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
The G-quadruplex （G4） elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This （34 DNA can form within or across single-stranded DNA molecules and ...The G-quadruplex （G4） elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This （34 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationaily identified 149,988 non-telomeric G4 motifs in maize （Zea mays L., B73 AGPv2）, 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5~ UTR and the other at the 5~ end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia （group VII ERFs）, oxidative stress （D J-1/GATasel）, and energy status （AMPK/ SnRK） pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.展开更多
In this assay, a label-free fluorescent sensing platform based on triple-helix molecular switch（THMS） and G-quadruplex was developed for the detection of tetracycline. We demonstrated this approach by using THMS, wh...In this assay, a label-free fluorescent sensing platform based on triple-helix molecular switch（THMS） and G-quadruplex was developed for the detection of tetracycline. We demonstrated this approach by using THMS, which consists of a central section with a shortened 8-mer aptamer sequence with high affinity to tetracycline and flanked by two arm segments. G-rich oligonucleotide can specifically bind to thioflavin T（Th T） as a signal transduction probe（STP）. In the absence of tetracycline, THMS remains stable, the fluorescence of background is low. By the addition of target tetracycline, the aptamer-target binding results in the formation of a structured aptamer-target complex, which disassembles the THMS and releases the STP. The free STP self-assembles into G-quadruplex and specifically binds to Th T which generates a obvious fluorescence enhancement. Using the triple-helix molecular switch, the developed aptamer-based fluorescent sensing platform showed a linear relationship with the concentration of tetracycline ranging from 0.2 to 20.0 nmol/L. The detection limit of tetracycline was determined to be970.0 pmol/L. The assay avoids complicated modifications or chemical labeling, making it simple and cost-effective. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection.展开更多
The G-quadruplexes formed from G-rich strands in the telomere and oncogene-promoter regions are regarded as new promising targets in the cancer therapy.A G-quadruplex in the downstream flanking region of the signal tr...The G-quadruplexes formed from G-rich strands in the telomere and oncogene-promoter regions are regarded as new promising targets in the cancer therapy.A G-quadruplex in the downstream flanking region of the signal transducer and activator of transcription 3（STAT3） gene was explored.Its folding patterns were proposed to be 3：2：2 and 3：3：1 loop isomers by the mutation analysis by CD spectroscopy.The structures were constructed and refined by molecular modeling method.展开更多
In this research, an unusually dimeric G-quadruplex of d（GGGTGGGTGGGTGGGT） （SI）, the potent nanomolar HIV-1 integrase inhibitor, was detected by nuclear magnetic resonance （NMR）. This result has been confirmed b...In this research, an unusually dimeric G-quadruplex of d（GGGTGGGTGGGTGGGT） （SI）, the potent nanomolar HIV-1 integrase inhibitor, was detected by nuclear magnetic resonance （NMR）. This result has been confirmed by electrospray ionization mass spectrometry （ESI-MS） and circular dichroism （CD）.展开更多
G-quadruplexes （G4s） play important roles in biological systems, such as telomere maintenance, replication, and transcription. Based on the DNA sequence, loop geometry, and the local environments, G4s can be classif...G-quadruplexes （G4s） play important roles in biological systems, such as telomere maintenance, replication, and transcription. Based on the DNA sequence, loop geometry, and the local environments, G4s can be classified into different conformations. It is important to detect different types of G4s to monitor the diseases related with G4s. Most ligands bind to G4s based on end-stacking modes, while rare ligands bind to G4s through groove binding modes. We have found that a cyanine dye DMSB interacts with parallel G4 by end-stacking and groove simultaneous binding mode. In this article, we found that DMSB could simply discriminate parallel G4s from other DNA motifs by using UV-vis spectrum. These results give some clues to develop high specificity G4 probes.展开更多
G-quadruplex ligands have been accepted as potential therapeutic agents for anticancer treatment. Thioflavin T （ThT）, a highly selective G-quadruplex ligand, can bind G-quadruplex with a fluorescent light-up signal ...G-quadruplex ligands have been accepted as potential therapeutic agents for anticancer treatment. Thioflavin T （ThT）, a highly selective G-quadruplex ligand, can bind G-quadruplex with a fluorescent light-up signal change and high specificity against DNA duplex. However, there are still different opinions that ThT induces/stabilizes G-quadruplex foldings/topologies in human telomere sequence. Here, a sensitive single-molecule nanopore technology was utilized to analyze the interactions between human telomeric DNA （Tel DNA） and ThT. Both translocation time and current blockade were measured to investigate the translocation behaviors. Furthermore, the effects of metal ion （K~ and Na~） and pH on the translocation behaviors were studied. Based on the single-molecule level analysis, there are some conclusions： （1） In the electrolyte solution containing 50 mmol/L I（Cl and 450 mmol/L NaCl, ThT can bind strongly with Tel DNA but nearly does not change the G-quadruplex form; （2） in the presence of high concentration K~, the ThT binding induces the structural change of hybrid G-quadruplex into antiparallel topology with an enhanced structural stability; （3） In either alkaline or acidic buffer, G-quadruplex form will change in certain degree. All above conclusions are helpful to deeply understand the interaction behaviors between Tel DNA and ThT. This nanopore platform, investigating G-quadruplex ligands at the single-molecule level, has great potential for the design of new drugs and sensors.展开更多
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.
