The influence of the G‐quartet structural integrity on the catalytic activity of the G‐quadruplex(G4)was investigated by comparing the G4‐DNAzyme performances of a series of G4s with a G‐vacancy site and a G‐trip...The influence of the G‐quartet structural integrity on the catalytic activity of the G‐quadruplex(G4)was investigated by comparing the G4‐DNAzyme performances of a series of G4s with a G‐vacancy site and a G‐triplex(G‐tri).The results presented herein not only confirm that the structural integrity of the 3'‐end G‐quartet is necessary for G4s to be catalytically competent but also show how to remediate G‐vacancy‐mediated catalytic activity losses via the addition of guanine surrogates in an approach referred to as G‐vacancy complementation strategy that is applicable to parallel G4s only.Furthermore,this study demonstrates that the terminal G‐quartet could act as a proximal coordinating group and cooperate with the flanking nucleotide to activate the hemin cofactor.展开更多
The active ingredients of ginger(Zingiber officinale)are 6-gingerol,8-gingerol,and 10-gingerol.Ginger is reported to be an antioxidant,anticancer,and anti-inflammatory agent because of its bioactive metabolites.The 3 ...The active ingredients of ginger(Zingiber officinale)are 6-gingerol,8-gingerol,and 10-gingerol.Ginger is reported to be an antioxidant,anticancer,and anti-inflammatory agent because of its bioactive metabolites.The 3 gingerols share a standard ring structure with different side chains.The maintenance of telomeric length by telomerase is a major issue in almost all cancers.Targeting TERRA G4 could provide a method to inhibit telomerase activity.Molecular docking,molecular dynamics simulations,molecular mechanics Poisson-Boltzmann surface area,principal component analysis,and free energy landscape analysis were performed to evaluate gingerol-TERRA G4 interactions,the extent and stability of these interactions,and the binding free energy and stability of the complexes of the 3 gingerols with TERRA G4.The results revealed that 10-gingerol has superior binding and stabilizing potential for TERRA G4 structures.These findings suggest that TERRA G4 could be a promising therapeutic target for cancer and that 10-gingerol may serve as a potential anticancer lead compound.Further in vitro and in vivo studies to determine the effective dose and toxicity are necessary to evaluate its safety and efficacy.展开更多
The human telomere sequence (TTAGGG)4 folds into an unusual conformation possessing three G-tetrads linked by TTA loops. The first loop is a propeller loop while the second and third loops are transverse loops. Using ...The human telomere sequence (TTAGGG)4 folds into an unusual conformation possessing three G-tetrads linked by TTA loops. The first loop is a propeller loop while the second and third loops are transverse loops. Using Circular Dichroism (CD) spectroscopy, we have investigated the effect of sequence context on the structures and stabilities of intramolecular G-quadruplexes related to the human telomere sequence by considering all permutations of T and A within the loops. The results indicate that changing only one base in any one loop can have a dramatic effect on the conformation of the quadruplex as well as its melting temperature, Tm. Thus, each sequence studied has a unique CD spectrum and Tm. In general, variants with a modified second loop are the most stable while the wild type sequence is the least stable. The observed difference in CD spectra and melting temperature are discussed in terms of base stacking within the loop and stacking of the loop bases with adjacent G-tetrads.展开更多
Tomato brown rugose fruit virus(ToBRFV) is a novel tobamovirus firstly reported in 2015 and poses a severe threat to the tomato industry. So far, it has spread to 10 countries in America, Asia, and Europe. In 2019, To...Tomato brown rugose fruit virus(ToBRFV) is a novel tobamovirus firstly reported in 2015 and poses a severe threat to the tomato industry. So far, it has spread to 10 countries in America, Asia, and Europe. In 2019, ToBRFV was identified in Shandong Province(ToBRFV-SD), China. In this study, it was shown that ToBRFV-SD induced mild to severe mosaic and blistering on leaves, necrosis on sepals and pedicles, and deformation, yellow spots, and brown rugose necrotic lesions on fruits. ToBRFV-SD induced distinct symptoms on plants of tomato, Capsicum annumm, and Nicotiana benthamiana, and caused latent infection on plants of Solanum tuberosum, Solanum melongena, and N. tabacum cv. Zhongyan 102. All the 50 tomato cultivars tested were highly sensitive to ToBRFV-SD. The complete genomic sequence of ToBRFV-SD shared the highest nucleotide and amino acid identities with isolate IL from Israel. In the phylogenetic tree constructed with the complete genomic sequence, all the ToBRFV isolates were clustered together and formed a sister branch with tobacco mosaic virus(TMV). Furthermore, a quadruplex RT-PCR system was developed that could differentiate ToBRFV from other economically important viruses affecting tomatoes, such as TMV, tomato mosaic virus, and tomato spotted wilt virus. The findings of this study enhance our understanding of the biological and molecular characteristics of ToBRFV and provide an efficient and effective detection method for multiple infections, which is helpful in the management of ToBRFV.展开更多
