A chronocoulometric aptamer sensor for adenosine monophosphate

The selective recognition of adenosine monophosphate by a half-duplex aptamer-modified electrode leads to a simple chronocoulometric aptasensor based on the changes in surface charges.     

Covalently bonded DNA aptamer chiral stationary phase for the chromatographic resolution of adenosine

In this work, a target-specific aptamer chiral stationary phase (CSP) based on the oligonucleotidic selector binding to silica particles through a covalent linkage was developed. An anti-d-adenosine aptamer was coupled, using an in-situ method, by way of an amide bond to macroporous carboxylic acid based silica. Frontal chromatography analysis was performed to evaluate the column properties, i.e., determination of the stationary phase binding capacity and the dissociation constant of the target-immobilized aptamer complex. It was found that such covalent immobilization was able to maintain the aptamer binding properties at a convenient level for an efficient enantioseparation. Subsequently, the separation of adenosine enantiomers was investigated under different operating conditions, including changes in the eluent’s ionic strength and the proportion of organic modifiers as well as column temperatures. It was demonstrated that, under various conditions of use and storage, the present CSP was stable over time.     

A single DNA aptamer functions as a biosensor for ricin

The use of microorganisms or toxins as weapons of death and fear is not a novel concept; however, the modes by which these agents of bioterrorism are deployed are increasingly clever and insidious. One mechanism by which biothreats are readily disseminated is through a nation's food supply. Ricin, a toxin derived from the castor bean plant, displays a strong thermostability and remains active at acidic and alkaline pHs. Therefore, the CDC has assigned ricin as a category B reagent since it may be easily amendable as a deliberate food biocontaminate. Current tools for ricin detection utilize enzymatic activity, immunointeractions and presence of castor bean DNA. Many of these tools are confounded by complex food matrices, display a limited dynamic range of detection and/or lack specificity. Aptamers, short RNA and single stranded DNA sequences, have increased affinity to their selected receptors, experience little cross-reactivity to other homologous compounds and are currently being sought after as biosensors for bacterial contaminants in food. This paper describes the selection and characterization of a single, dominant aptamer, designated as SSRA1, against the B-chain of ricin. SSRA1 displays one folding conformation that is stable across 4-63 °C (ΔG = -5.05). SSRA1 is able to concentrate at least 30 ng mL(-1) of ricin B chain from several liquid food matrices and outcompetes a currently available ELISA kit and ricin aptamer. Furthermore, we show detection of 25 ng mL(-1) of intact ricin A-B complex using SSRA1 combined with surface enhanced Raman scattering technique. Thus, SSRA1 would serve well as pre-analytical tool for processing of ricin from liquid foods to aid current diagnostics as well as a sensor for direct ricin detection.     

A label-free electrochemical biosensor based on a DNA aptamer against codeine

In order to develop a sensor for opium alkaloid codeine detection, DNA aptamers against codeine were generated by SELEX (systematic evolution of ligands by exponential enrichment) technique. An aptamer HL7-14, which is a 37-mer sequence with K_d values of 0.91 μM, was optimized by the truncation-mutation assay. The specificity investigation shows that HL7-14 exhibits high specificity to codeine over morphine, and almost cannot bind to other small molecule. With this new selected aptamer, a novel electrochemical label-free codeine aptamer biosensor based on Au-mesoporous silica nanoparticles (Au-MSN) as immobilized substrate has been proposed using [Fe(CN)₆]^3−/4− as electroactive redox probe. The linear range covered from 10 pM to 100 nM with correlation coefficient of 0.9979 and the detection limit was 3 pM. Our study demonstrates that the biosensor has good specificity, stability and well regeneration. It can be used to detect codeine.     

A DNA aptamer as a new target-specific chiral selector for HPLC

In this paper, a DNA aptamer, known to bind stereospecifically the D-enantiomer of an oligopeptide, i.e., arginine-vasopressin, was immobilized on a chromatographic support. The influence of various parameters (such as column temperature, eluent pH, and salt concentration) on the L- and D-peptide retention was investigated in order to provide information about the binding mechanism and then to define the utilization conditions of the aptamer column. The results suggest that dehydration at the binding interface, charge-charge interactions, and adaptive conformational transitions contribute to the specific D-peptide-aptamer complex formation. A very significant enantioselectivity was obtained in the optimal binding conditions, the D-peptide being strongly retained by the column while the L-peptide eluted in the void volume. A rapid baseline separation of peptide enantiomers was also achieved by modulating the elution conditions. Furthermore, it was established that the aptamer column was stable during an extended period of time. This work indicates that DNA aptamers, specifically selected against an enantiomer, could soon become very attractive as new target-specific chiral selectors for HPLC.     

