Enrichment of low abundance DNA/RNA by oligonucleotide-clicked iron oxide nanoparticles.

Detection of low abundance target DNA/RNA for clinical or research purposes is challenging because the target sequences can be hidden under a large background of human genomic or non-human metagenomic sequences. We describe a probe-based capture method to enrich for target sequences with DNA-clicked iron oxide nanoparticles. Our method was tested against commercial capture assays using streptavidin beads, on a set of probes derived from a common genotype of the hepatitis C virus. We showed that our method is more specific and sensitive, most likely due to the combination of an inert silica coating and a high density of DNA probes clicked to the nanoparticles. This facilitates target capture below the limits of detection for TaqMan qPCR, and we believe that this method has the potential to transform management of infectious diseases.

Biomining of MoS2 with Peptide-based Smart Biomaterials.

Biomining of valuable metals using a target specific approach promises increased purification yields and decreased cost. Target specificity can be implemented with proteins/peptides, the biological molecules, responsible from various structural and functional pathways in living organisms by virtue of their specific recognition abilities towards both organic and inorganic materials. Phage display libraries are used to identify peptide biomolecules capable of specifically recognizing and binding organic/inorganic materials of interest with high affinities. Using combinatorial approaches, these molecular recognition elements can be converted into smart hybrid biomaterials and harnessed for biotechnological applications. Herein, we used a commercially available phage-display library to identify peptides with specific binding affinity to molybdenite (MoS2) and used them to decorate magnetic NPs. These peptide-coupled NPs could capture MoS2 under a variety of environmental conditions. The same batch of NPs could be re-used multiple times to harvest MoS2, clearly suggesting that this hybrid material was robust and recyclable. The advantages of this smart hybrid biomaterial with respect to its MoS2-binding specificity, robust performance under environmentally challenging conditions and its recyclability suggests its potential application in harvesting MoS2 from tailing ponds and downstream mining processes.

Peptide-functionalized iron oxide magnetic nanoparticle for gold mining.

Here, we present our work on preparing a novel nanomaterial composed of inorganic binding peptides and magnetic nanoparticles for inorganic mining. Two previously selected and well-characterized gold-binding peptides from cell surface display, AuBP1 and AuBP2, were exploited. This nanomaterial (AuBP-MNP) was designed to fulfill the following two significant functions: the surface conjugated gold-binding peptide will recognize and selectively bind to gold, while the magnetic nano-sized core will respond and migrate according to the applied external magnetic field. This will allow the smart nanomaterial to mine an individual material (gold) from a pool of mixture, without excessive solvent extraction, filtration, and concentration steps. The working efficiency of AuBP-MNP was determined by showing a dramatic reduction of gold nanoparticle colloid concentration, monitored by spectroscopy. The binding kinetics of AuBP-MNP onto the gold surface was determined using surface plasmon resonance (SPR) spectroscopy, which exhibits around 100 times higher binding kinetics than peptides alone. The binding capacity of AuBP-MNP was demonstrated by a bench-top mining test with gold microparticles. Graphical abstract.

[Research of Straw Biomass Based on NIR by Wavelength Selection of IPLS-SPA].

The whole spectrum usually contains a lot of redundant information in the near-infrared spectroscopy model, the presence of redundant information will increase the model resolution time and increase the difficulty of parsing model, Therefore, how to select the characteristic wavelength quickly and effectly is very crucial. In this paper, we combined the algorithm based on SPA (successive projections algorithm ) with IPLS (interval partial least squares ) to selec the characteristic wavelength in the fermentation of wheat straw microbial biomass, A total of 85 samples prepared by measuring microbial biomass using glucosamine method, 68 samples are chosen as calibration set and 17 simples are chosen as verification set. First, the whole spectral region 520 points are segmented modeling according to the interval wavelength point size 10, 20, 30, 40 and 4 450~4 925 cm-1, 9 194~9 993 cm-1 two-band range are selected as the characteristic wavelength band, then pick out the new feature wavelength points by Successive Projections Algorithm band and Genetic Algorithm (GA), comprehensive analysis and comparison the result of model. The experimental results show that the using of IPLS-SPA algorithm to select the combination band 4 450~4 925 cm-1 & 9 194~9 993 cm-1 has the best modeling effect, compared with the modeling of whole spectrum, the wavelength points decrease from 520 to 10, the correction coefficient of determination R2 rised from 0. 884 9 to 0. 945 28, root mean square error (RMSE) dropped from 11. 104 9 to 8. 203 3, although the genetic algorithm model achieved the better accuracy, but the results are instable and have a strong randomness , while IPLS combined SPA method can select characteristic wavelength information stability and accurately, which can improve the model calculation speed and reduce the fitting difficulty of the model, it can be used as a new reference method for band selection. The results show that using near infrared spectroscopy method for straw biomass rapid detection is feasible.

