of the hybridization, an oxidation signal was observed at +0.8 V. The influences of pH, target concentration, and non-complimentary DNA on biosensor performance were examined. The proposed DNA biosensor has the ability to detect the target sequence in the range of concentration between 10.0 and 100.0 μM with a detection limit of 3.32 μM. The experimental results demonstrated that the prepared ZnONWs/Au electrodes are suitable platform for the immobilization of DNA.展开更多
DNA methylation plays a significant role in various biological events, and its precise determination is vital for the prognosis and treatment of cancer. Here, we proposed an ultrasensitive electrochemical biosensor fo...DNA methylation plays a significant role in various biological events, and its precise determination is vital for the prognosis and treatment of cancer. Here, we proposed an ultrasensitive electrochemical biosensor for the quantitative analysis of multiple methylation-locus in DNA sequence via DNA anchoring the gold nanoparticles (DNA-AuNPs) and bienzyme dual signal amplifications. After the target DNA captured by the DNA-AuNPs of the biosensor, the methyl-CpG binding protein MeCP2 could specifically conjugate to the methylation-loci in the double-stranded DNA. Successively, the glucose oxidase (GOD) and horseradish (HRP) co-labeled antibody captured the His tagged MeCP2, which leads to a cascade enzymatic catalysis of the substrates to yield a detectable electrochemical signal. Both the two strategies, including the high content of DNA-AuNPs and the associated catalysis of bienzyme, dramatically enhanced the sensitivity of the biosensor. The response current elevated with the increasing numbers of methylation-locus, thus the multiple methylated DNA was identified by detecting the corresponding current signals. This method could detect the methylated target as low as 0.1 fM, and showed a wide linear range from 10 - 15 M to 10 - 7 M. Besides, the long-term stability and repeatability of the biosensor were also validated. The prepared electrochemical immunosensor exhibits ultrasensitivity through the bienzyme labeling process, which can be applied for the detection of DNA methylation with low concentration.展开更多
Fiber-optic DNA biosensors are a kind of ana-lytic setups, which convert the Waston-Crick base pairs matching duplex or Hoogsteen’s tri-plex (T/A-T, C/G-C) formation into a readable analytical signals when functional...Fiber-optic DNA biosensors are a kind of ana-lytic setups, which convert the Waston-Crick base pairs matching duplex or Hoogsteen’s tri-plex (T/A-T, C/G-C) formation into a readable analytical signals when functionalized single- strands DNA (ssDNA) or double-strands DNA (dsDNA) of interest are immobilized on the sur-face of fiber-optic hybrids with target DNA or interacts with ligands. This review will provide the information about the fiber-optic DNA bio-sensors classified into two categories depend-ing on the end fiber and side fiber with or with-out the labels—label-free fiber-optic DNA bio-sensors and labeled fiber-optic DNA biosensor in recent years. Both are dissertated, and em-phasis is on the label-free fiber-optic DNA bio-sensors. Fiber-optic DNA biosensors had got great progresses because fiber-optic has more advantages over the other transducers and are easily processed by nanotechnology. So fiber- optic DNA biosensors have increasingly at-tracted more attention to research and develop the new fiber-optic DNA biosensors that inte-grated with the “nano-bio-info” technology for in vivo test, single molecular detection and on-line medical diagnosis. Finally, future pros-pects to the fiber-optic DNA biosensors are predicted.展开更多
Objective: To establish a DNA detection platform based on a tapered optical fiber to detect Leptospira DNA by targeting the leptospiral secY gene.Methods: The biosensor works on the principle of light propagating in t...Objective: To establish a DNA detection platform based on a tapered optical fiber to detect Leptospira DNA by targeting the leptospiral secY gene.Methods: The biosensor works on the principle of light propagating in the special geometry of the optical fiber tapered from a waist diameter of 125 to 12 μm. The fiber surface was functionalized through a cascade of chemical treatments and the immobilization of a DNA capture probe targeting the secY gene. The presence of the target DNA was determined from the wavelength shift in the optical transmission spectrum.Results: The biosensor demonstrated good sensitivity, detecting Leptospira DNA at 0.001 ng/μL, and was selective for Leptospira DNA without cross-reactivity with non-leptospiral microorganisms. The biosensor specifically detected DNA that was specifically amplified through the loop-mediated isothermal amplification approach.Conclusions: These findings warrant the potential of this platform to be developed as a novel alternative approach to diagnose leptospirosis.展开更多
基金supported by the National Natural Science Foundation of China(Nos.31571511 and 31871500)
文摘DNA double-stranded break(DSB)is one of the most catastrophic damages of genotoxic insult.Inappropriate repair of DNA DSBs results in the loss of genetic information,mutation,and the generation of harmful genomic rearrangements,which predisposes an organism to immunodeficiency,neurological damage,and cancer.The tumor repressor p53 plays a key role in DNA damage response,and has been found to be mutated in 50%of human cancer.p53,p63,and p73 are three members of the p53 gene family.Recent discoveries have shown that human p53 gene encodes at least 12 isoforms.Different p53 members and isoforms play various roles in orchestrating DNA damage response to maintain genomic integrity.This review briefly explores the functions of p53 and its isoforms in DNA DSB repair.
