Co-reporter:Ru-Ru Gao;Yu-Jie Li;Maierhaba Wumaier;Xiao-Chun Hu;Tian-Ming Yao
Nanoscale (2009-Present) 2017 vol. 9(Issue 27) pp:9589-9597
Publication Date(Web):2017/07/13
DOI:10.1039/C7NR03264A
Novel supramolecular coordination polymer nanoparticles (CPNs) were synthesized via the self-assembly of guanosine monophosphate (GMP) and lanthanide ions (Ln3+, including Tb3+, Eu3+ and Ce3+) in aqueous solution. These CPNs (GMP/Tb3+, GMP/Eu3+ and GMP/Ce3+) have an identical coordination environment but exhibit completely different luminescence properties responding to external stimuli such as dipicolinic acid (DPA), ethylene diamine tetraacetic acid (EDTA), pH and metal ions, which has inspired us to tune the emission color of the CPNs and perform multiple logic operations. Firstly, color-tunable luminescence from red to green can be easily achieved by modulating the doping ratio of Tb3+ and Eu3+ into GMP. Notably, trichromatic white light emitting CPNs can be successfully realized by simultaneously doping Tb3+, Eu3+ and Ce3+ into the host or just adjusting the pH of the solution. What's more, by employing GMP/Tb3+ CPNs as a logic operator, we have achieved the implementation of multilayered gate cascades (INH–INH, NOR–OR). When GMP/Eu3+ CPNs served as a logic operator, the logic elements can be integrated as another combinatorial gate (AND–INH). Moreover, by employing the red emission of Eu3+ and blue emission of GMP as the dual-output signal transducer, a set of parallel logic gates was established successfully. These results help elucidate the design rules by which simple logic can be integrated to construct cascaded logic gates and expand the applications of CPNs in light-emitting diode (LED) lamps and biological systems.
Co-reporter:Ru-Ru Gao;Tian-Ming Yao;Xiao-Yan Lv;Yan-Yan Zhu;Yi-Wei Zhang
Chemical Science (2010-Present) 2017 vol. 8(Issue 6) pp:4211-4222
Publication Date(Web):2017/05/30
DOI:10.1039/C7SC00361G
To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.
Co-reporter:Ru-Ru Gao, Shuo Shi, Ying Zhu, Hai-Liang Huang and Tian-Ming Yao
Chemical Science 2016 vol. 7(Issue 3) pp:1853-1861
Publication Date(Web):23 Nov 2015
DOI:10.1039/C5SC03570H
Boolean logic gates integrate multiple digital inputs into a digital output. Among these, logic gates based on nucleic acids have attracted a great deal of attention due to the prospect of controlling living systems in the way we control electronic computers. Herein, by employing Thioflavin T (ThT) as a signal transducer, we integrated multiple components based on RET (a type of proto-oncogene) into a logic gate combinatorial library, including basic logic gates (NOR, INHIBIT, IMPLICATION), a single three-input NOR gate, and combinatorial gates (INHIBIT–OR, NOT–AND–NOR). In this library, gates were connected in series where the output of the previous gate was the input for the next gate. Subsequently, by taking advantage of the library, some intelligent logic functions were realized. Expectedly, a biocomputing keypad-lock security system was designed by sequential logic operations. Moreover, a parity checker which can identify even numbers and odd numbers from natural numbers was established successfully. This work helps elucidate the design rules by which simple logic can be harnessed to produce diverse and complex calculations by rewiring communication between different gates. Together, our system may serve as a promising proof of principle that demonstrates increased computational complexity by linking multiple logic gates together.
Co-reporter:Juanjuan Li, Xiaochun Hu, Shuo Shi, Yiwei Zhang and Tianming Yao
Journal of Materials Chemistry A 2016 vol. 4(Issue 7) pp:1361-1367
Publication Date(Web):15 Jan 2016
DOI:10.1039/C5TB02032H
Early disease diagnosis is very important for the prevention or mitigation of metastasis. Effective and efficient methods are needed to improve the diagnosis and assessment of diseases. Thrombin is a biomarker for diagnosis of some diseases, such as pulmonary metastases and diseases associated with coagulation abnormalities. Lots of methods for detecting thrombin have been reported, however, most of them were based on a single aptamer and needed modification of aptamers, and label free sensors for thrombin detection based on an aptamer pair are challenging. In this work, we present three label free sensing platforms based on [Ru(bpy)2(o-mopip)]2+ (bpy = 2,2-bipyridine; o-mopip = 2-(2-methoxylphenyl)imidazo[4,5-f][1,10]phenanthroline) (OMO) and graphene oxide (GO) for thrombin detection. Thrombin detection using our three label free sensors is accomplished by specific target recognition based on aptamer pair TBA1/TBA2–thrombin, single aptamer TBA1–thrombin or TBA2–thrombin, respectively. Direct readouts of the target recognition is achieved by restoration of the fluorescence of OMO prequenched by GO. All of the three sensing platforms exhibited high sensitivity and selectivity. Furthermore, all sensing platforms were successfully applied to thrombin analysis in diluted bovine serum. According to the thrombin dependent response of the three platforms, the sensing platform based on aptamer pair TBA1 and TBA2 showed the highest sensitivity, widest linearity, best selectivity and recovery in diluted serum to thrombin. These results show that the sensing platform based on an aptamer pair have great potential for clinical diagnosis of disease-related biomarkers.