基金supported by USDA-ARS and grants from the National Science Foundation(PGRP IOS-1025954 to HWB,PGRP IOS1116561 to KEK and coworkers)the U.S.Department of Agriculture(NRI-Plant Biochemistry 07-03580 to KEK and coworkers)The Florida State University(CRC Planning Grant to HWB,OMNI award No.0000025471)
文摘The G-quadruplex （G4） elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This （34 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationaily identified 149,988 non-telomeric G4 motifs in maize （Zea mays L., B73 AGPv2）, 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5~ UTR and the other at the 5~ end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia （group VII ERFs）, oxidative stress （D J-1/GATasel）, and energy status （AMPK/ SnRK） pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.
基金supported by National Natural Science Foundation of China (Nos. 21205142, 31370104)The Research Innovation Program for Graduates of Central South University (No. 2016zzts580)
文摘In this assay, a label-free fluorescent sensing platform based on triple-helix molecular switch（THMS） and G-quadruplex was developed for the detection of tetracycline. We demonstrated this approach by using THMS, which consists of a central section with a shortened 8-mer aptamer sequence with high affinity to tetracycline and flanked by two arm segments. G-rich oligonucleotide can specifically bind to thioflavin T（Th T） as a signal transduction probe（STP）. In the absence of tetracycline, THMS remains stable, the fluorescence of background is low. By the addition of target tetracycline, the aptamer-target binding results in the formation of a structured aptamer-target complex, which disassembles the THMS and releases the STP. The free STP self-assembles into G-quadruplex and specifically binds to Th T which generates a obvious fluorescence enhancement. Using the triple-helix molecular switch, the developed aptamer-based fluorescent sensing platform showed a linear relationship with the concentration of tetracycline ranging from 0.2 to 20.0 nmol/L. The detection limit of tetracycline was determined to be970.0 pmol/L. The assay avoids complicated modifications or chemical labeling, making it simple and cost-effective. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection.
基金supported by the National Natural Science Foundation of China(Nos90913004 and 30821001)the Natural Science Foundation of Beijing(No7082101)+1 种基金Program for New Century Excellent Talents in UniversityBeijing Talents Foundation Beijing National Laboratory for Molecular Sciences
文摘The G-quadruplexes formed from G-rich strands in the telomere and oncogene-promoter regions are regarded as new promising targets in the cancer therapy.A G-quadruplex in the downstream flanking region of the signal transducer and activator of transcription 3（STAT3） gene was explored.Its folding patterns were proposed to be 3：2：2 and 3：3：1 loop isomers by the mutation analysis by CD spectroscopy.The structures were constructed and refined by molecular modeling method.
基金the National Natural Science Foundation of China(No.20472009)the Research Fund for the Doctoral Program of Higher Education.
文摘In this research, an unusually dimeric G-quadruplex of d（GGGTGGGTGGGTGGGT） （SI）, the potent nanomolar HIV-1 integrase inhibitor, was detected by nuclear magnetic resonance （NMR）. This result has been confirmed by electrospray ionization mass spectrometry （ESI-MS） and circular dichroism （CD）.
基金supported by Major National Basic Research Projects (973,No.2013CB733701)National Natural Science Foundation of China (Nos.81072576,91027033,21302188,21205121,21305145 and 31200576)Chinese Academy of Sciences (No.KJCX2-EW-N06-01)
文摘G-quadruplexes （G4s） play important roles in biological systems, such as telomere maintenance, replication, and transcription. Based on the DNA sequence, loop geometry, and the local environments, G4s can be classified into different conformations. It is important to detect different types of G4s to monitor the diseases related with G4s. Most ligands bind to G4s based on end-stacking modes, while rare ligands bind to G4s through groove binding modes. We have found that a cyanine dye DMSB interacts with parallel G4 by end-stacking and groove simultaneous binding mode. In this article, we found that DMSB could simply discriminate parallel G4s from other DNA motifs by using UV-vis spectrum. These results give some clues to develop high specificity G4 probes.
基金financially supported by the National Natural Science Foundation of China(No. 21475091)the Science andTechnology Department of Sichuan Province(No. 2015GZ0301)
文摘G-quadruplex ligands have been accepted as potential therapeutic agents for anticancer treatment. Thioflavin T （ThT）, a highly selective G-quadruplex ligand, can bind G-quadruplex with a fluorescent light-up signal change and high specificity against DNA duplex. However, there are still different opinions that ThT induces/stabilizes G-quadruplex foldings/topologies in human telomere sequence. Here, a sensitive single-molecule nanopore technology was utilized to analyze the interactions between human telomeric DNA （Tel DNA） and ThT. Both translocation time and current blockade were measured to investigate the translocation behaviors. Furthermore, the effects of metal ion （K~ and Na~） and pH on the translocation behaviors were studied. Based on the single-molecule level analysis, there are some conclusions： （1） In the electrolyte solution containing 50 mmol/L I（Cl and 450 mmol/L NaCl, ThT can bind strongly with Tel DNA but nearly does not change the G-quadruplex form; （2） in the presence of high concentration K~, the ThT binding induces the structural change of hybrid G-quadruplex into antiparallel topology with an enhanced structural stability; （3） In either alkaline or acidic buffer, G-quadruplex form will change in certain degree. All above conclusions are helpful to deeply understand the interaction behaviors between Tel DNA and ThT. This nanopore platform, investigating G-quadruplex ligands at the single-molecule level, has great potential for the design of new drugs and sensors.