[Rapid discriminating hogwash oil and edible vegetable oil using near infrared optical fiber spectrometer technique].

In the present study, a new method using near infrared spectroscopy combined with optical fiber sensing technology was applied to the analysis of hogwash oil in blended oil. The 50 samples were a blend of frying oil and "nine three" soybean oil according to a certain volume ratio. The near infrared transmission spectroscopies were collected and the quantitative analysis model of frying oil was established by partial least squares (PLS) and BP artificial neural network The coefficients of determina- tion of calibration sets were 0.908 and 0.934 respectively. The coefficients of determination of validation sets were 0.961 and 0.952, the root mean square error of calibrations (RMSEC) was 0.184 and 0.136, and the root mean square error of predictions (RMSEP) was all 0.111 6. They conform to the model application requirement. At the same time, frying oil and qualified edible oil were identified with the principal component analysis (PCA), and the accurate rate was 100%. The experiment proved that near infrared spectral technology not only can quickly and accurately identify hogwash oil, but also can quantitatively detect hog- wash oil. This method has a wide application prospect in the detection of oil.

Supramolecular isomerism of 2,2'-bipyrazine complexes with cis-(NH(3))(2)Pt(II): ligand rotational state and sequential orientation determine the 3D shape of metallacycles.

2,2'-Bipyrazine (2,2'-bpz) reacts with cis-(NH(3))(2)Pt(II) in water to give a variety of products, several of which were isolated and characterized by X-ray analysis: cis-[Pt(NH(3))(2)(2,2'-bpz-N4)(2)](NO(3))(2)·3H(2)O (1), [{cis-Pt(NH(3))(2)(2,2'-bpz-N4,N4')}(3)]-(PF(6))(5)NO(3)·7H(2)O (2a), [{cis-Pt(NH(3))(2)(2,2'-bpz-N4,N4')}(3)](BF(4))(2)-(SiF(6))(2)·15H(2)O (2b), and [{cis-Pt(NH(3))(2)(2,2'-bpz-N4,N4')}(4)]-(SO(4))(4)·22H(2)O (3). In 1, 2b, and 3 the 2,2'-bpz ligands adopt approximately C(2h) symmetries, hence the two pyrazine halves are in trans orientation, whereas in 2a all three 2,2'-bpz bridges are approximately C(2v) symmetric, with the pyrazine halves cis to each other. The topologies of the two triangular complexes 2a and 2b are consequently distinctly different, but nevertheless both cations act as hosts for anions. In 2a a PF(6)(-) and a NO(3)(-) anion are associated simultaneously with the +6 cation, whereas in 2b it is a BF(4)(-) anion and a water molecule, which are trapped in its cavity. There is no anion inclusion in case of the metallasquare 3. In principle, 3 can exist in a large number of stereoisomers, depending on the rotational states of the bridging 2,2'-bpz ligands. Isolation of a single rotamer form of 3 with C(2h) symmetric 2,2'-bpz ligands and an overall meso form is proposed to be a consequence of a highly efficient self-assembly process that starts from the precursor 1 and reaction with two cis-(NH(3))(2)Pt(II) units. This process leads to the isolated rotamer of 3 regardless of whether two cations 1 in head-head form react with two cis-(NH(3))(2)Pt(II), or whether the Δ enantiomer of the chiral head-tail form of 1 combines with its Λ enantiomer through two cis-(NH(3))(2)Pt(II) entities.