Co-reporter:Xin Wang, Lihong Pei, Xiumin Fan, Shuo Shi
Inorganic Chemistry Communications 2016 Volume 72() pp:7-12
Publication Date(Web):October 2016
DOI:10.1016/j.inoche.2016.07.010
•Two new [Ru(L)2(3-tppp)]2 + complexes have been synthesized and characterized.•The interaction of the title complex with two different forms of the human telomeric G-quadruplexes DNA was explored.•The present investigation led to the identification of potent G-quadruplex stabilizers with high selectivity over duplex DNA.•Both complexes show preference for mixed-hybrid G-quadruplex over antiparallel G-quadruplex.The binding properties of new complexes [Ru(L)2(3-tppp)]2 + (L = bpy, phen) towards two different forms of the human telomeric G-quadruplexes DNA have been investigated by UV–Vis spectroscopy, fluorescent indicator displacement (FID) assays, fluorescence resonance energy transfer (FRET) melting assays and molecular docking studies. The molecular docking studies indicated that both complexes interacted with 22AG with the stoichiometric ratio of 1:1, but the two complexes showed different G-quadruplexed DNA binding affinity. Complex 2 bound to the G-quadruplexes DNA more tightly than complex 1 did. Moreover, the FRET melting assay revealed that both complexes could be potential stabilizers for G-quadruplex architectures. These studies are useful not only for better understanding of the interaction between the target G-quadruplexes DNA and metal complexes but also valuable in defining the best strategy to prepare metal complexes as potential anticancer drugs.
Co-reporter:Hailiang Huang, Shuo Shi, Xing Gao, Ruru Gao, Ying Zhu, Xuewen Wu, Ruimin Zang, Tianming Yao
Biosensors and Bioelectronics 2016 Volume 79() pp:198-204
Publication Date(Web):15 May 2016
DOI:10.1016/j.bios.2015.12.024
•This method was successfully used to detect three different chemicals, adenosine, dopamine and 17β-estradiol, which turned out to be a universal biosensor.•This method was one of the simplest sensors which was rapid and portable for adenosine, dopamine and 17β-estradiol detection.•The advantage of label-free, low-cost, highly selective and repeatable made it of remarkable significance.Based on specific aptamer binding properties, a strategy for adenosine, dopamine and 17β-estradiol detection was realised by employing Ru complex and quantum dots (QDs) as fluorescence probes. Ru complex, which could quench the fluorescence of QDs, preferred to bind with aptamer DNA and resulted in the fluorescence rise of QDs. When the aptamer DNA was incubated with the target first, it could not bind with Ru complex and the fluorescence of QDs was quenched. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of adenosine, dopamine and 17β-estradiol with a limit of detection (LOD) of 101 nM, 19 nM and 37 nM, respectively. The experiments in fetal bovine serum were also carried out with good results. This universal method was rapid, label-free, low-cost, easy-operating and highly repeatable for the detection of adenosine, dopamine and 17β-estradiol. Qualitative detection by naked eyes was also available without complex instruments. It could also be extended to detect various analytes, such as metal ions, proteins and small molecules by using appropriate aptamers.
Co-reporter:Ying Zhu, Xiao-chun Hu, Shuo Shi, Ru-ru Gao, Hai-liang Huang, Yan-yan Zhu, Xiao-yan Lv, Tian-ming Yao
Biosensors and Bioelectronics 2016 Volume 79() pp:205-212
Publication Date(Web):15 May 2016
DOI:10.1016/j.bios.2015.12.015
•This method achieved success in detecting three different biomolecules both in PBS and FBS.•A label-free, low-cost and enzyme-free biosensor is developed for biomolecule detection.•Results for FBS samples demonstrated that our biosensor is applicable in real samples.•This assay is universal by re-building or modifying DNA sequences.We report here an ultrasensitive strategy based on the recognition-induced conformational alteration of aptamer and fluorescence turn-on abilities of guanine-rich (G-rich) DNA sequence in proximity to silver nanoclusters for adenosine triphosphate (ATP), adenosine (A) and thrombin (TB) detection. Herein, we designed two tailored DNA sequences noted as complementary DNA (abbreviated as c-DNA) and signal probe DNA (abbreviated as s-DNA), respectively. c-DNA is designed as a special structure consisting of a sequence complementary to aptamer at the 3′-end and a guanine-rich DNA sequence at the 5′-end; s-DNA contains a cytosine-rich sequence responsible for Ag NCs templated synthesis at the 3′-end and a link sequence (part of aptamer) complementary to partial of the c-DNA at the 5′-end. In the presence of target, the aptamer associated with the target, resulting in the formation of duplex DNA (dsDNA), the DNA–Ag NCs thereafter could close to the guanine-rich sequence, leading to enhanced fluorescence signal readout. The widespread application of the sensing system is achieved success in the detection of three biomolecules. ATP, adenosine and thrombin in the range of 0.5-8.0 μM, 0.5-7.0 μM and 50-900 nM could be linearly detected with the detection limits of 91.6 nM, 103.4 nM and 8.4 nM, respectively. This label-free and turn-on fluorescent sensing system employing the mechanism proposed here turns out to be sensitive, selective, and convenient for the detection of biomolecules without washing and separation steps.
