Enantioselective aptameric molecular recognition material: Design of a novel chiral stationary phase for enantioseparation of a series of chiral herbicides by capillary electrochromatography

Stereoselective RNA reaction with chiral 2'-OH acylating agents

The reactivity of RNA 2'-OH groups with acylating agents has recently been investigated for high-yield conjugation of RNA strands. To date, only achiral molecules have been studied for this reaction, despite the complex chiral structure of RNA. Here we prepare a set of chiral acylimidazoles and study their stereoselectivity in RNA reactions. Reactions performed with unfolded and folded RNAs reveal that positional selectivity and reactivity vary widely with local RNA macro-chirality. We further document remarkable effects of chirality on reagent reactivity, identifying an asymmetric reagent with 1000-fold greater reactivity than prior achiral reagents. In addition, we identify a chiral compound with higher RNA structural selectivity than any previously reported RNA-mapping species. Further, azide-containing homologs of a chiral dimethylalanine reagent were synthesized and applied to local RNA labeling, displaying 92% yield and 16 : 1 diastereoselectivity. The results establish that reagent stereochemistry and chiral RNA structure are critical elements of small molecule-RNA reactions, and demonstrate new chemical strategies for selective RNA modification and probing.

Preparative separation of enantiomers based on functional nucleic acids modified gold nanoparticles

The preparative-scale separation of chiral compounds is vitally important for the pharmaceutical industry and related fields. Herein we report a simple approach for rapid preparative separation of enantiomers using functional nucleic acids modified gold nanoparticles (AuNPs). The separation of DL-tryptophan (DL-Trp) is demonstrated as an example to show the feasibility of the approach. AuNPs modified with enantioselective aptamers were added into a racemic mixture of DL -Trp. The aptamer-specific enantiomer (L-Trp) binds to the AuNPs surface through aptamer-L-Trp interaction. The separation of DL-Trp is then simply accomplished by centrifugation: the precipitate containing L-Trp bounded AuNPs is separated from the solution, while the D-Trp remains in the supernatant. The precipitate is then redispersed in water. The aptamer is denatured under 95 °C and a second centrifugation is then performed, resulting in the separation of AuNPs and L-Trp. The supernatant is finally collected to obtain pure L-Trp in water. The results show that the racemic mixture of DL-Trp is completely separated into D-Trp and L-Trp, respectively, after 5 rounds of repeated addition of fresh aptamer-modified AuNPs to the DL-Trp mixture solution. Additionally, the aptamer-modified AuNPs can be repeatedly used for at least eight times without significant loss of its binding ability because the aptamer can be easily denatured and renatured in relatively mild conditions. The proposed approach could be scaled up and extended to the separation of other enantiomers by the adoption of other enantioselective aptamers.

Chiral recognition in separation science: an overview

Chiral recognition phenomena play an important role in nature as well as analytical separation sciences. In separation sciences such as chromatography and capillary electrophoresis, enantiospecific interactions between the enantiomers of an analyte and the chiral selector are required in order to observe enantioseparations. Due to the large structural variety of chiral selectors applied, different mechanisms and structural features contribute to the chiral recognition process. This chapter briefly illustrates the current models of the enantiospecific recognition on the structural basics of various chiral selectors.

Enantioselective and label-free detection of oligopeptide via fluorescent indicator displacement

In this work, a simple and label-free fluorescent method via fluorescent indicator displacement (FID) was proposed for enantioselectively determining d-enantiomer of arginine vasopressin (DV) using DV-specific DNA aptamer (V-apt) and one guanidiniophthalocyanine dye (Zn-DIGP). Zn-DIGP that preferentially binds to single-stranded DNA with fluorescence enhancement rather than duplexes occupies the long internal loop of V-apt and generates intensive fluorescence. Then DV is introduced into the solution containing Zn-DIGP and V-apt, and displaces the Zn-DIGP from the binding site of internal loop, leading to fluorescence decrease. But l-enantiomer cannot induce any fluorescence change due to the selectivity of V-apt. This established FID technique can detect DV with a detection limit of 100 nM and exhibits a broad linear range, and is able to discriminate enantiomers of arginine vasopressin unambiguously. Moreover chiral separation by chromatography, complicated experimental procedures and covalent modification of tags (such as organic dyes, redox-active metal complexes) are avoided in our strategy. This simple and label-free method is promising for fabricating diverse aptasensors to determine other biomolecules and drugs.

