DNA guanine(G)-quadruplexes(G4s)are unique secondary structures formed by two or more stacked Gtetrads in G-rich DNA sequences.These structures have been found to play a crucial role in highly transcribed genes,especi...DNA guanine(G)-quadruplexes(G4s)are unique secondary structures formed by two or more stacked Gtetrads in G-rich DNA sequences.These structures have been found to play a crucial role in highly transcribed genes,especially in cancer-related oncogenes,making them attractive targets for cancer therapeutics.Significantly,targeting oncogene promoter G4 structures has emerged as a promising strategy to address the challenge of undruggable and drug-resistant proteins,such as MYC,BCL2,KRAS,and EGFR.Natural products have long been an important source of drug discovery,particularly in the fields of cancer and infectious diseases.Noteworthy progress has recently been made in the discovery of naturally occurring DNA G4-targeting drugs.Numerous DNA G4s,such as MYC-G4,BCL2-G4,KRAS-G4,PDGFR-b-G4,VEGF-G4,and telomeric-G4,have been identified as potential targets of natural products,including berberine,telomestatin,quindoline,sanguinarine,isaindigotone,and many others.Herein,we summarize and evaluate recent advancements in natural and nature-derived DNA G4 binders,focusing on understanding the structural recognition of DNA G4s by small molecules derived from nature.We also discuss the challenges and opportunities associated with developing drugs that target DNA G4s.展开更多
Mercury ion(Hg^(2+)),a highly noxious of heavy metalion,has detrimental effects on the ecological environment and human health.Herein,we have developed an exonuclease III(Exo III)assisted catalytic hairpin assembly fo...Mercury ion(Hg^(2+)),a highly noxious of heavy metalion,has detrimental effects on the ecological environment and human health.Herein,we have developed an exonuclease III(Exo III)assisted catalytic hairpin assembly formation of a trivalent G-quadruplex/hemin DNAzyme for colorimetric detection of Hg^(2+).A hairpin DNA(Hr)was designed with thymine-Hg^(2+)-thymine pairs that catalyzed by Exo III is prompted to happen upon binding Hg^(2+).A released DNA fragment triggers the catalytic assembly of other three hairpins(H1,H2,and H3)to form many trivalent G-quadruplex/hemin DNA enzymes for signal output.The developed sensor shows a dynamic range from 2 pM to 2μM,with an impressively low detection limit of 0.32 pM for Hg^(2+)detection.Such a sensor also has good selectivity toward Hg^(2+)detection in the presence of other common metal ions.This strategy shows the great potential for visual detection with portable type.展开更多
Since the discovery of left-handed G-quadruplex(L-G4)structure formed by natural DNA,there has been a growing interest in its potential functions.This study utilised it to catalyse enantioselective Diels-Alder reactio...Since the discovery of left-handed G-quadruplex(L-G4)structure formed by natural DNA,there has been a growing interest in its potential functions.This study utilised it to catalyse enantioselective Diels-Alder reactions,considering its different optical rotation compared to an ordinary G4.It was determined that when L-G4 was used with a combination of copper(Ⅱ)ions,there was a good enantioselectivity(-52%ee)without further addition of ligands.When further consideration was given by adding G4 ligands,G4 was further stabilised,even obtaining a better enantioselectivity(up to-80%ee).Moreover,when using ligands that have regulatory effects on G4,the ee value can be adjusted.In this work,a minimal left-handed G4 was reported.A follow-up study was also con ducted,which recovers that the minimal left-handed G4 remains its catalytic effect and enantioselectivity,but is not so effective as the former case.This indicates that a complete G4 structure is relatively conducive to chiral catalysis.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