Pt(II) coordination to N1 of 9-methylguanine: why it facilitates binding of additional metal ions to the purine ring.

The preparation and X-ray crystal structure analysis of {trans-[Pt(MeNH(2))(2)(9-MeG-N1)(2)]}⋅{3 K(2)[Pt(CN)(4)]}⋅6 H(2)O (3 a) (with 9-MeG being the anion of 9-methylguanine, 9-MeGH) are reported. The title compound was obtained by treating [Pt(dien)(9-MeGH-N7)](2+) (1; dien=diethylenetriamine) with trans-[Pt(MeNH(2))(2)(H(2)O)(2)](2+) at pH 9.6, 60 °C, and subsequent removal of the [(dien)Pt(II)] entities by treatment with an excess amount of KCN, which converts the latter to [Pt(CN)(4)](2-). Cocrystallization of K(2)[Pt(CN)(4)] with trans-[Pt(MeNH(2))(2)(9-MeG-N1)(2)] is a consequence of the increase in basicity of the guanine ligand following its deprotonation and Pt coordination at N1. This increase in basicity is reflected in the pK(a) values of trans-[Pt(MeNH(2))(2)(9-MeGH-N1)(2)](2+) (4.4±0.1 and 3.3±0.4). The crystal structure of 3 a reveals rare (N7,O6 chelate) and unconventional (N2,C2,N3) binding patterns of K(+) to the guaninato ligands. DFT calculations confirm that K(+) binding to the sugar edge of guanine for a N1-platinated guanine anion is a realistic option, thus ruling against a simple packing effect in the solid-state structure of 3 a. The linkage isomer of 3 a, trans-[Pt(MeNH(2))(2)(9-MeG-N7)(2)] (6 a) has likewise been isolated, and its acid-base properties determined. Compound 6 a is more basic than 3 a by more than 4 log units. Binding of metal entities to the N7 positions of 9-MeG in 3 a has been studied in detail for [(NH(3))(3)Pt(II)], trans-[(NH(3))(2)Pt(II)], and [(en)Pd(II)] (en=ethylenediamine) by using (1)H NMR spectroscopy. Without exception, binding of the second metal takes place at N7, but formation of a molecular guanine square with trans-[(Me(2)NH(2))Pt(II)] cross-linking N1 positions and trans-[(NH(3))(2)Pt(II)] cross-linking N7 positions could not be confirmed unambiguously, despite the fact that calculations are fully consistent with its existence.

A neutral Pt3 stack unsupported by any bridging ligand.

Pt···Pt···Pt interactions via their d(8) orbitals, combined with π-π stacking of deprotonated, chelating 2-(3'-pyrazolyl)pyridine (pyzpy) ligands, are responsible for trans-Pt(pyzpy)(2) (2) crystallization in a stack of three molecules unsupported by any bridging ligand.

Mono- and dinuclear platinum(II) compounds with 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine. Structure, cytotoxic activity and reaction with 5'-GMP.

Mono- and dinuclear platinum(II) coordination compounds of formula cis-[PtCl(2)(NH(3))(dmtp)], 1, cis-[PtCl(2)(dmtp)(2)], 2 and {H(+)[C(28)H(32)Cl(2)N(16)Pt(2)](2+)(NO(3))(3)(H(2)O)(6)}, 3, in which dmtp is 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine have been synthesized and characterized by infrared and by (1)H, (13)C, (195)Pt NMR spectroscopy. The coordination units of the cationic species of formula [Pt(2)(mu-dmtp)(2)Cl(2)(dmtp)(2)](2+) are built up by two platinum atoms in a square-planar environment. Two sites are occupied by two 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp) bridging ligands which are linked to both metal atoms through their nitrogen atoms in positions 3 and 4. The other two positions are occupied by one monodentate 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp) molecule and a coordinated chloride. This compound is the first in which the same triazolopyrimidine ligand (dmtp) coordinates to a metal ion in two different ways, i.e. bridging bidentate and non-bridging monodentate. In addition, the interaction of compounds 1 and 2 with 5'-GMP was investigated in solution by (1)H NMR spectroscopy. The cytotoxicity of all the new platinum(II) compounds were studied by using two different cell lines: T47D (breast cancer) and HCV29T (bladder cancer).