文摘In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.
基金The authors thank Alexandra Surcel and Carey L Hendrix Lord for helpful comments on this manuscript.The work in our laboratory is supported by grants from the National Science Foundation(IBN-0077832,MCB-9896340,MCB-0092075)the National Institutes of Health(R0 1 GM63871)+3 种基金the US Department of Agriculture(2001-35301-10570 and 2003-35301-13313)Wuxing L was partially supported by the Intercollege Graduate Degree Program in Plant PhysiologyHong M gratefully acknowledges the support of the John Simon Guggenheim Foundationthe National Institutes of Health(F33 GM72245-1).
文摘Meiotic prophase I is a long and complex phase. Homologous recombination is an important process that occurs between homologous chromosomes during meiotic prophase I. Formation of chiasmata, which hold homologous chromosomes together until the metaphase I to anaphase I transition, is critical for proper chromosome segregation. Recent studies have suggested that the SPO 11 proteins have conserved functions in a number of organisms in generating sites of double-stranded DNA breaks （DSBs） that are thought to be the starting points of homologous recombination. Processing of these sites of DSBs requires the function of RecA homologs, such as RAD5 1, DMC 1, and others, as suggested by mutant studies; thus the failure to repair these meiotic DSBs results in abnormal chromosomal alternations, leading to disrupted meiosis. Recent discoveries on the functions of these RecA homologs have improved the understanding of the mechanisms underlying meiotic homologous recombination.
基金supported by the National Natural Science Foundation of China(11272193 and 10872121)the Shanghai Leading Academic Discipline Project(S30106)
文摘In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal and electrical properties of DNA biofilm. In this paper, the elastic properties of dsDNA biofilm are studied. First, the Parsegian＇s empirical potential based on a mesoscopic liq- uid crystal theory is employed to describe the interaction energy among coarse-grained DNA cylinders. Then, con- sidering a Gaussian distribution of DNA interaxial distance, the thought experiment method is used to derive an analyti- cal expression for Young＇s modulus of DNA biofilm with a stochastic packing pattern for the first time. Results show that Young＇s modulus of DNA biofilm is on the order of 10 MPa. These findings could provide a simple and effective method to evaluate the mechanical properties of soft biofilm on snbstrate.
基金Project supported by the National Natural Science Foundation of China (Grant No.11974366)the Fundamental Research Funds for the Central Universities+2 种基金Chinathe Supercomputer Center of the Chinese Academy of Sciencesthe Shanghai Supercomputer Center of China。
文摘The adsorption dynamics of double-stranded DNA(dsDNA)molecules on a graphene oxide(GO)surface are important for applications of DNA/GO functional structures in biosensors,biomedicine and materials science.In this work,molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules(from 4 bp to24 bp)on the GO surface.The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface.For short dsDNA(4 bp)molecules,the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface.For long dsDNA molecules(from 8 bp to 24 bp)adsorption is stable.By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface,we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp.We attributed this behavior to the flexibility of dsDNA molecules.With increasing length,the flexibility of dsDNA molecules also increases,and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal.This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.