Co-reporter:Xing Gao, Shuo Shi, Jun-Liang Yao, Juan Zhao and Tian-Ming Yao
Dalton Transactions 2015 vol. 44(Issue 44) pp:19264-19274
Publication Date(Web):07 Oct 2015
DOI:10.1039/C5DT03373J
[Ru(phen)2dppz]2+ and other closely related ruthenium(II) complexes containing π-extended ligands were found to be non or weakly emissive in water, while exhibiting significant luminescence intensity growth when bound to DNA, however, a satisfactory interpretation has not been provided on this “light switch” mechanism. In the present study, we investigated the vertical transitions and triplet excited states of [Ru(phen)2dppz]2+ (1), [Ru(phen)2dppzi]2+ (2) and [Ru(phen)2dppz-idzo]2+ (3) in the gas phase and aqueous solution, through time dependent-density functional theory (TDDFT). Based on the optimized 3MLCT and 3LLCT structures and energies, we found that the 3MLCT state might be responsible for the emissions of the complexes. Interesting connections between the singlet vertical transitions and the luminescence properties were noticed. Through ZORA-TDDFT calculation with perturbative SOC, we evaluated the intersystem crossing between the lowest singlet excited state, and both 3MLCT state and 3LLCT state, which gave a reasonable explanation for the luminescence properties of these complexes.
Co-reporter:Dr. Shuo Shi;Xing Gao;Hailiang Huang;Juan Zhao ; Tianming Yao
Chemistry - A European Journal 2015 Volume 21( Issue 38) pp:13390-13400
Publication Date(Web):
DOI:10.1002/chem.201501830
Abstract
In an effort to explore the effect of ancillary ligands on the spectral properties and overall G-quadruplex DNA binding behavior, two new ruthenium(II) complexes [Ru(phen)2(dppzi)]2+ (1) and [Ru(dmp)2(dppzi)]2+ (2) (phen=1,10-phenanthroline, dmp=2,9-dimethyl-1,10-phenanthroline, dppzi=dipyrido[3,2-a:2′,3′-c]phenazine-10,11-imidazole) were prepared. Complex 1 can emit luminescence in the absence and presence of G-quadruplexes DNA. However, with CH3 substituent on the 2- and 9-positions of the phen ancillary ligand, no detectable luminescence is observed for complex 2 in any organic solvent or in the absence and/or presence of G-quadruplex DNA. Experimental and molecular docking studies indicated that both complexes interacted with the human telomeric repeat AG3(T2AG3)3 (22AG) G-quadruplex with the stoichiometric ratio of 1:1, but the two complexes showed different G-quadruplex DNA binding affinity. Complex 1 binds to the G-quadruplexes DNA more tightly than complex 2 does. Our results demonstrate that methyl groups on the phen ancillary ligand significantly affect the spectral properties and the overall DNA binding behavior of the complexes. Such difference in spectral properties and DNA binding affinities of these two complexes can be reasonably explained by DFT/TD-DFT calculations. This work provides guidance not only on exploring the G-quadruplexes DNA binding behavior of complexes, but also understanding the unique luminescence mechanism.
Co-reporter:Dr. Shuo Shi;Jin-Hong Xu;Xing Gao;Hai-Liang Huang ;Dr. Tian-Ming Yao
Chemistry - A European Journal 2015 Volume 21( Issue 32) pp:11435-11445
Publication Date(Web):
DOI:10.1002/chem.201501093
Abstract
Polymorphic DNA G-quadruplex recognition has attracted great interest in recent years. The strong binding affinity and potential enantioselectivity of chiral [Ru(bpy)2(L)]2+ (L=dipyrido[3,2-a:2′,3′-c]phenazine, dppz-10,11-imidazolone; bpy=2,2′-bipyridine) prompted this investigation as to whether the two enantiomers, Δ and Λ, can show different effects on diverse structures with a range of parallel, antiparallel and mixed parallel/antiparallel G-quadruplexes. These studies provide a striking example of chiral-selective recognition of DNA G-quadruplexes. As for antiparallel (tel-Na+) basket G-quadruplex, the Λ enantiomers bind stronger than the Δ enantiomers. Moreover, the behavior reported here for both enantiomers stands in sharp contrast to B-DNA binding. The chiral selectivity toward mixed parallel/antiparallel (tel-K+) G-quadruplex of both compounds is weak. Different loop arrangements can change chiral complex selectivity for both antiparallel and mixed parallel/antiparallel G-quadruplex. Whereas both Δ and Λ isomers bind to parallel G-quadruplexes with comparable affinity, no appreciable stereoselective G-quadruplex binding of the isomers was observed. In addition, different binding stoichiometries and binding modes for Δ and Λ enantiomers were confirmed. The results presented here indicate that chiral selective G-quadruplex binding is not only related to G-quadruplex topology, but also to the sequence and the loop constitution.