Enantioselective capillary electrochromatography: recent developments and new trends

Since its development in the early 1970s, CEC has been studied quite extensively, but unfortunately its use is still mostly located at an academic level. Reasons for this are the limited availability of commercially available stationary phases (SPs) and columns, along with some practical limitations, such as column fragility, lack of column robustness and reproducibility. Nevertheless, CEC maintains a place among the separation techniques, probably because of its unique feature to combine two separation principles. Also in the field of chiral separations, CEC is often used as a separation technique and already showed its potential for this kind of analyses. This overview will focus on the recent applications, i.e. between 2006 and 2010, in enantioselective analysis by means of CEC. For the selected applications, the used SPs (chiral selectors) and their potential for future method development or screening purposes will be evaluated and critically discussed.

A mirror-image tetramolecular DNA quadruplex

L-DNA, the mirror image of natural DNA forms structures of opposite chirality. We demonstrate here that a short guanine rich L-DNA strand forms a tetramolecular quadruplex with the same properties as a D-DNA strand of identical sequence, besides an inverted circular dichroism spectra. L- and D-strands self exclude when mixed together, showing that the controlled parallel self-assembly of different G-rich strands can be obtained through L-DNA use.

Recent advances of enantioseparations in capillary electrophoresis and capillary electrochromatography

A comprehensive survey of recent developments and applications of capillary electromigration techniques for enantioseparations from January 2006 to June 2010 is presented. The techniques include capillary electrophoresis, chip capillary electrophoresis and capillary electrochromatography. The separation principles and the chiral recognition mechanisms are discussed. Additionally, on-line preconcentrations in chiral capillary electrophoresis are also reviewed.

Microcalorimetrics studies of the thermodynamics and binding mechanism between L-tyrosinamide and aptamer

In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.

Recent accomplishments in the field of enantiomer separation by CEC

The present review intends to summarize recent developments in the field of enantioselective separations and analysis by CEC. It covers studies published in English language in common peer-reviewed journals within the period between 2003 and 2006. Both, methods making use of chiral mobile phase additives as well as chiral stationary phases for electrochromatographic enantiomer separations, are reviewed. Achievements that have been made on the various column technologies, such as open-tubular, particle-packed, inorganic, organic and particle-fixed (hybrid-type) monolithic as well as molecularly imprinted polymer phases, are discussed.

SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands

SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.

Fluid dynamics in capillary and chip electrochromatography

This review is concerned with the phenomenological fluid dynamics in capillary and chip electrochromatography (EC) using high-surface-area random porous media as stationary phases. Specifically, the pore space morphology of packed beds and monoliths is analyzed with respect to the nonuniformity of local and macroscopic EOF, as well as the achievable separation efficiency. It is first pointed out that the pore-level velocity profile of EOF through packed beds and monoliths is generally nonuniform. This contrasts with the plug-like EOF profile in a single homogeneous channel and is caused by a nonuniform distribution of the local electrical field strength in porous media due to the continuously converging and diverging pores. Wall effects of geometrical and electrokinetic nature form another origin for EOF nonuniformities in packed beds which are caused by packing hard particles against a hard wall with different zeta potential. The influence of the resulting, systematic porosity fluctuations close to the confining wall over a distance of a few particle diameters becomes aggravated at low column-to-particle diameter ratio. Due to the hierarchical structure of the pore space in packed beds and silica-based monoliths which are characterized by discrete intraparticle (intraskeleton) mesoporous and interparticle (interskeleton) macroporous spatial domains, charge-selective transport prevails within the porous particles and the monolith skeleton under most general conditions. It forms the basis for electrical field-induced concentration polarization (CP). Simultaneously, a finite and -- depending on morphology -- often significant perfusive EOF is realized in these hierarchically structured materials. The data collected in this review show that the existence of CP and its relative intensity compared to perfusive EOF form fundamental ingredients which tune the fluid dynamics in EC employing monoliths and packed beds as stationary phases. This addresses the (electro)hydrodynamics, associated hydrodynamic dispersion, as well as the migration and retention of charged analytes.