文摘An effective procedure for constructing a DNA biosensor is developed based on covalent immobilization of NH2 labeled,single strand DNA（NH2-ssDNA） onto a self-assembled diazo-thiourea and gold nanoparticles modified Au electrode（diazo-thiourea/GNM/Au）.Gold nano-particles expand the electrode surface area and increase the amount of immobilized thiourea and single stranded DNA（ssDNA） onto the electrode surface.Diazo-thiourea film provides a surface with high conductibility for electron transfer and a bed for the covalent coupling of NH2-ssDNA onto the electrode surface.The immobilization and hybridization of the probe DNA on the modified electrode is studied by differential pulse voltammetry（DPV） using methylene blue（MB） as a well-known electrochemical hybridization indicator.The linear range for the determination of complementary target ssDNA is from 9.5（±0.1） × 10^-13 mol/L to1.2（±0.2） x 10^-9 mol/L with a detection limit of 1.2（±0.1） 〉 10^-13 mol/L.
基金supported by the National Natural Science Foundation of China (No. 20707034, 20877091,20890112, 20921063)the National Basic Research Program (973) of China (No. 09CB421605,2010CB933500, 2011CB936001)
文摘An E. coli SOS-EGFP biosensor which expresses enhanced green fluorescent protein as a reporter protein under the control of recA gene promoter in SOS response was constructed for detection of DNA damage and evaluation of DNA damaging chemicals. The chemicals that may cause substantial DNA damage will trigger SOS response in the constructed bacterial biosensor, and then the reporter egfp gene under the control of recA promoter is stimulated to express as a fluorescent protein, allowing fast and sensitive fluorescence detection. Interestingly, this biosensor can be simultaneously applied for evaluation of genotoxicity and cytotoxicity. The SOS-EGFP bacterial biosensor provides a sensitive, specific and simple method for detecting known and potential DNA damaging chemicals.
基金This study is financially supported by the National Natural Science Foundation of China (No. 60508012)the Natural Sci-ence Foundation of Zhejiang Province (No. Y106725)+1 种基金the Natural Science Foundation of Ningbo (No. 2006A610048)the Scientific and Technological Project Funding of Zhejiang Province (No. 2006C31040).
文摘A DNA biosensor with [Ru（DA-bpy）3]Cl2（DA-bpy：4,4＇-diamino-2,2＇-bipyridine） （RuL） as the electrochemical probe was prepared on pyrolytic graphite electrode （PGE） through the supramolecular interaction between RuL complex and DNA template. Cyclic voltammetry of RuL-DNA film showed a pair of stable and reversible peaks corresponding to the Ru（Ⅲ）/Ru（Ⅲ） redox potential of-0.165 V versus AglAgCl in pa 7.4 0.1 mol·L^-1Tris-HCl. The electron transfer was expected across the double-strand DNA by an ＂electron tunneling＂ mechanism. When the DNA biosensor was immerged in gold （Ⅲ） buffer solution, the current peak signal （I） of the RuL-DNA supramolecular depressed and △I was linear in the concentration range of Au ion from 1×10^-7 to 2×10^-5 mol·L^-1 with a regression coefficient of 0.9879. The detection limit was 5×10^-8 mol·L^-1. The developed procedures were applied to the analysis of synthetic samples of real materials with good sensitivity and selectivity.
基金supported by the National Natural Science Foundation of China (Nos. 91749115 and 81872298)the Natural Science Foundation of Jiangxi Province (No. 20181BAB205044), China。
文摘DNA is the hereditary material in humans and almost all other organisms. It is essential for maintaining accurate transmission of genetic information. In the life cycle, DNA replication, cell division, or genome damage, including that caused by endogenous and exogenous agents, may cause DNA aberrations. Of all forms of DNA damage, DNA double-strand breaks(DSBs) are the most serious. If the repair function is defective, DNA damage may cause gene mutation, genome instability, and cell chromosome loss, which in turn can even lead to tumorigenesis. DNA damage can be repaired through multiple mechanisms. Homologous recombination(HR) and non-homologous end joining(NHEJ) are the two main repair mechanisms for DNA DSBs. Increasing amounts of evidence reveal that protein modifications play an essential role in DNA damage repair.Protein deubiquitination is a vital post-translational modification which removes ubiquitin molecules or polyubiquitinated chains from substrates in order to reverse the ubiquitination reaction. This review discusses the role of deubiquitinating enzymes(DUBs) in repairing DNA DSBs. Exploring the molecular mechanisms of DUB regulation in DSB repair will provide new insights to combat human diseases and develop novel therapeutic approaches.