(1)H NMR spectroscopic identification of binding modes of 2,2'-bipyridine ligands in complexes of square-planar d(8) metal ions.

The reaction of [M(bpy)](2+) (M = Pd(II) and/or Pt(II); bpy = 2,2'-bipyridine) moieties with model nucleobases leads to a variety of products, viz. 1 : 1, 1 : 2 and 2 : 2 (head-tail, ht, or head-head, hh) complexes. By carefully analysing the H5 (H5') resonances of the bpy ligands, which in all cases occur furthest upfield, and with additional indicators (concentration dependence of H6, H6' resonances; (195)Pt-(1)H coupling constants, if observable; absolute shifts of H5, H5'), it is possible to assign binding situations of bpy ligands, even in multinuclear complexes with several [M(bpy)](2+) entities in different environments present. The analysis presented here is carried out on X-ray structurally established cases of [M(bpy)](2+) complexes, including three new ones, [Pt(1-MeC-N3)(2)(bpy)](NO(3))(2).2.5H(2)O (), ht-[(bpy)Pd(N3-1-MeC(-)-N4)(2)Pd(bpy)](ClO(4))(2).3H(2)O () and ht-[(bpy)Pd(N1-ampy(-)-N2)(2)Pd(bpy)](NO(3))(2).3H(2)O (). The data provide a consistent picture, useful for the future assignment of similar bpy complexes in the absence of X-ray structural evidence.

Regioselective de novo synthesis of cyanohydroxypyridines with a concerted cycloaddition mechanism.

An efficient cycloaddition reaction of 1-alkoxy-1-azadienes with alpha,alpha-dicyanoalkenes is described, which gives facile access to highly substituted 3-hydroxypyridines in very good yields and with complete regiocontrol and chemoselectivity. The reaction path was investigated in detail by quantum mechanics calculations, reporting that a concerted cycloaddition mechanism and thermodynamic control synergistically contribute to the observed selectivity.

On the interrelationship of mu-OH bridged dimers, trimers, and tetramers of (en)PtII and their Ag+ adducts.

[(en)Pt(mu-OH)2Pt(en)]2+, a dinuclear mu-hydroxo bridged complex (with en = ethylenediamine) crystallizes with excess AgNO3 in high yield as the trinuclear complex [((en)Pt(mu-OH)2Pt(en))Ag](NO3)3 (Pt2Ag, 1) from water. The two halves of the complex are significantly bent (dihedral angle 42.2 degrees ) and the three metals form a triangle with the following distances: Pt1...Pt2, 2.9729(9) angstroms, Pt1...Ag1, 2.818(1) angstroms and Pt2...Ag1, 2.809(1) angstroms. The shortness of the Pt...Ag distances and the dispositions of the three metal ions strongly suggest that dative bonds from Pt to Ag are responsible for the bending of the two halves of the edge-sharing dinuclear [(en)Pt(mu-OH)2Pt(en)]2+ complex. This scenario appears to be yet another cause of bending of edge-sharing dinuclear mu-OH bridged metal complexes of d8 metal ions, adding to those involving Pt...Pt bonding, or anion binding, among others. Comparison with related mu-OH dimers of cis-(NH3)2PtII or (tmeda)PtII (tmeda = N,N,N',N'-tetramethylethylenediamine), which do not display Ag+ binding, suggests that the feature of Ag+ binding is not common to all cis-bis(am(m)ine) complexes of PtII. Interestingly the complete removal of Ag+ from 1 does not lead to the mu-OH dimer but rather to the known mu-OH tetramer [((en)Pt(mu-OH))4]4+.

Cyclic, trinuclear PdII complex of cytidine with pronounced double cone structure.