The DNA G quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G quadruplex using single molecule fluorescence resonance energy...The DNA G quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G quadruplex using single molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single molecule level was consistent with ensemble measurement展开更多
Mercury(Hg^(2+))has been recognized as a global pollutant with a toxic,mobile,and persistent nature.It adversely affects the ecosystem and human health.Already developed biosensors for Hg^(2+)detection majorly suffer ...Mercury(Hg^(2+))has been recognized as a global pollutant with a toxic,mobile,and persistent nature.It adversely affects the ecosystem and human health.Already developed biosensors for Hg^(2+)detection majorly suffer from poor sensitivity and specificity.Herein,a colorimetric/fluorimetric dual-mode sensing approach is designed for the quantitative detection of Hg^(2+).This novel sensing approach utilizes nanofluorophores,i.e.,fluorescent copper nanoclusters-doped zirconia metal-organic framework(CuNCs@Zr-MOF)nanoconjugate(blue color)and N-methyl mesoporphyrin IX(NMM)(red color)in combination with peroxidase-mimicking G-quadruplex DNAzyme(PMDNAzyme).In the presence of Hg^(2+),dabcyl conjugated complementary DNA with T-T mismatches form the stable duplex with the CuNCs@Zr-MOF@G-quadruplex structure through T-Hg^(2+)-T base pairing.It causes the quenching of fluorescence of CuNCs@Zr-MOF(463 nm)due to the Förster resonance energy transfer(FRET)system.Moreover,the G-quadruplex(G4)structure of the aptamer enhances the fluorescence emission of NMM(610 nm).Besides this,the peroxidase-like activity of G4/hemin DNAzyme offers the colorimetric detection of Hg^(2+).The formation of duplex with PMDNAzyme increases the catalytic activity.This novel biosensing probe quantitatively detected Hg^(2+)using both fluorimetry and colorimetry approaches with a low detection limit of 0.59 and 36.3 nM,respectively.It was also observed that the presence of interfering metal ions in case of real aqueous samples does not affect the performance of this novel biosensing probe.These findings confirm the considerable potential of the proposed biosensing probe to screen the concentration of Hg^(2+)in aquatic products.展开更多
Refers to:•Evaluation of DNA aduct damage using G-quadruplex-based DNAzyme•Microfluidic chemostatic bioreactor for high-throughput screening and sustainable co-harvesting of biomass and biodiesel in microalgae The aff...Refers to:•Evaluation of DNA aduct damage using G-quadruplex-based DNAzyme•Microfluidic chemostatic bioreactor for high-throughput screening and sustainable co-harvesting of biomass and biodiesel in microalgae The affiliation of one of the authors of the above articles,Dr.Xingcai Zhang,was incorrectly published as his previous positions at the Mas-sachusetts Institute of Technology and Harvard University.This note serves to alert the readers that Dr.Zhang was not affiliated with the Massachusetts Institute of Technology or Harvard University at the time of publication.The Editor would like to apologize for any inconvenience caused.展开更多
Introduction:A quadruplex digital polymerase chain reaction(dPCR)method was developed for the simultaneous detection of Salmonella spp.,Shigella spp.,Vibrio cholerae,and V.parahaemolyticus in wastewater to enhance pat...Introduction:A quadruplex digital polymerase chain reaction(dPCR)method was developed for the simultaneous detection of Salmonella spp.,Shigella spp.,Vibrio cholerae,and V.parahaemolyticus in wastewater to enhance pathogen identification velocity and efficiency.This study established detection limits for these bacterial pathogens and validated the method using environmental wastewater samples.Methods:Specific primers and probes were designed targeting the invA gene of Salmonella,ipaH gene of Shigella,tlh gene of V.parahaemolyticus,and cholera toxin gene ctxA of V.cholerae.The quadruplex dPCR assay underwent rigorous evaluation for analytical sensitivity and specificity.Detection limits were determined using spiked wastewater samples,and the method’s effectiveness was assessed through preliminary testing of 60 environmental wastewater samples.Results:The quadruplex dPCR assay was optimized at an annealing temperature of 58°C.In spiked wastewater samples,the detection limits were 390 CFU/100 mL for Salmonella,11 CFU/100 mL for Shigella,660 CFU/100 mL for V.cholerae,and 640 CFU/100 mL for V.parahaemolyticus.Analysis of 60 municipal wastewater samples revealed pathogen concentrations ranging from 100.9–14,560 copies/100 mL for Shigella,86.5–7,329 copies/100 mL for Salmonella,and 84.5–865.7 copies/100 mL for V.parahaemolyticus.Conclusions:The developed quadruplex dPCR assay demonstrates robust capability for comprehensive surveillance of intestinal bacterial pathogens in wastewater,offering reliable detection even at low concentrations.展开更多
Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadrupiex structure in vitro. Circular dichroism (CD) spectroscopic studies ...Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadrupiex structure in vitro. Circular dichroism (CD) spectroscopic studies show that TTAGGG, (TTAGGG)2 and (TTAGGG)4 can all form quadrupiex in vitro and exist mainly as parallel quadrupiex without metal ions. Both K+ and Na+ can stabilize the tetrameric structure and facilitate the forming of anti-parallel conformation. Furthermore, the conformations of quadrupiex can also be affected by sequence length, the nature and concentration of metal ions.展开更多
Under different conditions, oligonucleotides can form several different DNA structures such as duplex, triplex and quadruplex. All these structures exhibit an obvious difference in their CD spectra. The common charact...Under different conditions, oligonucleotides can form several different DNA structures such as duplex, triplex and quadruplex. All these structures exhibit an obvious difference in their CD spectra. The common characteristic is that they show a negative band at 240 nm, while in the range of 260-300 nm, the spectra are different from each other. Many factors such as chain direction, sugar puckering mode, orientation of the glycosyl bond, base stacking and sequence can affect their conformation and then show diversity and complexity in their spectra. By studying and comparing these spectra, more information about their conformations can be obtained to help predict some new structures. Furthermore, the spectra can also provide a base to study their potential biological functions.展开更多
Under different conditions, oligonucleotides can form several alternative DNA structures such as duplex, triplex and quadruplex. All these structures can interact with ethidium bromide (EB) and make its fluorescence i...Under different conditions, oligonucleotides can form several alternative DNA structures such as duplex, triplex and quadruplex. All these structures can interact with ethidium bromide (EB) and make its fluorescence intensity change. The fluorescence spectra and other related parameters provided by static fluorescence techniques showed that the interaction mechanisms between EB and these structures were not always the same. Among them, B type duplex and triplex DNA adopt an intercalative mode when binding to the EB, which has a relatively high efficiency of energy transfer and the fluorescence of EB cannot be quenched easily. While for the parallel duplex DNA, the interaction mode is an outside binding in which energy transfer can hardly happen and its fluorescence intensity as well as Stern-Volmer constant is almost the same to the free EB. For the quadruplex, the binding mechanism to EB is more complex. Results from the energy transfer and quenching studies indicate that the two interaction modes noted above probably coexist at the same time.展开更多
文摘The influence of the G‐quartet structural integrity on the catalytic activity of the G‐quadruplex(G4)was investigated by comparing the G4‐DNAzyme performances of a series of G4s with a G‐vacancy site and a G‐triplex(G‐tri).The results presented herein not only confirm that the structural integrity of the 3'‐end G‐quartet is necessary for G4s to be catalytically competent but also show how to remediate G‐vacancy‐mediated catalytic activity losses via the addition of guanine surrogates in an approach referred to as G‐vacancy complementation strategy that is applicable to parallel G4s only.Furthermore,this study demonstrates that the terminal G‐quartet could act as a proximal coordinating group and cooperate with the flanking nucleotide to activate the hemin cofactor.
文摘The active ingredients of ginger(Zingiber officinale)are 6-gingerol,8-gingerol,and 10-gingerol.Ginger is reported to be an antioxidant,anticancer,and anti-inflammatory agent because of its bioactive metabolites.The 3 gingerols share a standard ring structure with different side chains.The maintenance of telomeric length by telomerase is a major issue in almost all cancers.Targeting TERRA G4 could provide a method to inhibit telomerase activity.Molecular docking,molecular dynamics simulations,molecular mechanics Poisson-Boltzmann surface area,principal component analysis,and free energy landscape analysis were performed to evaluate gingerol-TERRA G4 interactions,the extent and stability of these interactions,and the binding free energy and stability of the complexes of the 3 gingerols with TERRA G4.The results revealed that 10-gingerol has superior binding and stabilizing potential for TERRA G4 structures.These findings suggest that TERRA G4 could be a promising therapeutic target for cancer and that 10-gingerol may serve as a potential anticancer lead compound.Further in vitro and in vivo studies to determine the effective dose and toxicity are necessary to evaluate its safety and efficacy.