基金supported by the National Natural Science Foundation of China (Nos.21802064,21275127)Natural Science Foundation of Fujian Province,China (Nos.2018J01435,2017J01419)Foundation of Key Laboratory of Sensor Analysis of Tumor Marker,Ministry of Education,Qingdao University of Science and Technology
文摘The core-shell structured Au@Bi2S3 nanorods have been prepared through direct in-situ growth of Bi2S3 at the surface of pre-synthesized gold nanorods.The product was characterized by X-ray diffraction,transmission electron microscopy and energy-dispersive X-ray spectroscopy.Then the obtained Au@Bi2S3 nanorods were coated onto glassy carbon electrode to act as a scaffold for fabrication of electrochemical DNA biosensor on the basis of the coordination of-NH2 modified on 5’-end of probe DNA and Au@Bi2S3.Electrochemical characterization assays demonstrate that the Au@Bi2S3 nanorods behave as an excellent electronic transport channel to promote the electron transfer kinetics and increase the effective surface area by their nanosize effect.The hybridization experiments reveal that the Au@Bi2S3 matrix-based DNA biosensor is capable of recognizing complementary DNA over a wide concentration ranging from 10 fmol/L to 1 nmol/L.The limit of detection was estimated to be 2 fmol/L(S/N=3).The biosensor also presents remarkable selectivity to distinguish fully complementa ry sequences from basemismatched and non-complementary ones,showing great promising in practical application.
基金funded by the National Natural Science Foundation of China(Nos.21103059,51136002 and 51076079)the China Key Technologies R&D Program(No.2012BAJ02B03)
文摘In the present study, a disposable electrochemical DNA nano-biosensor is proposed for the rapid detection of genotoxic compounds and bio-analysis of water pollution. The DNA nano-biosensor is prepared by immobilizing DNA on Au nanoparticles and a self-assembled monolayer of cysteamine modified Au electrode. The assembly processes of cysteamine, Au nanoparticles and DNA were characterized by cyclic voltammetry （CV）. The Au nanoparticles enhanced DNA immobilization resulting in an increased guanine signal. The interaction of the analyte with the immobilized DNA was measured through the variation of the electrochemical signal of guanine by square wave voltammetry （SWV）. The biosensor was able to detect the known genotoxic compounds： 2-anthramine, acridine orange and 2- naphthylamine with detection limits of 2, 3 and 50 nmol/L, respectively. The biosensor was also used to test actual water samples to evaluate the contamination level. Additionally, the comparison of results from the classical genotoxiciw bioassay has confirmed the applicability of the method for real samoles.
基金supported by grants from National Natural Sciences Foundation of China (No.30872237)the National Basic Research Program of China(No.2007CB512900)
文摘Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently occurring cancers.Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the hepatocarcinogenesis.More and more researches were designed to find the relationship of the two.In this study,we investigated whether HBV DNA integration occurred at sites of DNA double-strand breaks(DSBs),one of the most detrimental DNA damage.An 18-bp I-SceI homing endonuclease recognition site was introduced into the DNA of HepG2 cell line by stable DNA transfection,then cells were incubated in patients’ serum with high HBV DNA copies and at the same time,DSBs were induced by transient expression of I-SceI after transfection of an I-SceI expression vector.By using nest PCR,the viral DNA was detected at the sites of the break.It appeared that integra-tion occurred between part of HBV x gene and the I-SceI induced breaks.The results suggested that DSBs,as the DNA damages,may serve as potential targets for hepadnaviral DNA insertion and the integrants would lead to widespread host genome changes necessarily.It provided a new site to investi-gate the integration.
基金supported by the National Key Research and Development Program of China(2017YFC1001102)National Natural Science Foundation of China(81760507)
文摘DNA damage in oocytes can cause infertility and birth defects. DNA double-strand breaks （DSBs） are highly deleterious and can substantially impair genome integrity. Homologous recombination （HR）-mediated DNA DSB repair plays dominant roles in safeguarding oocyte quantity and quality. However, little is known regarding the key players of the HR repair pathway in oocytes. Here, we identified oocyte-specific gene Ooep as a novel key component of the HR repair pathway in mouse oocytes. OOEP was required for efficient ataxia telangiectasia mutated （ATM） kinase activation and Rad51 recombinase （RAD51） focal accumulation at DNA DSBs. Ooep null oocytes were defective in DNA DSB repair and prone to apoptosis upon exogenous DNA damage insults. Moreover, Ooep null oocytes exhibited delayed meiotic maturation. Therefore, OOEP played roles in preserving oocyte quantity and quality by maintaining genome stability. Ooep expression decreased with the advance of maternal age, suggesting its involvement in maternal aging.