G-quadruplexes are stable secondary structures formed with guanine rich sequences,which are widely distributed in genome.Chemical compounds stabilizing G-quadruplexes exhibited inhibition on tumor cells.However,the fe...G-quadruplexes are stable secondary structures formed with guanine rich sequences,which are widely distributed in genome.Chemical compounds stabilizing G-quadruplexes exhibited inhibition on tumor cells.However,the feasibility of G-quadruplex structures as drug targets needs to be validated.In this study,Sunitinib,an antitumor drug targeting tyrosine kinases was found to stabilize telomere G-quadruplex.The stabilization was further enhanced by the combined usage with Berberine,an isoquinoline alkaloid.Circular dichroism spectra showed the synergistic effect comes from inducing the conformation conversion of telomere G-quadruplex.The combination of Berberine with Sunitinib resulted in 1.7-fold enhancement in cell apoptosis rate with the percentage of apoptotic cells reaching about 70%.The confocal microscopy immunofluorescence images showed the combination of Berberine and Sunitinib induced the formation of G-quadruplex at the telomere in A549 cancer cells.This study suggested that more clinic drugs could work by targeting G-quadruplex structures.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 in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world ...G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences(PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database(http://jsjds.hzau.edu.cn/MBPC/Vi PGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads(G2-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads(G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested that the G2-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.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
A simple, rapid, highly sensitive electrochem-ical sensor for potassium ion （K^＋） based on the confor-mationai change of DNA sequence containing guanine-rich segments is presented. In the presence of K^＋, guanine-...A simple, rapid, highly sensitive electrochem-ical sensor for potassium ion （K^＋） based on the confor-mationai change of DNA sequence containing guanine-rich segments is presented. In the presence of K^＋, guanine-rich DNA sequence folds to G-quadruplex structure, allowing a ferrocene tag to transfer electrons to the electrode. Gold nanoparticles （AuNPs）, which are self-assembled on the surface of a bare gold electrode by using 4-aminothio-phenol as a medium, offer a big surface area to immobilize a large number of aptamers and improve the sensitivity of the sensor. The square-wave voltammetry peak current increases with K^＋ concentration. The plots of peak current against K^＋ concentration and the logarithm of K^＋ con- centration are linear over the range from 0.1 to 1.0 mmol·L^-1 and from 1 to 30 mmol·L^-1, respectively. A lower detection limit of 0.1 mmol·L^-1 K^＋ is obtained for AuNPs-modified sensor, which greatly surpasses that （100 mmol·L^-1） of the sensor without AuNPs modification by three orders of magnitude. Thus, the sensor with AuNPs amplification is expected to open new opportunities for highly sensitive detection of other biomolecules in the future.展开更多
The Bloom helicase （BLM） gene product encodes a DNA helicase that functions in homologous recombination repair to prevent genomic instability. BLM is highly active in binding and unfolding G-quadruplexes （G4）, whi...The Bloom helicase （BLM） gene product encodes a DNA helicase that functions in homologous recombination repair to prevent genomic instability. BLM is highly active in binding and unfolding G-quadruplexes （G4）, which are non- canonical DNA structures formed by Hoogsteen base-pairing in guanine-rich sequences. Here we use single-molecule fluorescence resonance energy transfer （smFRET） to study the molecular mechanism of BLM-catalysed G4 unfolding and show that BLM unfolds G4 in two pathways. Our data enable us to propose a model in which the HRDC domain functions as a regulator of BLM, depending on the position of the HRDC domain of BLM in action： when HRDC binds to the G4 sequence, BLM may hold G4 in the unfolded state; otherwise, it may remain on the unfolded G4 transiently so that G4 can refold immediately.展开更多
Human telomeric G-quadruplex plays a crucial role in regulating the genome stability. Despite extensive studies on structures and kinetics of monomeric G-quadruplex, the interaction between G-quadruplexes is still in ...Human telomeric G-quadruplex plays a crucial role in regulating the genome stability. Despite extensive studies on structures and kinetics of monomeric G-quadruplex, the interaction between G-quadruplexes is still in debate. In this work,we employ magnetic tweezers to investigate the folding and unfolding kinetics of two contiguous G-quadruplexes in 100-mM K~＋buffer. The interaction between G-quadruplexes and the consequent effect on the kinetics of G-quadruplex are revealed. The linker sequence between G-quadruplexes is further found to play an important role in the interaction between two G-quadruplexes. Our results provide a high-resolution insight into kinetics of multimeric G-quadruplexes and genome stability.展开更多