Co-reporter:Xuyue Zheng, Tianming Yao, Ying Zhu, Shuo Shi
Biosensors and Bioelectronics 2015 Volume 66() pp:103-108
Publication Date(Web):15 April 2015
DOI:10.1016/j.bios.2014.11.013
•This platform is simple, label-free and highly repeatable for the detection of l-histidine.•DNA-Ag NCs exhibited reversible “light switch” effect in the presence of Cu2+ and l-histidine successively.•Biosensor offers nanomolar sensitivity (4.3 nm) and wide detection range (0.20–80 μM).•The proposed assay was successfully used to determine l-histidine in urine samples.In the present study, a new strategy based on Cu2+ mediated DNA-templated silver nanoclusters (DNA-Ag NCs) was developed, as a label-free, on–off–on fluorescent probe for the detection of l-histidine. Eight synthesized DNA oligonucleotides (D1–D8) were experimentally tested, and D5-Ag NCs was finally selected for l-histidine detection due to its best fluorescent properties. The fluorescence emission of D5-Ag NCs could be quenched by Cu2+ via electron or energy transfer. Upon addition of l-histidine, the chelation between Cu2+ and the imidazole group of l-histidine leads to Cu2+ liberation from D5-Ag NCs, and subsequently results in a dramatic fluorescence enhancement of the probe. The method displayed a good selectivity toward l-histidine over all the other amino acids, with a linear relationship in the range of 0.20–80 μM, and a limit of detection (LOD) of 4.3 nM. The strategy was also successfully applied to detect l-histidine in diluted human urine, exhibiting great opportunities for practical application in biological system.
Co-reporter:Hailiang Huang, Shuo Shi, Xuyue Zheng, Tianming Yao
Biosensors and Bioelectronics 2015 Volume 71() pp:439-444
Publication Date(Web):15 September 2015
DOI:10.1016/j.bios.2015.04.076
•This sensor presented the lowest LOD for coralyne detection among all reported.•This method was successfully used to detect two different chemicals, coralyne and mercury ions, which had never been reported.•This platform was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions.•An exonuclease III (Exo III)-aided DNA recycling amplification strategy was introduced to highly improve the limit of detection.Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2–100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg2+ taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg2+ detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers.
Co-reporter:Xiao-Hui Lu, Shuo Shi, Jun-Liang Yao, Xing Gao, Hai-Liang Huang, Tian-Ming Yao
Journal of Inorganic Biochemistry 2014 140() pp: 64-71
Publication Date(Web):
DOI:10.1016/j.jinorgbio.2014.07.003
Co-reporter:Yanlin Cao, Shuo Shi, Linlin Wang, Junliang Yao, Tianming Yao
Biosensors and Bioelectronics 2014 Volume 55() pp:174-179
Publication Date(Web):15 May 2014
DOI:10.1016/j.bios.2013.12.009
•This work represents the first example for heparin detection based on QDs and complex.•The limit of detection is much lower than any reported outcome and the sensitivity is higher.•The selectivity could be visualized with the naked eye.•Our assay is very convenient and can readily be used to detect heparin immediately without other treatments.A new strategy for the detection of heparin is developed by utilizing quantum dots (QDs) and a functional ruthenium polypyridyl complex [Ru(phen)2(dppz-idzo)]2+ (phen=1,10-phenanthroline, dppz-idzo=dipyrido-[3,2-a:2',3'-c] phenazine-imidazolone). The emission of CdTe QDs is found to be quenched by Ru complex due to electron transfer. Upon addition of the polyanionic heparin, it could remove the quencher (Ru complex) from the surface of QDs owing to the electrostatic and/or hydrogen bonding interactions between heparin and Ru complex, which led to significant fluorescence recovery of CdTe QDs. The fluorescence intensity enhanced with the increase of heparin and a linear relationship was observed in the range of 21–77 nM for heparin detection in buffer solution and the limit of detection (LOD) is 0.38 nM. Moreover, the strategy was successfully applied to detect heparin as low as 0.68 nM with a linear range of 35–98 nM in fetal bovine serum samples. The selectivity results of the fluorescence assay revealed that our system displayed excellent fluorescence selectivity towards heparin over its analogues, such as chondroitin 4-sulfate (Chs) or hyaluronic acid (Hya). This fluorescence “switch on” assay for heparin is label-free, convenient, sensitive and selective, which can be used to detect heparin in biological systems even with the naked eyes.
Co-reporter:Wenliang Sun, Junliang Yao, Tianming Yao and Shuo Shi
Analyst 2013 vol. 138(Issue 2) pp:421-424
Publication Date(Web):09 Nov 2012
DOI:10.1039/C2AN36142F
Using molecular light switch Ru complex Ru(bpy)2(dppz)2+ and CdTe quantum dots (QDs), we have designed a label-free DNA fluorescent sensor for the detection of Ag+ in aqueous solution.
