Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands - d(G(4)T(4)G(4)), d(G(3)T(4)G(4)), d(G(3)T(4)G(3)), and d(G(4)T(4)G(3)) - have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH4+ in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d(G(3)T(4)G(3)) and d(G(4)T(4)G(3)) are unstable, being converted into trimolecular and tetramolecular structures with increasing concentrations of NH4+ in the solution. Circular dichroism (CD) spectra reveal structural changes during the process of strand stoichiometric transitions, in which the relative orientation of strands in the quadruplexes changes from an antiparallel to a parallel arrangement. Such changes were observed for the strand d(G(4)T(4)G(3)), but not for the strand d(G(3)T(4)G(3)). The present work provides a significant insight into the formation of various DNA quadruplexes, especially the higher-order species.

Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

Single-walled carbon nanotubes binding to human telomeric i-motif DNA: significant acceleration of S1 nuclease cleavage rate

Single-walled carbon nanotubes (SWNTs) binding to human telomeric i-motif DNA can significantly accelerate S1 nuclease cleavage rate by increasing the enzyme turnover number.

Interactions of the human telomeric DNA with terbium-amino acid complexes

The human telomeric DNA can form four-stranded structures: the G-rich strand adopts a G-quadruplex conformation stabilized by G-quartets and the C-rich strand may fold into an I-motif based on intercalated C (.) C+ base pairs. There is intense interests in the design and synthesis of compounds which can target telomeric DNA and inhibit the telomerase activity. Here we report the thermodynamic studies of the two newly synthesized terbium-amino acid complexes bound to the human telomeric G-quadruplex and I-motif DNA which were studied by means of UV-Visible, DNA meltings, fluorescence and circular dichroism. These two complexes can bind to the human telomeric DNA and have shown different features on DNA stability, binding stoichiometry, and sequence-dependent fluorescence enhancement. To our knowledge, this is the first report to show terbium-amino acid complexes can interact with the human telomeric DNA.

Nano-reactors for controlling the selectivity of the free radical grafting of maleic anhydride onto polypropylene in the melt

This paper reports on a successful application of the concept of nanoreactors to effectively controlling the selectivity of the free radical grafting of maleic anhydride (MAH) onto polypropylene (PP) in the melt, an industrially relevant process. More specifically, a free radical initiator of type ROOR was first confined into (or encapsulated by) the galleries of an organically modified montmorillonite (o-MMT) whose interdistance was 2.4 nm. Primary free radicals (RO center dot) formed inside the o-MMT galleries had to diffuse out before they could react with the PP backbone. The controlled release of the primary free radicals significantly increased the grafting degree of MAH onto PP and greatly reduced the level of the chain scission of the latter. Those results were better understood by electron spin resonance studies on model systems and by Monte Carlo simulations.

Neodymium oxide-assisted melt free-radical grafting of maleic anhydride on isotactic-polypropylene by reactive extrusion

Rare earth oxide, neodymium oxide (Nd2O3), -assisted melt free-radical grafting of maleic anhydride (MAH) on isotactic-polypropylene (i-PP) was carried out by reactive extrusion. The experimental results reveal that the addition of Nd2O3 into reactive system leads to an enhancement of the grafting degree of MAH, along with an elevated degradation of i-PP matrix. When Nd2O3 content is 4.5 mmol %, the increment of the grafting degree of MAH (maximally) is up to about 30% compared with that of the related system without adding Nd2O3, while the severest degradation of i-PP matrix simultaneously occurs. On the basis of the reaction mechanism of PP-g-MAH proposed before, the sequence of beta-scission and grafting reaction is discussed in detail. It is found that, for the reactive system studied, most tertiary macroradicals first undergo beta-scission, and then, grafting reaction with MAH takes place at the new radical chain ends. The imported Nd2O3 has no effect on the aforementioned reaction mechanism, whereas it enhances the initiating efficiency of the initiator, dicumyl peroxide (DCP).

Thermal degradation kinetics of uncapped and end-capped poly(propylene carbonate)

In order to improve its thermal stability, poly(propylene carbonate)(PPC) was end-capped by different active agents. Thermogravimetric data show that the degradation temperature of uncapped PPC was lower than that of end-capped PPC. The kinetic parameters of thermal degradation of uncapped and end-capped PPC were calculated according to Chang's method. The results show that different mechanisms operate during the whole degradation temperature range for uncapped PPC. In the first stage, chain unzipping dominates the degradation. With increasing temperature, competing multi-step reactions occur. In the last stage, random chain scission plays an important role in degradation. For end-capped PPC, random chain scission dominates the whole degradation process.

Monte Carlo simulation of the grafting of maleic anhydride onto polypropylene at higher temperature

The graft of maleic anhydride (MAH) onto isotactic polypropylene (iPP) initiated by dicumyl peroxide (DCP) at 190 degreesC was studied by means of the Monte Carlo method. The ceiling temperature theory, i.e., no possibility for the homopolymerization of MA-H to occur at higher temperatures, was used in this study. The simulation results show that most MAH monomers were grafted onto the radical chain ends arising from beta scission at a lower MAH concentration, whereas the amount of MAH monomers attached to the tertiary carbons was much larger than that grafted onto the radical chain ends at a higher MAH concentration for various DCP concentrations. This conclusion gives a good interpretation for the disagreement on the grafting sites along a PP chain. Moreover, it was found that the grafting degree increased considerably up to a peak value; thereafter, it decreased continuously with increasing MA-H concentration. The peak shifted in the lower MAH concentration direction and became lower and lower with increasing DCP concentration. When the DCP concentration was below 0.1 wt %, the peak was hardly observed. Those results are in good agreement with the experiments.

Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation

The conformational transition of DNA induced by the interaction between DNA and a cationic lipid vesicle, didodecyidimethylammonium bromide (DDAB), had been investigated by circular dichroism (CD) and UV spectroscopy methods. We used singular value decomposition least squares method (SVDLS) to analyze the experimental CD spectra. Although pH value influenced the conformation of DNA in solution, the results showed that upon binding to double helical DNA, positively charged liposomes induced a conformational transition of DNA molecules from the native B-form to more compact conformations. At the same time, no obvious conformational changes occurred at single-strand DNA (ssDNA). While the cationic lipid vesicles and double-strand DNA (dsDNA) were mixed at a high molar ratio of DDAB vesicles to dsDNA, the conformation of dsDNA transformed from the B-form to the C-form resulting in an increase in duplex stability (DeltaT(m) = 8 +/- 0.4 degreesC). An increasing in T-m was also observed while the cationic lipid vesicles interacted with ssDNA.

The kinetics of the thermal decomposition of poly(3-hydroxybutyrate) and maleated poly(3-hydroxybutyrate)

The thermal decomposition mechanism of maleated poly(3-hydroxybutyrate) (PHB) was investigated by FTIR and H-1 NMR. The results of experiments showed that the random chain scission of maleated PHB obeyed the six-membered ring ester decomposition process. The thermal decomposition behavior of PHB and maleated PHB with different graft degree were studied by thermogravimetry (TGA) using various heating-up rates. The thermal stability of maleated PHB was evidently better than that of PHB. With increase in graft degree, the thermal decomposition temperature of maleated PHB gradually increased and then declined. Activation energy E. as a kinetic parameter of thermal decomposition was estimated by the Flynn-Wall-Ozawa and Kissinger methods, respectively. It could be seen that approximately equal values of activation energy were obtained by both methods.

Functionalization of isotactic polypropylene with maleic anhydride by reactive extrusion: mechanism of melt grafting

In this work, chemical structures and molecular parameters of grafted materials of PP-g-MAH prepared by melt reactive extrusion were studied by using electrospray ionization-mass spectrometer and gel permeation chromatography. It was found that the initial radicals, due to homolitic scission of dicumyl peroxide could be combined with maleic anhydride (MAH) monomers as well as polypropylene (PP) molecular chains. The homopolymerization of MAH cannot occur and the MAH radicals undergo a dismutational reaction under the processing condition (180-190 degreesC). A modified mechanism of melt grafting MAH onto PP has been proposed tentatively on the basis of our experimental results and other experimental findings published in the literature. (C) 2001 Elsevier Science Ltd. All rights reserved.

Cleavage of nucleotides by Ce4+ and the lanthanide metal complexes

The cleavage of adenosine-5'-monophosphate (5'-AMP) and guanosine-5'-monophosphate (S-GMP) by Ce4+ and lanthanide complex of 2-carboxyethylgermanium sesquioxide (Ge-132) in acidic and near neutral conditions was investigated by NMR, HPLC and measuring the liberated inorganic phosphate at 37 degrees C and 50 degrees C, The results showed that 5'-GMP and 5'-AMP was converted to guanine (G), 5'-monophosphate (depurination of 5'-GMP), ribose (depurination and dephosphorylation of 5'-GMP), phosphate and adenine (A), 5'-monophosphate (depurination of 5'-AMP), ribose (depurination and dephosphorylation of 5'-AMP), phosphate respectively by Ce4+. In presence of lanthanide complexes, 5'-GMP and 5'-AMP were converted to guanosine (Guo) and phosphate and adenosine (Ado) and phosphate respectively. The mechanism of cleaving 5'-GMP and 5'-AMP is hydrolytic scission.

Determination of the secondary structure of the king cobra neurotoxin CM-11

The king cobra neuotoxin CM-11 is a small protein with 72 amino acid residues. After its complete assignments of H-1-NMR resonance's were obtained using various 2D-NMR technologies, including of DQF-COSY, clean-TOCSY AND NOESY, the secondary structure was analysed by studying the various NOEs extracted from the NOESY spectra and the distribution of chemical shifts. The secondary structure was finally determined by MCD as follows: a triple-strand antiparallel beta sheet with I20-W36, R37-A43 and V53--S59 as its beta strands, a short alpha helix formed by W30-G35 and four turns formed by P7-K10, C14-G17, K50-V53 and D61-N64.

WAXD and SAXS study on gamma-radiation damage to polyamide-1010 crystal structure

In the present work we attempt to settle the controversy on the district wherein the radiation induced reaction preferentially occurs through examining the structural changes of the irradiated polyamide-1010 specimens on both the crystallographic and the supermolecular level by using WAXD and SAXS techniques. Experimental results indicated that the chain crosslinking and scission of the irradiated specimens occur mainly in the amorphous region and on the crystal surface (or interphase), and extend into the inner portion of the crystal with increasing radiation dose.