The detection of biomarkers is of great significance in the diagnosis of numerous diseases,especially cancer.Herein,we developed a sensitive and universal fluorescent aptasensor strategy based on magnetic beads,DNA G-...The detection of biomarkers is of great significance in the diagnosis of numerous diseases,especially cancer.Herein,we developed a sensitive and universal fluorescent aptasensor strategy based on magnetic beads,DNA G-quadruplex,and exonuclease Ⅲ(Exo Ⅲ).In the presence of a target protein,a label-free single strand DNA(ssDNA)hybridized with the aptamer was released as a trigger DNA due to specific recognition between the aptamer and target.Subsequently,ssDNA initiates the ExoⅢ-aided recycling to amplify the fluorescence signal,which was caused by N-methylmesoporphyrin IX(NMM)insertion into the G-quadruplex structure.This proposed strategy combines the excellent specificity between the aptamer and target,high sensitivity of the fluorescence signal by G-quadruplex and ExoⅢ-aided recycling amplification.We selected(50-1200 nmol/L)MUC1,a common tumor biomarker,as the proof-of-concept target to test the specificity of our aptasenso r.Results reveal that the sensor sensitively and selectively detected the target protein with limits of detection(LODs)of 3.68 and 12.83 nmol/L in buffer solution and 10%serum system,respectively.The strategy can be easily applied to other targets by simply substituting corresponding aptamers and has great potential in the diagnosis and monitoring of several diseases.展开更多
Several probes containing benzothiazole-guided conjugated systems(BGCS) were designed and synthesized, and two molecules(BGCS5 and BGCS6) of which were discovered as selective probes targeting c-MYC Pu22 G-quadruplex ...Several probes containing benzothiazole-guided conjugated systems(BGCS) were designed and synthesized, and two molecules(BGCS5 and BGCS6) of which were discovered as selective probes targeting c-MYC Pu22 G-quadruplex DNA. The fluorescence intensity of BGCS5 and BGCS6 in the presence of c-MYC Pu22 far exceeds that of the typical G4 probe TO1. Especially, the fluorescence of BGCS6 increased almost193-fold in the presence of c-MYC Pu22 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10–30 folds than those in the presence of other DNAs, which will be useful tools for disease detection in mammals.展开更多
G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of li...G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K^(+)/Na^(+))is about the base stacking free energies indicates that there will be a competition among the binding of M^(+)-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.展开更多
G-quadruplex(G4) is widely known as a non-classical secondary structure of nucleic acid. With the indepth study of G4, it is an urgent need for a phosphorescent probe with a high G4 binding ability to evaluate the lev...G-quadruplex(G4) is widely known as a non-classical secondary structure of nucleic acid. With the indepth study of G4, it is an urgent need for a phosphorescent probe with a high G4 binding ability to evaluate the level of G4 in the cytoplasm. Thus, this study designed and synthesized Ir-PDP where an Ir(Ⅲ)complex was used as a phosphorescent emitter. Meanwhile, two installed PDPs(pyridostatin derivatives)were used to improve the combination ability with G4 and reduced the cytotoxicity of the Ir(Ⅲ) complex.Compared with other nucleic acid secondary structures, Ir-PDP produced a higher phosphorescence lifetime after interacting with G4. Ir-PDP was distributed in the cytoplasm of living cells, and two-photon phosphorescence lifetime imaging can detect the binding events of the probe in the cytoplasm. The addition of G4 binder PDS significantly regulated cytoplasmic phosphorescence lifetime. The project explored a new sensing pathway to observe the binding manners of probes in the cytoplasm through the phosphorescence lifetime of probes.展开更多
基金supported by the National Institutes of Health(R01CA177585,U01CA240346,and R01CA153821)(DY)the Purdue Center for Cancer Research(P30CA023168)+2 种基金the National Natural Science Foundation of China(82173707 and 82322065)the Program for Jiangsu Province Innovative Research Scholar(JSSCRC2021512)the“Double First-Class”University Project(CPUQNJC22_08).