A label-free electrochemical RNA aptamer for selective detection of theophylline

In this work, we report a novel electrochemical RNA aptamer for the selective detection of theophylline. Firstly, gold nanoparticles were electrodeposited on the surface of glassy carbon (GC) electrode to form a gold nanoparticles modified electrode. Secondly, the designed single-stranded RNA (ssRNA) was immobilized on gold nanoparticles through a thiol linker as a probe RNA. Then, the complement stranded RNA, which can combine with the probe ssRNA to form a double-stranded RNA (dsRNA) with a recognition unit of theophylline, was linked on the probe RNA through a hybrid reaction in the presence of theophylline. Doxorubicin was selected as an electrochemical indicator. The proposed RNA aptamer presents an excellent selectivity for the detection of theophylline. The detectable concentration range of theophylline is from 2.0 to 50.0 μM with a limit of detection of 1.2 μM.     

A gold nanoparticle based approach for screening triplex DNA binders

Nanoparticle assemblies interconnected with DNA triple helixes can be used to colorimetrically screen for triplex DNA binding molecules and simultaneously determine their relative binding affinities based on melting temperatures. Nanoparticles assemble only when DNA triple helixes form between DNA from two different particles and a third strand of free DNA. In addition, the triple helix structure is unstable at room temperature and only forms in the presence of triplex DNA binding molecules which stabilize the triple helix. The resulting melting transition of the nanoparticle assembly is much sharper and at a significantly higher Tm than the analogous triplex structure without nanoparticles. Upon nanoparticle assembly, a concomitant red-to-blue color change occurs. The assembly process and color change do not occur in the presence of duplex DNA binders and therefore provide a significantly better screening process for triplex DNA binding molecules compared to standard methods.     

Formation and stability of a Janus-Wedge type of DNA triplex

A new type of DNA targeting with the formation of a Janus-Wedge (J-W) triple helix is described. The "wedge" residue (W) attached to a PNA backbone is designed to insert itself into double-stranded DNA and base pair with both Watson-Crick faces. To study the stability of such an assembly, we have examined the formation of the J-W triplex with dC8 - T8 target sequence. The use of this target sequence permits the study of this new helix form without competing Watson-Crick interactions between the two target residues. Studies indicate that the W strand binds to both target strands, with defined polarity and a stability (-15.2 kcal/mol) that is roughly the sum of the two independent duplex interactions.     

ATP detection using a label-free DNA aptamer and a cationic tetrahedralfluorene

A simple and sensitive method for ATP detection using a label-free DNA aptamer as the recognition element and ethidium bromide (EB) as the signal reporter is reported. The ATP-binding aptamer undergoes a conformational switch from the aptamer duplex to the aptamer/target complex upon target binding, which induces the fluorescence change of intercalated EB emission. Good selectivity between ATP and CTP, GTP or UTP has been demonstrated, which is due to the specific recognition between the ATP aptamer and ATP. Using EB alone as a signal reporter, the ATP detection limit was estimated to be approximately 0.2 mM. When a light harvesting cationic tetrahedralfluorene was used as an energy donor to sensitize the intercalated EB emission, a 10-fold increase in detection limit and a 2-fold increase in detection selectivity was demonstrated. The sensitivity and selectivity of the tetrahedralfluorene sensitized assay is comparable to or better than most fluorescent ATP assays with multiple labels.     

A selective supramolecular photochemical sensor for dopamine

Dopamine (DA) is an important biomarker for diseases and biological disorders. Existing techniques for DA detection suffer from drawbacks including low sensitivity and selectivity as well as interfering signals from non-target molecules. A simple and selective photochemical sensor for the determination of DA in a supramolecular manner is presented. This approach utilises the complexation properties of a highly fluorescent water-soluble complex of perylene bis(diimide) dye with the macrocyclic host cucurbit[8]uril. The method can be used for the determination of DA in aqueous media, with detection limits below 2 × 10^? 5 M, even in the presence of known interferents including ascorbic acid and the catecholamines epinephrine and norepinepherine.     

Characterization and application of a DNA aptamer binding to L-tryptophan

DNA aptamers for specific recognition of L-tryptophan have been evolved by a SELEX (systematic evolution of ligands by exponential enrichment) technique. Truncation-mutation experiments suggest that a 34-mer sequence, Trp3a-1, possesses the strongest binding ability to L-tryptophan. Trp3a-1 is predicted to adopt a loop-stem secondary structure, in which the loop may further fold into a binding pocket for L-tryptophan with the help of the stem. The specificity investigation shows that Trp3a-1 strongly binds to L-tryptophan, has almost no binding to other amino acids, and weakly binds to some tryptophan analogs and peptides containing the L-tryptophan residue. The binding of Trp3a-1 to L-tryptophan is mainly contributed to by hydrogen bonds and precise stacking formed between the binding pocket of Trp3a-1 and all groups on L-tryptophan. This aptamer has also been proved to be an effective ligand for the chiral separation of D/L-tryptophan. L-tryptophan and its derivatives are known to play important biological roles; this aptamer ligand could be used as a tool for the analysis of tryptophan and other related studies.     