Co-reporter:Ting-Ting Cheng, Jun-Liang Yao, Xing Gao, Wenliang Sun, Shuo Shi and Tian-Ming Yao
Analyst 2013 vol. 138(Issue 12) pp:3483-3489
Publication Date(Web):17 Apr 2013
DOI:10.1039/C3AN00242J
In the present study, a new strategy for heparin detection and quantification in biological media, such as fetal bovine serum (FBS), is developed by monitoring the emission change of a functional ruthenium polypyridyl complex ([Ru(phen)2dppz-idzo]2+, complex 1) in buffer solution. Polyanionic heparin is found to interact with a positively charged Ru-complex through electrostatic effects and/or hydrogen bonding interactions, which leads to a significant fluorescence enhancement of the Ru-complex. To get insight into this fluorescence “switch on” behavior, the binding model of the Ru-complex to heparin is established by employing molecular docking simulations based on the fluorescence and UV absorption results. The selectivity results of the fluorescence assay reveal that our complex displayed good fluorescence selectivity towards heparin over its analogues, such as chondroitin 4-sulfate (Chs) or hyaluronic acid (Hya), which have lower charge density and/or structural compatibility as compared to that of heparin. Quantification of heparin is also performed and a linear calibration curve is observed in the range of 0.01–4.87 U mL−1 (the limit of detection is 0.01 U mL−1) for heparin detection in diluted FBS solution. This “one-step” fluorescence “switch on” assay for heparin detection is label-free, convenient, sensitive and selective, and has a long emission wavelength and large Stokes shift.
Co-reporter:Jun-Liang Yao, Xing Gao, Wenliang Sun, Shuo Shi and Tian-Ming Yao
Dalton Transactions 2013 vol. 42(Issue 16) pp:5661-5672
Publication Date(Web):23 Jan 2013
DOI:10.1039/C3DT32640C
A new ruthenium complex, [Ru(bpy)2dppz-idzo]2+ (bpy = 2,2′-bipyridine, dppz-idzo = dipyrido-[3,2-a:2′,3′-c] phenazine-imidazolone), was synthesized and characterized. The luminescent titrations showed that the Ru-complex exhibited an outstanding “light switch” effect with an emission enhancement factor of about 300 in the presence of G-quadruplex DNA in a K+ solution. This remarkable “light switch” behavior can even be observed by the naked eye under irradiation with UV light. To get an insight into the “light switch” mechanism, quantum-chemical calculations were performed based on the DFT/TDDFT/PCM method at the B3LYP/6-31G* level. Furthermore, the CD titrations and thermal melting experiments indicated that [Ru(bpy)2dppz-idzo]2+ could not only induce the formation of an antiparallel G-quadruplex structure in the absence of monocations, but also has the ability to stabilize the G-quadruplex architecture, implying potential applications in anticancer therapeutics. Both the “light switch” effect and the structure stabilization ability of [Ru(bpy)2dppz-idzo]2+ were found to be superior to the well-known DNA molecular “light switch” [Ru(bpy)2dppz]2+. Finally, a “sandwich-like” binding model was proposed on the basis of molecular docking simulations.
Co-reporter:Junliang Yao, Xing Gao, Wenliang Sun, Tianming Yao, Shuo Shi, and Liangnian Ji
Biochemistry 2013 Volume 52(Issue 11) pp:
Publication Date(Web):February 26, 2013
DOI:10.1021/bi400240c
Inhibition of anomalous aggregation of tau protein would be an attractive therapeutic target for Alzheimer’s disease (AD). In this study, tannic acid (TA), a polymeric plant polyphenol, and its monomer, gallic acid (GA), were introduced as the references to afford a molecular framework that integrates tau binding properties and inhibitory effects. Using a thioflavin S fluorescence assay and electron microscopy, we demonstrated that TA could competently inhibit the in vitro aggregation of tau peptide R3, corresponding to the third repeat unit of the microtubule-binding domain, with an IC50 of 3.5 μM, while GA’s inhibition was comparatively piddling (with an IC50 of 92 μM). In the isothermal titration calorimetry experiment, we found that TA could strongly bind to R3 with a large amount of heat released. Circular dichroism spectra showed TA dose-dependently suppressed the conformational transition of R3 from a random coil structure to a β-sheet structure during the aggregation process. Finally, a structural model was built using molecular docking simulation to elucidate the possible binding sites for TA on the tau peptide surface. Our results suggest that TA recognizably interacts with tau peptide by forming a hairpin binding motif, a key framework required for inhibiting tau polymerization, in addition to hydrogen bonding, hydrophilic–hydrophobic interactions, and static electrical interactions, as reported previously. The inhibitory effect of TA on human full-length tau protein (tau441) was also verified by electron microscopy. This finding hints at the possibility of TA as a leading compound of anti-AD drugs and offers a new stratagem for the rational molecular design of a tau aggregation inhibitor.
Co-reporter:Shuo Shi, Hai-Liang Huang, Xing Gao, Jun-Liang Yao, Chun-Yan Lv, Juan Zhao, Wen-Liang Sun, Tian-Ming Yao, Liang-Nian Ji
Journal of Inorganic Biochemistry 2013 Volume 121() pp:19-27
Publication Date(Web):April 2013
DOI:10.1016/j.jinorgbio.2012.12.011
Two new polypyridine ligands and their corresponding ruthenium(II) complexes have been prepared and characterized. The interactions of both complexes with human telomere quadruplex DNA (both the antiparallel basket and the mixed-hybrid G-quadruplex) have been studied by circular dichroism (CD), CD melting, UV-visible (UV-Vis), fluorescent intercalator displacement (FID) assays and molecular docking studies. The results show that both complexes can stabilize G-quadruplexes DNA and two complexes show different binding affinity for different G-quadruplexes DNA. The 1:1 stoichiometry was confirmed in the buffered solutions by the UV-Vis spectrophotometer using Job's plot method and molecular docking studies. We have also investigated the interaction between the complexes and duplex DNA to gain some insight into the selectivity of the complexes for G-quadruplex structures. FID studies have shown that the complexes have a modest selectivity for G-quadruplex versus duplex DNA.A comparative G-quadruplexes DNA binding of two structurally analogue Ru(II) complexes were explored and explained.Highlights► Two new ligands and their corresponding ruthenium(II) complexes were synthesized and characterized. ► A comparative study of the binding of two structurally analogous Ru(II) complexes to G-quadruplexes DNA were explored. ► Modification of the ligands significantly affects the spectral properties and overall DNA-binding behavior of the complexes.