文摘DNA guanine(G)-quadruplexes(G4s)are unique secondary structures formed by two or more stacked Gtetrads in G-rich DNA sequences.These structures have been found to play a crucial role in highly transcribed genes,especially in cancer-related oncogenes,making them attractive targets for cancer therapeutics.Significantly,targeting oncogene promoter G4 structures has emerged as a promising strategy to address the challenge of undruggable and drug-resistant proteins,such as MYC,BCL2,KRAS,and EGFR.Natural products have long been an important source of drug discovery,particularly in the fields of cancer and infectious diseases.Noteworthy progress has recently been made in the discovery of naturally occurring DNA G4-targeting drugs.Numerous DNA G4s,such as MYC-G4,BCL2-G4,KRAS-G4,PDGFR-b-G4,VEGF-G4,and telomeric-G4,have been identified as potential targets of natural products,including berberine,telomestatin,quindoline,sanguinarine,isaindigotone,and many others.Herein,we summarize and evaluate recent advancements in natural and nature-derived DNA G4 binders,focusing on understanding the structural recognition of DNA G4s by small molecules derived from nature.We also discuss the challenges and opportunities associated with developing drugs that target DNA G4s.
基金Supported by The Science and Technology Project of General Administration of Quality Supervision,Inspection and Quarantine (2015IK126)The Science and Technology Project of Changsha City of Hunan Province of China (KQ1602124).
文摘Mercury ion(Hg^(2+)),a highly noxious of heavy metalion,has detrimental effects on the ecological environment and human health.Herein,we have developed an exonuclease III(Exo III)assisted catalytic hairpin assembly formation of a trivalent G-quadruplex/hemin DNAzyme for colorimetric detection of Hg^(2+).A hairpin DNA(Hr)was designed with thymine-Hg^(2+)-thymine pairs that catalyzed by Exo III is prompted to happen upon binding Hg^(2+).A released DNA fragment triggers the catalytic assembly of other three hairpins(H1,H2,and H3)to form many trivalent G-quadruplex/hemin DNA enzymes for signal output.The developed sensor shows a dynamic range from 2 pM to 2μM,with an impressively low detection limit of 0.32 pM for Hg^(2+)detection.Such a sensor also has good selectivity toward Hg^(2+)detection in the presence of other common metal ions.This strategy shows the great potential for visual detection with portable type.
基金This work was supported by the National Natural Science Foundation of China(Nos.21432008,91753201,and 21721005).
文摘Since the discovery of left-handed G-quadruplex(L-G4)structure formed by natural DNA,there has been a growing interest in its potential functions.This study utilised it to catalyse enantioselective Diels-Alder reactions,considering its different optical rotation compared to an ordinary G4.It was determined that when L-G4 was used with a combination of copper(Ⅱ)ions,there was a good enantioselectivity(-52%ee)without further addition of ligands.When further consideration was given by adding G4 ligands,G4 was further stabilised,even obtaining a better enantioselectivity(up to-80%ee).Moreover,when using ligands that have regulatory effects on G4,the ee value can be adjusted.In this work,a minimal left-handed G4 was reported.A follow-up study was also con ducted,which recovers that the minimal left-handed G4 remains its catalytic effect and enantioselectivity,but is not so effective as the former case.This indicates that a complete G4 structure is relatively conducive to chiral catalysis.
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Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(Grant No.2015RC013)The Fundamental Research Funds for the Central Universities(Grant No.2662017PY113,2662015PY208,2662015BQ048)+2 种基金National Natural Science Foundation of China(Grant No.21502060,21708011)Open fund of The State Key Laboratory of Bio-organic and Natural Products Chemistry,CAS(Grant No.SKLBNPC16343)Open fund of Beijing National Laboratory For Molecular Sciences
文摘G-quadruplexes are stable secondary structures formed with guanine rich sequences,which are widely distributed in genome.Chemical compounds stabilizing G-quadruplexes exhibited inhibition on tumor cells.However,the feasibility of G-quadruplex structures as drug targets needs to be validated.In this study,Sunitinib,an antitumor drug targeting tyrosine kinases was found to stabilize telomere G-quadruplex.The stabilization was further enhanced by the combined usage with Berberine,an isoquinoline alkaloid.Circular dichroism spectra showed the synergistic effect comes from inducing the conformation conversion of telomere G-quadruplex.The combination of Berberine with Sunitinib resulted in 1.7-fold enhancement in cell apoptosis rate with the percentage of apoptotic cells reaching about 70%.The confocal microscopy immunofluorescence images showed the combination of Berberine and Sunitinib induced the formation of G-quadruplex at the telomere in A549 cancer cells.This study suggested that more clinic drugs could work by targeting G-quadruplex structures.
