SERS opens a new way in aptasensor for protein recognition with high sensitivity and selectivity

SERS aptasensors for protein recognition based on Au nanoparticles labeled with aptamers and Raman reporters have been developed, which opens a new way for protein recognition of high sensitivity and selectivity.

CE with electrochemical detection for investigation of label-free recognition of amino acid amides by guanine-rich DNA aptamers

In this work, we report a simple and effective investigation into adaptive interactions between guanine-rich DNA aptamers and amino acid amides by CE with electrochemical (EC) detection. Argininamide (Arm) and tyrosinamide (Tym) were chosen as model molecules. On a copper electrode, Arm generated a good EC signal in 60 mM NaOH at 0.7 V (vs Ag/ AgCl), while Tym. was detected well on a platinum electrode at 1. 3 V in 20 mM phosphate of pH 7.0. Based on their EC properties, the ligands themselves were used as indicators for the adaptive interactions investigated by CE-EC, making any step of labeling and/or modification of aptamers with indicators exempted. Hydrophilic ionic liquid was used as an additive in running buffer of CE to improve the sensitivity of Arm detection, whereas the additive was not used for Tym. detection due to its negative effect. Two guanine-rich DNA aptamers were used for molecular recognition of Arm and Tym. When the aptamers were incubated with ligands, they bound the model molecules with high affinity and specificity, reflected by obvious decreases in the signals of ligands but no changes in those of the control molecules. However, the ligands were hardly affected by the control ssDNAs after incubation. The results revealed the specific recognition of Arm and Tym. by the aptamers.

Aptamer-based label-free method for hemin recognition and DNA assay by capillary electrophoresis with chemiluminescence detection

An aptamer-based label-free approach to hemin recognition and DNA assay using capillary electrophoresis with chemiluminescence detection is introduced here. Two guanine-rich DNA aptamers were used as the recognition element and target DNA, respectively. In the presence of potassium ions, the two aptamers folded into the G-quartet structures, binding hemin with high specificity and affinity. Based on the G-quartet-hemin interactions, the ligand molecule was specifically recognized with a K (d)approximate to 73 nM, and the target DNA could be detected at 0.1 mu M. In phosphate buffer of pH 11.0, hemin catalyzed the H2O2-mediated oxidation of luminol to generate strong chemiluminescence signal; thus the target molecule itself served as an indicator for the molecule-aptamer interaction, which made the labeling and/or modification of aptamers or target molecules unnecessary. This label-free method for molecular recognition and DNA detection is therefore simple, easy, and effective.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Structural diversity of lanthanide-amino acid complexes under near physiological pH conditions and their recognition of single-stranded DNA

We reported here four structures of lanthanide-amino acid complexes obtained under near physiological pH conditions and their individual formula can be described as [Tb-2(DL-Cys)(4)(H2O)(8)]Cl-2 (1), [Eu-4(mu(3)-OH)(4)(L-Asp)(2)(L-HAsp)(3)(H2O)(7)] Cl center dot 11.5H(2)O (2), [Eu-8-(L-HVal) (16)(H2O)(32)]Cl-24 center dot 12.5H(2)O (3), and [Tb-2(DL-HVal)(4)(H2O)(8)]Cl-6 center dot 2H(2)O (4). These complexes showed diverse structures and have shown potential application in DNA detection. We studied the interactions of the complexes with five single-stranded DNA and found different fluorescence enhancement, binding affinity and binding stoichiometry when the complexes are bound to DNA.

NMR and pattern recognition studies on the acute biochemical effects of Lu(NO3)(3)

Pattern recognition methods were applied to the analysis of 600 MHz H-1 NMR spectra of urine from rats dosed with compounds that induced organ-specific damage in the liver and kidney. Male Wistar rats were separated into groups (n=4) and each was treated with one of following compounds: HgCl2, CCl4, Lu(NO3)(3) and Changle (a kind of rare earth complex mixed with La, Ce, Pr and Nd). Urine samples from the rats dosed with HgCl2, CCl4 and Lu(NO3)(3) were collected over a 24 h time course and the samples from the rats administrated with Changle were gained after 3 months. These samples were measured by 600 MHz NMR spectroscopy. Each spectrum was data-processed to provide 223 intensity-related descriptors of spectra. Urine spectral data corresponding to the time intervals, 0-8 h (HgCl2 and CCl4), 4-8 (Lu(NO3)(3)) h and 90 d (Changle) were analyzed using principal component analysis (PCA). Successful classification of the toxicity and biochemical effects of Lu(NO3)(3) was achieved.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Electrochemical recognition of alkali metal ions at the micro-water 1,2-dichloroethane interface using a calix[4]arene derivative

In this paper, a calix[4]arene derivative, 5,11,17,23-butyl-25,26,27,28-tetra-(ethanoxycarbonyl)-methoxy-calix[4]arene (L), is investigated as a host to recognize alkali metal ions (Li+, Na+, K+, Rb+ and Cs+) at the interface between two immiscible electrolyte solutions (ITIES). Well-defined cyclic voltammograms are obtained at the micro- and nano-water \ 1,2-dichloroethane (W \ DCE) interfaces supported at micro- and nano-pipets.

Aggregation behavior of amphiphilic D-pi-A molecules bearing recognition group

Aggregation behavior of two amphiphilic D-pi -A molecules bearing barbituric acid as both recogniton group and electron-drawing substituent, 5-(4-dodecyl oxybenzylidene)-(1H, 3H)-2,4,6-pyrimidine trione (PB12) and 5-(4-N,N-didodecyl aminobenzylidene)-(1H,3H)-2,4,6-pyrimidine trione (AB(12)) was studied by UV-visible, fluorescence, and surface voltaic spectroscopies (SPS). The experimental results indicate that PB12 tends to form J-aggregate and AB(12) tends to form H-aggregate under increasing concentration. An intramolecular twisted charge transfer (TICT) emission around 500 nm is observed when J-aggregate is formed between PB12 molecules, and an excimer emission around 600 nm is observed when H-aggregate is formed between AB(12) molecules.

SeGPX activity of three organoselenium-containing cyclodextrins and their scavenging effects on HO center dot

Three organoselenium-containing derivatives of beta-cyclodextrins (beta-CD), mono-6-benzylseleno-6-deoxy-beta-cyclodextrin (compound 1), 6,6'-trimethylenediseleno bridged beta-cyclodextrin dimer(compound 2) and 6,6'- (o-phenylene)diseleno bridged beta-cyclodextrin dimer (compound 3) functioned as mimics of selenium-containing glutathione peroxidase(SeGPX). Acting on H2O2 and GSH, the SeGPX activities of these compounds were 0.83-, 0.26-, and 1. 23-fold of that of Ebselen (0.99 U/mu mol), respectively. The relationship between the structure and the function of these compounds was studied. The results suggested that the hydrophobicity and rigidity of phenyl group is the main reason that accounted for the higher activity of compounds 3 and 1. Phenyl group not only provided the hydrophobic circumstance which is necessary for the catalytic function of selenium, but also make it possible that the cyclodextrin unit of compounds 1 and 3 combines the substrate with a more effective direction. Fluorometric techniques were utilized to determine the yields of the hydroxyl radical produced by Fenton reactions through the formation of hydroxy benzoic acids from benzoate. Compared with Ebselen which showed a significant inhibition effect on the formation of HO., these organoselenium-containing cyclodextrins showed a little scavenging effect on the formation of HO. throughout the whole process.