Co-reporter:Jun-Liang Yao, Xing Gao, Wenliang Sun, Xue-Zhong Fan, Shuo Shi, and Tian-Ming Yao
Inorganic Chemistry 2012 Volume 51(Issue 23) pp:12591-12593
Publication Date(Web):November 19, 2012
DOI:10.1021/ic301305q
Herein, we report a new strategy for developing an on–off–on molecular “light switch” by utilizing the pH value to control the “conformational switch” of G-quadruplex DNA. A novel ruthenium(II) complex with an emission enhancement factor of 150 was synthesized and introduced to detect the switch by the naked eye. The “light switch” can be repeatedly cycled off and on through the addition of H+ and OH–, respectively. The conformational transitions of G-quadruplex DNA in K+ solution at different pH values in the acidic region were evidenced by circular dichroism and fluorescence titrations. Computational calculations by applying density functional theory (DFT)/time-dependent DFT and molecular docking were also carried out to gain insight into the “light-switch” mechanism.
Co-reporter:Shuo Shi, Juan Zhao, Xing Gao, Chunyan Lv, Li Yang, Jian Hao, Hailiang Huang, Junliang Yao, Wenliang Sun, Tianming Yao and Liangnian Ji
Dalton Transactions 2012 vol. 41(Issue 19) pp:5789-5793
Publication Date(Web):29 Mar 2012
DOI:10.1039/C2DT30076A
We report a new G-quadruplex DNA “light switch”, where the light switch can be cycled on and off through the successive introduction of G-quadruplex DNA and [Fe(CN)6]4− ions.
Co-reporter:Wenliang Sun, Tianming Yao and Shuo Shi
Analyst 2012 vol. 137(Issue 7) pp:1550-1552
Publication Date(Web):21 Feb 2012
DOI:10.1039/C2AN16181H
A simple, label-free method for the detection of thrombin has been developed based on the conformational transition of aptamer in the presence of the target by using a molecular light switch, Ru polypyridine complex, and quantum dots as novel fluorescence probes in aqueous solution.
Co-reporter:Shuo Shi, Chunyan Lv, Xing Gao, Juan Zhao, Junliang Yao, Wenliang Sun, Hailing Huang, Tianming Yao, Liangnian Ji
Inorganic Chemistry Communications 2012 Volume 24() pp:212-215
Publication Date(Web):October 2012
DOI:10.1016/j.inoche.2012.07.015
A new complex [Ru(bpy)2(bppp)]2 + (bpy = 2,2′-bipyridine, bppp = 12-bromo-pyrido[2′,3′:5,6]pyrazino[2,3-f][1,10]phenanthroline) has been synthesized and characterized. The interaction of the title complex with two different forms of the human telomeric G-quadruplexes DNA was explored by means of CD spectroscopy, CD melting, fluorescent intercalator displacement (FID) and molecular docking studies. Results indicated that [Ru(bpy)2(bppp)]2 + not only induce formation of antiparallel G-quadruplex structure in the absence of metal cations, but also have the ability to stabilize the G-quadruplexes DNA.A new complex [Ru(bpy)2(bppp)]2 + was synthesized and different binding behavior of two different forms of the human telomeric G-quadruplexes was indicated.Highlights► A new complex [Ru(bpy)2(bppp)]2+ was synthesized and characterized. ► Two different forms of the G- quadruplexes DNA binding were explored. ► It induces the formation of antiparallel G-quadruplex structure. ► It can stabilize both forms of the G-quadruplexes DNA.
Co-reporter:Dan-Jing Yang;Tian-Ming Yao;Liang-Nian Ji
BioMetals 2012 Volume 25( Issue 2) pp:361-372
Publication Date(Web):2012 April
DOI:10.1007/s10534-011-9505-7
The group IIB elements, especially Cd(II) and Hg(II), are increasingly considered as potential environmental neurotoxins. This study demonstrates that the Alzheimer’s tau fragment R2, corresponding to the second repeat of the microtubule-binding domain, can bind to Zn(II), Cd(II) and Hg(II). Isothermal titration calorimetry experiments suggest that the most likely coordination site is the thiol group of Cys291, and this is further confirmed by a control experiment using a C291A mutant peptide. Circular dichroism spectrum reveals that the coordination of group IIB cations, especially Hg(II), can induce pronounced conformational conversions in natively unfolded R2, from random coil to other ordered structures. ThS fluorescence assays and electron microscopy indicate that the group IIB cations promote heparin-induced aggregation of R2, giving relatively small R2 filaments. The efficiency in promoting aggregation, as well as inducing conformational conversion, varies strongly with the cation’s polarizability. Based on these results, a model is proposed in which the cooperative folding of R2 through cross-bridging of group IIB cations is suggested to be a key factor in promoting aggregation, in addition to the effective neutralization of coulombic charge–charge repulsion by heparin, the poly-anion inducer. Our results provide clues to understanding the potential pathogenic role of group IIB metals in the development of neurofibrillary tangles, a typical hallmark of Alzheimer’s disease.