文摘The human telomere sequence (TTAGGG)4 folds into an unusual conformation possessing three G-tetrads linked by TTA loops. The first loop is a propeller loop while the second and third loops are transverse loops. Using Circular Dichroism (CD) spectroscopy, we have investigated the effect of sequence context on the structures and stabilities of intramolecular G-quadruplexes related to the human telomere sequence by considering all permutations of T and A within the loops. The results indicate that changing only one base in any one loop can have a dramatic effect on the conformation of the quadruplex as well as its melting temperature, Tm. Thus, each sequence studied has a unique CD spectrum and Tm. In general, variants with a modified second loop are the most stable while the wild type sequence is the least stable. The observed difference in CD spectra and melting temperature are discussed in terms of base stacking within the loop and stacking of the loop bases with adjacent G-tetrads.
基金supported by the grants from the National Natural Science Foundation of China (31720103912 and 31801704)the ’Taishan Scholar’ Construction Project, China (TS201712023)。
文摘Tomato brown rugose fruit virus(ToBRFV) is a novel tobamovirus firstly reported in 2015 and poses a severe threat to the tomato industry. So far, it has spread to 10 countries in America, Asia, and Europe. In 2019, ToBRFV was identified in Shandong Province(ToBRFV-SD), China. In this study, it was shown that ToBRFV-SD induced mild to severe mosaic and blistering on leaves, necrosis on sepals and pedicles, and deformation, yellow spots, and brown rugose necrotic lesions on fruits. ToBRFV-SD induced distinct symptoms on plants of tomato, Capsicum annumm, and Nicotiana benthamiana, and caused latent infection on plants of Solanum tuberosum, Solanum melongena, and N. tabacum cv. Zhongyan 102. All the 50 tomato cultivars tested were highly sensitive to ToBRFV-SD. The complete genomic sequence of ToBRFV-SD shared the highest nucleotide and amino acid identities with isolate IL from Israel. In the phylogenetic tree constructed with the complete genomic sequence, all the ToBRFV isolates were clustered together and formed a sister branch with tobacco mosaic virus(TMV). Furthermore, a quadruplex RT-PCR system was developed that could differentiate ToBRFV from other economically important viruses affecting tomatoes, such as TMV, tomato mosaic virus, and tomato spotted wilt virus. The findings of this study enhance our understanding of the biological and molecular characteristics of ToBRFV and provide an efficient and effective detection method for multiple infections, which is helpful in the management of ToBRFV.
文摘The DNA G quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G quadruplex using single molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single molecule level was consistent with ensemble measurement
基金Funding:S.K.thanks the Department of Biotechnology(DBT),Government of India,for research grant(award BT/PR18868/BCE/8/1370/2016 dated 2018 January 31)M.N.is grateful to CSIR for the SRA fellowship(no.B-12857,dated 2021 October 21).
文摘Mercury(Hg^(2+))has been recognized as a global pollutant with a toxic,mobile,and persistent nature.It adversely affects the ecosystem and human health.Already developed biosensors for Hg^(2+)detection majorly suffer from poor sensitivity and specificity.Herein,a colorimetric/fluorimetric dual-mode sensing approach is designed for the quantitative detection of Hg^(2+).This novel sensing approach utilizes nanofluorophores,i.e.,fluorescent copper nanoclusters-doped zirconia metal-organic framework(CuNCs@Zr-MOF)nanoconjugate(blue color)and N-methyl mesoporphyrin IX(NMM)(red color)in combination with peroxidase-mimicking G-quadruplex DNAzyme(PMDNAzyme).In the presence of Hg^(2+),dabcyl conjugated complementary DNA with T-T mismatches form the stable duplex with the CuNCs@Zr-MOF@G-quadruplex structure through T-Hg^(2+)-T base pairing.It causes the quenching of fluorescence of CuNCs@Zr-MOF(463 nm)due to the Förster resonance energy transfer(FRET)system.Moreover,the G-quadruplex(G4)structure of the aptamer enhances the fluorescence emission of NMM(610 nm).Besides this,the peroxidase-like activity of G4/hemin DNAzyme offers the colorimetric detection of Hg^(2+).The formation of duplex with PMDNAzyme increases the catalytic activity.This novel biosensing probe quantitatively detected Hg^(2+)using both fluorimetry and colorimetry approaches with a low detection limit of 0.59 and 36.3 nM,respectively.It was also observed that the presence of interfering metal ions in case of real aqueous samples does not affect the performance of this novel biosensing probe.These findings confirm the considerable potential of the proposed biosensing probe to screen the concentration of Hg^(2+)in aquatic products.