Isolation of a fluorophore-specific DNA aptamer with weak redox activity

Background: In vitro selection experiments with pools of random-sequence nucleic acids have been used extensively to isolate molecules capable of binding specific ligands and catalyzing self-modification reactions.Results: In vitro selection from a random pool of single-stranded DNAs has been used to isolate molecules capable of recognizing the fluorophore sulforhodamine B with high affinity. When assayed for the ability to promote an oxidation reaction using the reduced form of a related fluorophore, dihydrotetramethylrosamine, a number of selected clones show low levels of catalytic activity. Chemical modification and site-directed mutagenesis experiments have been used to probe the structural requirements for fluorophore binding. The aptamer recognizes its ligand with relatively high affinity and is also capable of binding related molecules that share extended aromatic rings and negatively charged functional groups.Conclusions: A guanosine-rich single-stranded DNA is capable of binding fluorophores with relatively high affinity and of weakly promoting a multiple-turnover reaction. A simple motif consisting of a three-tiered G-quartet stacked upon a standard Watson-Crick duplex appears to be responsible for this activity. The corresponding sequence might provide a useful starting point for the evolution of novel, improved deoxyribozymes that generate fluorescent signals by promoting multiple-turnover reactions.     

A highly selective fluorescent sensor for distinguishing cadmium from zinc ions based on a quinoline platform

A fluorescent sensor, N-(quinolin-8-yl)-2-(quinolin-8-yloxy)acetamide (HL), based on 8-aminoquinoline and 8-hydroxyquinoline platforms has been synthesized. This sensor displays high selectivity and sensitive fluorescence enhancement to Cd(2+) in ethanol. Moreover, sensor HL can distinguish Cd(2+) from Zn(2+) via two different sensing mechanisms (photoinduced electron transfer for Cd(2+); internal charge transfer for Zn(2+)). The composition of the complex Cd(2+)/HL or Zn(2+)/L(-) has been found to be 1:1, based on the fluorescence/absorption titration and further confirmed by X-ray crystallography.     

金属有机骨架衍生 Ni基材料催化烷烃选择氧化

N掺杂碳基纳米材料由于具有高稳定性、良好的导电性、较大的孔体积和比表面积等特点而受到了国内外广泛的关注,在气体吸附、催化、电化学以及燃料电池等许多领域表现出潜在应用价值. N掺杂碳材料的制备主要采用两种方法,即后合成法和原位合成法.后合成法是指采用含 N化合物(如尿素等)对已合成的碳材料进行处理,但所制材料中 N含量往往偏低,且 N活性位不够稳定.要得到 N含量较高且稳定的 N掺杂碳材料常常采用原位合成法,即以富氮前体作为模板,在热解过程中 N原位嵌入碳纳米材料中,因而具有结构稳定, N含量丰富等优点.
　　金属有机骨架(MOFs)材料是一种新型的类沸石类多孔材料,是由金属离子和有机配体通过配位键键合而成的拓扑结构.该类材料具有较高的孔隙率和比表面积以及结构可调控性等特点.通过调节金属中心和配体种类,引入含 N配体,可以得到不同类型的含 N的 MOFs.此外,含 N的 MOFs在一定温度下热解能有效减少 N元素的流失,因此, MOFs是一类优秀的用于制备 N掺杂碳基纳米材料的模板材料.近年来,以含 N的金属有机骨架材料为模板,通过简单热解一步合成 N掺杂碳基纳米催化剂,已成为国内外研究的热点之一.
　　本文在惰性气氛中采用直接热解 Ni基 MOF方法制备了 N掺杂 C包裹的 Ni纳米颗粒,并利用 X射线粉末衍射(PXRD)、N2吸附脱附、扫描电子显微镜(SEM)、透射电子显微镜(TEM)、原子吸收光谱(AAS)、X射线光电子能谱(XPS)等对该复合材料的组成和结构进行了表征.
　　 PXRD测试结果表明,经过热解,催化剂中出现了大量的金属 Ni粒子,说明 Ni-MOF中的 Ni2+离子在热解过程中被原位还原成了 Ni纳米颗粒. N2吸附脱附结果表明,热解前的 Ni-MOF结构中只存在微孔结构,但是热解 Ni@C-N材料中生成了大量的介孔或大孔结构,从而有利于反应底物与催化剂活性位点的接触. SEM结果表明,在较低的温度下热解,催化剂可以保持 MOFs原来的构型,且结构疏松多孔;而在较高的温度下热解,如800oC,将有大量的碳纳米管生成. TEM结果表明,随着热解温度升高,催化剂中 Ni纳米颗粒逐渐增大.从 HRTEM测试结果可以清晰看出,高温热解时有石墨烯结构生成,并且生成的 Ni纳米颗粒原位嵌入了石墨烯结构中,因而有利于 Ni纳米颗粒的分散,从而提高催化剂的活性. XPS结果进一步证明,热解过程中, Ni2+被原位还原成了零价的 Ni纳米粒子,此外, N 1s谱图也进一步证明 N在热解过程中原位嵌入了生成的石墨烯结构中.
　　随后,以乙基苯选择性氧化为模型反应,测试了 Ni@C-N材料的催化活性.结果表明,该材料在烷烃选择氧化反应中表现出很高的催化活性和选择性,尤其是 Ni@C-N-900-8h,在温和的反应条件下,可有效催化一系列饱和烷烃的选择氧化,获得很高的氧化产物收率,且重复利用多次后其活性和选择性没有明显的下降.     