Co-reporter:Shuo Shi, Juan Zhao, Xiaoting Geng, Tianming Yao, Hailiang Huang, Tianlin Liu, Lengfeng Zheng, Zonghui Li, Danjing Yang and Liangnian Ji
Dalton Transactions 2010 vol. 39(Issue 10) pp:2490-2493
Publication Date(Web):22 Jan 2010
DOI:10.1039/B916094A
[Ru(phen)2(dppz)]2+can serve as a prominent molecular “light switch” for G-quadruplexes and i-motif, but it preferentially binds to G-quadruplexes over i-motif.
Co-reporter:Shuo Shi, Tian Xie, Tian-Ming Yao, Chao-Ran Wang, Xiao-Ting Geng, Dan-Jing Yang, Lin-Jie Han, Liang-Nian Ji
Polyhedron 2009 28(7) pp: 1355-1361
Publication Date(Web):
DOI:10.1016/j.poly.2009.02.035
Co-reporter:Shuo Shi, Xin Wang, Wenliang Sun, Xiangyang Wang, Tianming Yao, Liangnian Ji
Methods (15 December 2013) Volume 64(Issue 3) pp:305-314
Publication Date(Web):15 December 2013
DOI:10.1016/j.ymeth.2013.07.004
DNA based biosensors have become increasingly important in medical diagnostics, genetic and drug screening, and forensics in this post-genomic era. Chemical labeling methods suffer from several drawbacks, which are tedious, cost-expensive and time-consuming, thus the development of simple and general label free strategies is being demanded. The present article introduces a new model of biosensor device based on both metallointercalators and nanomaterials, with the aim of highlighting, in particular, the use of the “label-free” strategy for the construction of simple and inexpensive sensing platforms. In this work, two strategies were developed for designing “label-free” sensors: (1) metallointercalators act as the quencher to nanomaterials; (2) nanomaterials act as the quencher to metallointercalators. These methods take advantage of the sensitive luminescence signal change of metallointercalators or nanomaterials upon analytes binding. By monitoring the luminescence change, we were able to detect metal ions and biomolecules. Compared to other label-free fluorescent methods, these “label-free” DNA biosensors provide fast, simple, economical, sensitive and selective detection of target analytes with specific probes.Download full-size image
Co-reporter:Ru-Ru Gao, Tian-Ming Yao, Xiao-Yan Lv, Yan-Yan Zhu, Yi-Wei Zhang and Shuo Shi
Chemical Science (2010-Present) 2017 - vol. 8(Issue 6) pp:
Publication Date(Web):
DOI:10.1039/C7SC00361G
Co-reporter:Xing Gao, Shuo Shi, Jun-Liang Yao, Juan Zhao and Tian-Ming Yao
Dalton Transactions 2015 - vol. 44(Issue 44) pp:NaN19274-19274
Publication Date(Web):2015/10/07
DOI:10.1039/C5DT03373J
[Ru(phen)2dppz]2+ and other closely related ruthenium(II) complexes containing π-extended ligands were found to be non or weakly emissive in water, while exhibiting significant luminescence intensity growth when bound to DNA, however, a satisfactory interpretation has not been provided on this “light switch” mechanism. In the present study, we investigated the vertical transitions and triplet excited states of [Ru(phen)2dppz]2+ (1), [Ru(phen)2dppzi]2+ (2) and [Ru(phen)2dppz-idzo]2+ (3) in the gas phase and aqueous solution, through time dependent-density functional theory (TDDFT). Based on the optimized 3MLCT and 3LLCT structures and energies, we found that the 3MLCT state might be responsible for the emissions of the complexes. Interesting connections between the singlet vertical transitions and the luminescence properties were noticed. Through ZORA-TDDFT calculation with perturbative SOC, we evaluated the intersystem crossing between the lowest singlet excited state, and both 3MLCT state and 3LLCT state, which gave a reasonable explanation for the luminescence properties of these complexes.