基金Financial support was from Hunan Provincial Natural Science Foundation(Nos.2023JJ40210,2023JJ40211)Hunan Provincial Innovation Training Program for College Students(No.202211342042)+2 种基金Hunan Provincial Natural Science Foundation(No.2021JJ10001)Key Areas Research and Development Plan of Hunan Province(No.2021SK2038)Huxiang High Level Talent Gathering Project(No.2021RC5011)。
文摘Nowadays,due to excellent biological and polymeric characteristics,DNA has been widely noted as an emerging building block to construct diverse materials for biosensing,in vivo imaging,drug delivery,and disease therapy.Particularly,relying on programmability,predictability,and stability of DNA,DNA walkers have opened new and exciting opportunities in modern life sciences for target detection and biological analysis,which are constructed by self-assembly of DNA or combining DNA with other nanomaterials(e.g.,quantum dots,gold nanoparticles,magnetic nanoparticles,polymers).Compared with conventional nanomaterials(lanthanide-doped upconversion nanoparticles,magnetic nanomaterials,carbon dots,silicon dots,and so on),DNA walkers showed convenient modification,lower biotoxicity,excellent biocompatibility and high biostability,improving the biological application.Meanwhile,with high-speed operating efficiency and sustainable operation,DNA walkers powered by strand displacement reaction or protein enzyme/DNAzyme reaction,have highly sensitive detection and signal amplification abilities,which are applied in biosensing,material assembly and synthesis,and early cancer diagnosis.Worthily,DNA walkers could be regarded as signal amplifiers,which enhanced the signal transduction and amplified biosensor sensing signals.Herein,we systematically and comprehensively summarized the operating principles of various DNA walkers,categorized rational design of the DNA walker,and outlined the application of DNA walker in biosensors.Furthermore,the challenges and future trends of DNA walkers were discussed.
文摘Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break(DSB)signaling.P53-binding protein 1(53BP1)plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining(NHEJ)-mediated DSB repair pathway that rejoins DSB ends.New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination(HR)signaling.This review focuses on the up-and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair,which in turn promotes the sensitivity of poly(ADP-ribose)polymerase inhibitor(PARPi)in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.
基金Project supported by the National Natural Science Foundation of China (Nos. 30627002 and 60725102)the Interdisciplinary Research Foundation of Zhejiang University (No. 2009-15), China
文摘Titanium dioxide (TiO2) thin film was deposited on the surface of the light addressable potentiometric sensor (LAPS) to modify the sensor surface for the non-labeled detection of DNA molecules. To evaluate the effect of ultraviolet (UV) treatment on the silanization level of TiO2 thin film by 3-aminopropyltriethoxysilane (APTS),fluorescein isothiocyanate (FITC) was used to label the amine group on the end of APTS immobilized onto the TiO2 thin film. We found that,with UV irradiation,the silanization level of the irradiated area of the TiO2 film was improved compared with the non-irradiated area under well-controlled conditions. This result indicates that TiO2 can act as a coating material on the biosensor surface to improve the effect and efficiency of the covalent immobilization of biomolecules on the sensor surface. The artificially synthesized probe DNA molecules were covalently linked onto the surface of TiO2 film. The hybridization of probe DNA and target DNA was monitored by the recording of I-V curves that shift along the voltage axis during the process of reaction. A significant LAPS signal can be detected at 10 μmol/L of target DNA sample.
基金the Ministry of Higher Education Malaysia for the ERGS grant(600/RMI/st/ERGS/5/3/fst12/2011)Universiti Teknologi MARA for financial support via postgraduate teaching assistant scheme(UPTA)to Nur Azimah Mansor for conducting this research.