A label-free DNA reduced graphene oxide-based fluorescent sensor for highly sensitive and selective detection of hemin

G-quadruplex structure aptamer (PS2.M) can capture acridine orange (AO) from reduced graphene oxide (rGO). When the AO-PS2.M/rGO mixture is incubated with hemin, the specific binding of hemin with PS2.M results in a release of AO from PS2.M and return of AO back to rGO. Based on the quenching of fluorescence, the target hemin was detected sensitively and selectively, giving a detection limit of 50 nM.     

A solid-state electrochemiluminescence sensing platform for detection of adenosine based on ferrocene-labeled structure-switching signaling aptamer

A solid-state electrochemiluminescence sensing platform based on ferrocene-labeled structure-switching signaling aptamer (Fc-aptamer) for highly sensitive detection of small molecules is developed successfully using adenosine as a model analyte. Such special sensing platform included two main parts, an electrochemiluminescence (ECL) substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Au nanoparticle and Ruthenium (II) tris-(bipyridine) (Ru(bpy)₃²⁺-AuNPs) onto Au electrode. An anti-adenosine aptamer labeled by ferrocene acted as the ECL intensity switch. A short complementary ssDNA for the aptamer was applied to hybridizing with the aptamer, yielding a double-stranded complex of the aptamer and the ssDNA on the electrode surface. The introduction of adenosine triggered structure switching of the aptamer. As a result, the ssDNA was forced to dissociate from the sensing platform. Such structural change of the aptamer resulted in an obvious ECL intensity decrease due to the increased quenching effect of Fc to the ECL substrate. The analytic results were sensitive and specific.     

A new highly selective fluorescent K+ sensor

We describe the synthesis, properties, and application of a new fluorescent potassium chemosensor, KS2, for K(+) sensing and imaging in live cells. By virtue of a strong electron-withdrawing group, 2-dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofuran (TCF), with a triazacryptand ligand, the new sensor can respond to K(+) up to 1.6 M. This is the first highly selective intracellular sensor suitable for sensing K(+) over a broad and high concentration range. Confocal fluorescence microscopy has established the utility of KS2 for live-cell K(+) detection. The application of KS2 combined with other sensors will be of great benefit for investigating cellular metabolism, detecting and diagnosing diseases including cancer, and monitoring responses to therapy.     

DNA aptamer folding on gold nanoparticles: from colloid chemistry to biosensors

We have investigated the effect of the folding of DNA aptamers on the colloidal stability of gold nanoparticles (AuNPs) to which an aptamer is tethered. On the basis of the studies of two different aptamers (adenosine aptamer and K+ aptamer), we discovered a unique colloidal stabilization effect associated with aptamer folding: AuNPs to which folded aptamer structures are attached are more stable toward salt-induced aggregation than those tethered to unfolded aptamers. This colloidal stabilization effect is more significant when a DNA spacer was incorporated between AuNP and the aptamer or when lower aptamer surface graft densities were used. The conformation that aptamers adopt on the surface appears to be a key factor that determines the relative stability of different AuNPs. Dynamic light scattering experiments revealed that the sizes of AuNPs modified with folded aptamers were larger than those of AuNPs modified with unfolded (but largely collapsed) aptamers in salt solution. From both the electrostatic and steric stabilization points of view, the folded aptamers that are more extended from the surface have a higher stabilization effect on AuNP than the unfolded aptamers. On the basis of this unique phenomenon, colorimetric biosensors have been developed for the detection of adenosine, K+, adenosine deaminase, and its inhibitors. Moreover, distinct AuNP aggregation and redispersion stages can be readily operated by controlling aptamer folding and unfolding states with the addition of adenosine and adenosine deaminase.