Co-reporter:Juanjuan Li, Xiaochun Hu, Shuo Shi, Yiwei Zhang and Tianming Yao
Journal of Materials Chemistry A 2016 - vol. 4(Issue 7) pp:NaN1367-1367
Publication Date(Web):2016/01/15
DOI:10.1039/C5TB02032H
Early disease diagnosis is very important for the prevention or mitigation of metastasis. Effective and efficient methods are needed to improve the diagnosis and assessment of diseases. Thrombin is a biomarker for diagnosis of some diseases, such as pulmonary metastases and diseases associated with coagulation abnormalities. Lots of methods for detecting thrombin have been reported, however, most of them were based on a single aptamer and needed modification of aptamers, and label free sensors for thrombin detection based on an aptamer pair are challenging. In this work, we present three label free sensing platforms based on [Ru(bpy)2(o-mopip)]2+ (bpy = 2,2-bipyridine; o-mopip = 2-(2-methoxylphenyl)imidazo[4,5-f][1,10]phenanthroline) (OMO) and graphene oxide (GO) for thrombin detection. Thrombin detection using our three label free sensors is accomplished by specific target recognition based on aptamer pair TBA1/TBA2–thrombin, single aptamer TBA1–thrombin or TBA2–thrombin, respectively. Direct readouts of the target recognition is achieved by restoration of the fluorescence of OMO prequenched by GO. All of the three sensing platforms exhibited high sensitivity and selectivity. Furthermore, all sensing platforms were successfully applied to thrombin analysis in diluted bovine serum. According to the thrombin dependent response of the three platforms, the sensing platform based on aptamer pair TBA1 and TBA2 showed the highest sensitivity, widest linearity, best selectivity and recovery in diluted serum to thrombin. These results show that the sensing platform based on an aptamer pair have great potential for clinical diagnosis of disease-related biomarkers.
Co-reporter:Shuo Shi, Juan Zhao, Xiaoting Geng, Tianming Yao, Hailiang Huang, Tianlin Liu, Lengfeng Zheng, Zonghui Li, Danjing Yang and Liangnian Ji
Dalton Transactions 2010 - vol. 39(Issue 10) pp:NaN2493-2493
Publication Date(Web):2010/01/22
DOI:10.1039/B916094A
[Ru(phen)2(dppz)]2+can serve as a prominent molecular “light switch” for G-quadruplexes and i-motif, but it preferentially binds to G-quadruplexes over i-motif.
Co-reporter:Shuo Shi, Juan Zhao, Xing Gao, Chunyan Lv, Li Yang, Jian Hao, Hailiang Huang, Junliang Yao, Wenliang Sun, Tianming Yao and Liangnian Ji
Dalton Transactions 2012 - vol. 41(Issue 19) pp:NaN5793-5793
Publication Date(Web):2012/03/29
DOI:10.1039/C2DT30076A
We report a new G-quadruplex DNA “light switch”, where the light switch can be cycled on and off through the successive introduction of G-quadruplex DNA and [Fe(CN)6]4− ions.
Co-reporter:Ru-Ru Gao, Shuo Shi, Ying Zhu, Hai-Liang Huang and Tian-Ming Yao
Chemical Science (2010-Present) 2016 - vol. 7(Issue 3) pp:NaN1861-1861
Publication Date(Web):2015/11/23
DOI:10.1039/C5SC03570H
Boolean logic gates integrate multiple digital inputs into a digital output. Among these, logic gates based on nucleic acids have attracted a great deal of attention due to the prospect of controlling living systems in the way we control electronic computers. Herein, by employing Thioflavin T (ThT) as a signal transducer, we integrated multiple components based on RET (a type of proto-oncogene) into a logic gate combinatorial library, including basic logic gates (NOR, INHIBIT, IMPLICATION), a single three-input NOR gate, and combinatorial gates (INHIBIT–OR, NOT–AND–NOR). In this library, gates were connected in series where the output of the previous gate was the input for the next gate. Subsequently, by taking advantage of the library, some intelligent logic functions were realized. Expectedly, a biocomputing keypad-lock security system was designed by sequential logic operations. Moreover, a parity checker which can identify even numbers and odd numbers from natural numbers was established successfully. This work helps elucidate the design rules by which simple logic can be harnessed to produce diverse and complex calculations by rewiring communication between different gates. Together, our system may serve as a promising proof of principle that demonstrates increased computational complexity by linking multiple logic gates together.
Co-reporter:Jun-Liang Yao, Xing Gao, Wenliang Sun, Shuo Shi and Tian-Ming Yao
Dalton Transactions 2013 - vol. 42(Issue 16) pp:NaN5672-5672
Publication Date(Web):2013/01/23
DOI:10.1039/C3DT32640C
A new ruthenium complex, [Ru(bpy)2dppz-idzo]2+ (bpy = 2,2′-bipyridine, dppz-idzo = dipyrido-[3,2-a:2′,3′-c] phenazine-imidazolone), was synthesized and characterized. The luminescent titrations showed that the Ru-complex exhibited an outstanding “light switch” effect with an emission enhancement factor of about 300 in the presence of G-quadruplex DNA in a K+ solution. This remarkable “light switch” behavior can even be observed by the naked eye under irradiation with UV light. To get an insight into the “light switch” mechanism, quantum-chemical calculations were performed based on the DFT/TDDFT/PCM method at the B3LYP/6-31G* level. Furthermore, the CD titrations and thermal melting experiments indicated that [Ru(bpy)2dppz-idzo]2+ could not only induce the formation of an antiparallel G-quadruplex structure in the absence of monocations, but also has the ability to stabilize the G-quadruplex architecture, implying potential applications in anticancer therapeutics. Both the “light switch” effect and the structure stabilization ability of [Ru(bpy)2dppz-idzo]2+ were found to be superior to the well-known DNA molecular “light switch” [Ru(bpy)2dppz]2+. Finally, a “sandwich-like” binding model was proposed on the basis of molecular docking simulations.
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