文摘Herein we report an electrochemical DNA biosensor for the rapid detection of sequence (5’ AAT GGA TTT ATC TGC TCT TCG 3’) specific for the breast cancer 1 (BRCA1) gene. The proposed electrochemical genosensor is based on short oligonucleotide DNA probe immobilized onto zinc oxide nanowires (ZnONWs) chemically synthesized onto gold electrode via hydrothermal technique. The morphology studies of the ZnONWs, performed by field emission scanning electron microscopy (FESEM), showed that the ZnO nanowires are uniform, highly dense and oriented perpendicularly to the substrate. Recognition event between the DNA probe and the target was investigated by differential pulse voltammetry (DPV) in 0.1 M acetate buffer solution (ABS), pH 7.00;as a result of the hybridization, an oxidation signal was observed at +0.8 V. The influences of pH, target concentration, and non-complimentary DNA on biosensor performance were examined. The proposed DNA biosensor has the ability to detect the target sequence in the range of concentration between 10.0 and 100.0 μM with a detection limit of 3.32 μM. The experimental results demonstrated that the prepared ZnONWs/Au electrodes are suitable platform for the immobilization of DNA.
文摘DNA methylation plays a significant role in various biological events, and its precise determination is vital for the prognosis and treatment of cancer. Here, we proposed an ultrasensitive electrochemical biosensor for the quantitative analysis of multiple methylation-locus in DNA sequence via DNA anchoring the gold nanoparticles (DNA-AuNPs) and bienzyme dual signal amplifications. After the target DNA captured by the DNA-AuNPs of the biosensor, the methyl-CpG binding protein MeCP2 could specifically conjugate to the methylation-loci in the double-stranded DNA. Successively, the glucose oxidase (GOD) and horseradish (HRP) co-labeled antibody captured the His tagged MeCP2, which leads to a cascade enzymatic catalysis of the substrates to yield a detectable electrochemical signal. Both the two strategies, including the high content of DNA-AuNPs and the associated catalysis of bienzyme, dramatically enhanced the sensitivity of the biosensor. The response current elevated with the increasing numbers of methylation-locus, thus the multiple methylated DNA was identified by detecting the corresponding current signals. This method could detect the methylated target as low as 0.1 fM, and showed a wide linear range from 10 - 15 M to 10 - 7 M. Besides, the long-term stability and repeatability of the biosensor were also validated. The prepared electrochemical immunosensor exhibits ultrasensitivity through the bienzyme labeling process, which can be applied for the detection of DNA methylation with low concentration.
文摘Fiber-optic DNA biosensors are a kind of ana-lytic setups, which convert the Waston-Crick base pairs matching duplex or Hoogsteen’s tri-plex (T/A-T, C/G-C) formation into a readable analytical signals when functionalized single- strands DNA (ssDNA) or double-strands DNA (dsDNA) of interest are immobilized on the sur-face of fiber-optic hybrids with target DNA or interacts with ligands. This review will provide the information about the fiber-optic DNA bio-sensors classified into two categories depend-ing on the end fiber and side fiber with or with-out the labels—label-free fiber-optic DNA bio-sensors and labeled fiber-optic DNA biosensor in recent years. Both are dissertated, and em-phasis is on the label-free fiber-optic DNA bio-sensors. Fiber-optic DNA biosensors had got great progresses because fiber-optic has more advantages over the other transducers and are easily processed by nanotechnology. So fiber- optic DNA biosensors have increasingly at-tracted more attention to research and develop the new fiber-optic DNA biosensors that inte-grated with the “nano-bio-info” technology for in vivo test, single molecular detection and on-line medical diagnosis. Finally, future pros-pects to the fiber-optic DNA biosensors are predicted.
基金funded by Universiti Putra Malaysia through the Geran Inisiatif Putra Siswazah (GP-IPS/2019/9678200)。
文摘Objective: To establish a DNA detection platform based on a tapered optical fiber to detect Leptospira DNA by targeting the leptospiral secY gene.Methods: The biosensor works on the principle of light propagating in the special geometry of the optical fiber tapered from a waist diameter of 125 to 12 μm. The fiber surface was functionalized through a cascade of chemical treatments and the immobilization of a DNA capture probe targeting the secY gene. The presence of the target DNA was determined from the wavelength shift in the optical transmission spectrum.Results: The biosensor demonstrated good sensitivity, detecting Leptospira DNA at 0.001 ng/μL, and was selective for Leptospira DNA without cross-reactivity with non-leptospiral microorganisms. The biosensor specifically detected DNA that was specifically amplified through the loop-mediated isothermal amplification approach.Conclusions: These findings warrant the potential of this platform to be developed as a novel alternative approach to diagnose leptospirosis.