文摘Refers to:•Evaluation of DNA aduct damage using G-quadruplex-based DNAzyme•Microfluidic chemostatic bioreactor for high-throughput screening and sustainable co-harvesting of biomass and biodiesel in microalgae The affiliation of one of the authors of the above articles,Dr.Xingcai Zhang,was incorrectly published as his previous positions at the Mas-sachusetts Institute of Technology and Harvard University.This note serves to alert the readers that Dr.Zhang was not affiliated with the Massachusetts Institute of Technology or Harvard University at the time of publication.The Editor would like to apologize for any inconvenience caused.
基金Supported by the National Key Research and Development Program(2022YFC3201704-01)from the Ministry of Science and Technology of the People’s Republic of Chinathe Key Project of the Capital’s Funds for Health Improvement and Research,China(2022-1G-4231).
文摘Introduction:A quadruplex digital polymerase chain reaction(dPCR)method was developed for the simultaneous detection of Salmonella spp.,Shigella spp.,Vibrio cholerae,and V.parahaemolyticus in wastewater to enhance pathogen identification velocity and efficiency.This study established detection limits for these bacterial pathogens and validated the method using environmental wastewater samples.Methods:Specific primers and probes were designed targeting the invA gene of Salmonella,ipaH gene of Shigella,tlh gene of V.parahaemolyticus,and cholera toxin gene ctxA of V.cholerae.The quadruplex dPCR assay underwent rigorous evaluation for analytical sensitivity and specificity.Detection limits were determined using spiked wastewater samples,and the method’s effectiveness was assessed through preliminary testing of 60 environmental wastewater samples.Results:The quadruplex dPCR assay was optimized at an annealing temperature of 58°C.In spiked wastewater samples,the detection limits were 390 CFU/100 mL for Salmonella,11 CFU/100 mL for Shigella,660 CFU/100 mL for V.cholerae,and 640 CFU/100 mL for V.parahaemolyticus.Analysis of 60 municipal wastewater samples revealed pathogen concentrations ranging from 100.9–14,560 copies/100 mL for Shigella,86.5–7,329 copies/100 mL for Salmonella,and 84.5–865.7 copies/100 mL for V.parahaemolyticus.Conclusions:The developed quadruplex dPCR assay demonstrates robust capability for comprehensive surveillance of intestinal bacterial pathogens in wastewater,offering reliable detection even at low concentrations.
文摘Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadrupiex structure in vitro. Circular dichroism (CD) spectroscopic studies show that TTAGGG, (TTAGGG)2 and (TTAGGG)4 can all form quadrupiex in vitro and exist mainly as parallel quadrupiex without metal ions. Both K+ and Na+ can stabilize the tetrameric structure and facilitate the forming of anti-parallel conformation. Furthermore, the conformations of quadrupiex can also be affected by sequence length, the nature and concentration of metal ions.
文摘Under different conditions, oligonucleotides can form several different DNA structures such as duplex, triplex and quadruplex. All these structures exhibit an obvious difference in their CD spectra. The common characteristic is that they show a negative band at 240 nm, while in the range of 260-300 nm, the spectra are different from each other. Many factors such as chain direction, sugar puckering mode, orientation of the glycosyl bond, base stacking and sequence can affect their conformation and then show diversity and complexity in their spectra. By studying and comparing these spectra, more information about their conformations can be obtained to help predict some new structures. Furthermore, the spectra can also provide a base to study their potential biological functions.
基金Project supported by the Ninth Five-Year Plan Key Project Grant of the Chinese Academy of Sciences
文摘Under different conditions, oligonucleotides can form several alternative DNA structures such as duplex, triplex and quadruplex. All these structures can interact with ethidium bromide (EB) and make its fluorescence intensity change. The fluorescence spectra and other related parameters provided by static fluorescence techniques showed that the interaction mechanisms between EB and these structures were not always the same. Among them, B type duplex and triplex DNA adopt an intercalative mode when binding to the EB, which has a relatively high efficiency of energy transfer and the fluorescence of EB cannot be quenched easily. While for the parallel duplex DNA, the interaction mode is an outside binding in which energy transfer can hardly happen and its fluorescence intensity as well as Stern-Volmer constant is almost the same to the free EB. For the quadruplex, the binding mechanism to EB is more complex. Results from the energy transfer and quenching studies indicate that the two interaction modes noted above probably coexist at the same time.