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 the National Natural Science Foundation of China(21732002,22077043,31672558,31871305,21907036)Opening Foundation of State Key Laboratory of Freshwater Ecology and Biotechnology,China(2020FB08)+2 种基金the Fundamental Research Funds for the(2662018PY021,2662019PY003,2662020PY001)Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(2016RC011)HZAU-AGIS Cooperation Fund(SZYJY2021010)。
文摘G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences(PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database(http://jsjds.hzau.edu.cn/MBPC/Vi PGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads(G2-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads(G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested that the G2-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.
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.
基金financially supported by the National Natural Science Foundation of China(No.20903008)
文摘A simple, rapid, highly sensitive electrochem-ical sensor for potassium ion （K^＋） based on the confor-mationai change of DNA sequence containing guanine-rich segments is presented. In the presence of K^＋, guanine-rich DNA sequence folds to G-quadruplex structure, allowing a ferrocene tag to transfer electrons to the electrode. Gold nanoparticles （AuNPs）, which are self-assembled on the surface of a bare gold electrode by using 4-aminothio-phenol as a medium, offer a big surface area to immobilize a large number of aptamers and improve the sensitivity of the sensor. The square-wave voltammetry peak current increases with K^＋ concentration. The plots of peak current against K^＋ concentration and the logarithm of K^＋ con- centration are linear over the range from 0.1 to 1.0 mmol·L^-1 and from 1 to 30 mmol·L^-1, respectively. A lower detection limit of 0.1 mmol·L^-1 K^＋ is obtained for AuNPs-modified sensor, which greatly surpasses that （100 mmol·L^-1） of the sensor without AuNPs modification by three orders of magnitude. Thus, the sensor with AuNPs amplification is expected to open new opportunities for highly sensitive detection of other biomolecules in the future.
基金supported by the National Natural Science Foundation of China(Grant Nos.11674382,11574381,and 11574382)the Key Research Program of Frontier Sciences,Chinese Academy of Sciences(Grant No.QYZDJ-SSW-SYS014)
文摘The Bloom helicase （BLM） gene product encodes a DNA helicase that functions in homologous recombination repair to prevent genomic instability. BLM is highly active in binding and unfolding G-quadruplexes （G4）, which are non- canonical DNA structures formed by Hoogsteen base-pairing in guanine-rich sequences. Here we use single-molecule fluorescence resonance energy transfer （smFRET） to study the molecular mechanism of BLM-catalysed G4 unfolding and show that BLM unfolds G4 in two pathways. Our data enable us to propose a model in which the HRDC domain functions as a regulator of BLM, depending on the position of the HRDC domain of BLM in action： when HRDC binds to the G4 sequence, BLM may hold G4 in the unfolded state; otherwise, it may remain on the unfolded G4 transiently so that G4 can refold immediately.
基金supported by the National Natural Science Foundation of China(Grant Nos.11474346 and 11774407)the Key Research Program of Frontier Sciences,Chinese Academy of Sciences(Grant No.QYZDB-SSW-SLH045)the National Key Research and Development Program,China(Grant No.2016YFA0301500)
文摘Human telomeric G-quadruplex plays a crucial role in regulating the genome stability. Despite extensive studies on structures and kinetics of monomeric G-quadruplex, the interaction between G-quadruplexes is still in debate. In this work,we employ magnetic tweezers to investigate the folding and unfolding kinetics of two contiguous G-quadruplexes in 100-mM K~＋buffer. The interaction between G-quadruplexes and the consequent effect on the kinetics of G-quadruplex are revealed. The linker sequence between G-quadruplexes is further found to play an important role in the interaction between two G-quadruplexes. Our results provide a high-resolution insight into kinetics of multimeric G-quadruplexes and genome stability.
基金supported by grants from the National Natural Science Foundation of China (No.21472060)Shenzhen Municipal government (Nos.JCYJ20160301153959476 and JCYJ20160324163734374)Shenzhen Reform Commission (Disciplinary Development Program for Chemical Biology)
文摘The detection of biomarkers is of great significance in the diagnosis of numerous diseases,especially cancer.Herein,we developed a sensitive and universal fluorescent aptasensor strategy based on magnetic beads,DNA G-quadruplex,and exonuclease Ⅲ(Exo Ⅲ).In the presence of a target protein,a label-free single strand DNA(ssDNA)hybridized with the aptamer was released as a trigger DNA due to specific recognition between the aptamer and target.Subsequently,ssDNA initiates the ExoⅢ-aided recycling to amplify the fluorescence signal,which was caused by N-methylmesoporphyrin IX(NMM)insertion into the G-quadruplex structure.This proposed strategy combines the excellent specificity between the aptamer and target,high sensitivity of the fluorescence signal by G-quadruplex and ExoⅢ-aided recycling amplification.We selected(50-1200 nmol/L)MUC1,a common tumor biomarker,as the proof-of-concept target to test the specificity of our aptasenso r.Results reveal that the sensor sensitively and selectively detected the target protein with limits of detection(LODs)of 3.68 and 12.83 nmol/L in buffer solution and 10%serum system,respectively.The strategy can be easily applied to other targets by simply substituting corresponding aptamers and has great potential in the diagnosis and monitoring of several diseases.
基金financially supported by the Innovation and Application of Key Technologies of Quality-improving and Efficiency-increasing of Fengtou Ginger Industry (No. 2020–620–002–06)Natural Science Foundation of Hubei Province (No. 2020CFB717)+2 种基金support from the Program for Leading Talents of Hubei Academy of Agricultural Sciences (No. L2018031)the Youth Science Foundation of Hubei Academy of Agricultural Sciences (No. 2021NKYJJ17)Hubei Agricultural Science Innovation centre (No. 2019–620–000–001–27)。
文摘Several probes containing benzothiazole-guided conjugated systems(BGCS) were designed and synthesized, and two molecules(BGCS5 and BGCS6) of which were discovered as selective probes targeting c-MYC Pu22 G-quadruplex DNA. The fluorescence intensity of BGCS5 and BGCS6 in the presence of c-MYC Pu22 far exceeds that of the typical G4 probe TO1. Especially, the fluorescence of BGCS6 increased almost193-fold in the presence of c-MYC Pu22 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10–30 folds than those in the presence of other DNAs, which will be useful tools for disease detection in mammals.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11705160 and 11647074)。
文摘G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K^(+)/Na^(+))is about the base stacking free energies indicates that there will be a competition among the binding of M^(+)-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.
基金supported by the National Natural Science Foundation of China (Nos. 92153303 and 21721005)。
文摘G-quadruplex(G4) is widely known as a non-classical secondary structure of nucleic acid. With the indepth study of G4, it is an urgent need for a phosphorescent probe with a high G4 binding ability to evaluate the level of G4 in the cytoplasm. Thus, this study designed and synthesized Ir-PDP where an Ir(Ⅲ)complex was used as a phosphorescent emitter. Meanwhile, two installed PDPs(pyridostatin derivatives)were used to improve the combination ability with G4 and reduced the cytotoxicity of the Ir(Ⅲ) complex.Compared with other nucleic acid secondary structures, Ir-PDP produced a higher phosphorescence lifetime after interacting with G4. Ir-PDP was distributed in the cytoplasm of living cells, and two-photon phosphorescence lifetime imaging can detect the binding events of the probe in the cytoplasm. The addition of G4 binder PDS significantly regulated cytoplasmic phosphorescence lifetime. The project explored a new sensing pathway to observe the binding manners of probes in the cytoplasm through the phosphorescence lifetime of probes.