Reaction of PdII(tmeda) (tmeda=N,N,N',N'-tetramethylethylenediamine) with the RNA nucleoside cytidine (Cytd) yields a cyclic nucleoside complex containing three metal entities and three cytidine anions, with metal cross-links involving N(3) and N(4)H(-) sites. [{Pd(Cytd(-)-N3,N4)(tmeda)}3](ClO4)3.6H2O has a characteristic double cone structure with the methyl groups of the tmeda ligands representing the lower rim and the ribose moieties forming the upper rim. The Pd3 triangle is equilateral (5.193(1)A). In the solid state structure, one of the ClO(4)(-) counter ions links the lower and the upper rims of adjacent cones, thereby leading to a 1D chain. No host-guest chemistry has been detected with a series of N-heterocyclic ligands in water.

(Z)-Methyl 2-methoxy-imino-3-oxo-butanoate.

The title compound, C(6)H(9)NO(4), was prepared stereoselectively as a precursor for 1-aza-dienes in a study of hetero-Diels-Alder reactions. The configuration of the C=N double bond was found to be Z, corroborating earlier assignments of similar compounds based only on NMR and IR spectroscopic analysis.

Tetrakis- and tris(1-Methyluracil) complexes of Pt(II): formation and properties of a carbon-bonded nucleobase species as well as of heternonuclear derivatives.

The reaction of K2PtCl4 with an excess of 1-methyluracilate (1-MeU) in water at 60 degrees C leads to the formation of two major products, K2[Pt(1-MeU-N3)4].10H2O (1) and trans-K[Pt(1-MeU-N3)2(1-MeU-C5)(H2O)].3H2O (2). Addition of CuCl2 to an aqueous solution of 2 yields the mixed-metal complex trans-[PtCl(1-MeU-N3,O4)2(1-MeU-C5,O4)Cu(H2O)].H2O (4). Single-crystal X-ray analysis was carried out for 1 and 4. In both compounds, the heterometals (K+ in 1 and Cu2+ in 4) are bonded to exocyclic oxygens atoms of the 1-MeU ligands, giving rise to intermetallic distances of 3.386(2) and 3.528(2) A in 1 and 2.458(1) A in 4. The shortness of the Pt-Cu separation in 4 is consistent with a dative bond between PtII and CuII. The aqua ligand in 2 is readily substituted by a series of other ligands (e.g., 1-MeC, 9-MeGH, and CN-), as demonstrated by 1H NMR spectroscopy, with 3J(195Pt-1H(6)) coupling constants being sensitive indicators. Acid-base equilibria of 1 and 2 have been studied in detail and reveal some unexpected features: 1 has a relatively high basicity, with protonation starting below pH 5, and first and second pKa values being ca. 3.4 and 0.4, respectively. These pKa values are markedly higher than those of related neutral 2:1 or cationic 1:1 complexes and are attributed to both charge effects (-2 charge of 1) and a favorable stabilization of oxygen-protonated species by the arrangement of four exocyclic oxygen groups of 1-MeU ligands at either sides of the platinum coordination planes. Whereas in 2, H+ affinities of the three uracil ligands are in the normal range, there is a surprisingly low acidity of N(3)H of the C5-bonded uracil with a pKa of approximately 12.2, which compares with 9.75 for free 1-methyluracil. This implies that the C5-bonded PtII does not induce the typical acidifying effect of a PtII metal entity when bonded to a ring nitrogen atom of a neutral nucleobase. Rather, the effect is qualitatively similar to that of a metal ion bonded to N3 of an anionic 1-MeU ligand, which likewise increases its overall basicity as compared to neutral 1-MeUH.

Pd2Ag triangle supported by two micro3-amidopyridine ligands.

[Pd(tmeda)(Hampy-N1)(H2O)]2+ (tmeda=N,N,N',N'-tetramethylethylenediamine; Hampy=2-aminopyridine) forms in the presence of Ag+ at pH 8-9 a triangular Pd2Ag complex containing two deprotonated ampy- ligands. It has been crystallized and structurally characterized with nitrate anions and a second co-crystallized AgNO3, [{Pd(ampy)(tmeda)}2Ag(micro-NO3)2Ag(NO3)2]. The two amidopyridine ligands are triply bridging, binding to Ag+ in a monodentate fashion viaN1, and to two PdII centres in a micro2-bridging fashion via the monodeprotonated N2 position. The resulting four-membered Pd(ampy)2Pd metallacycle is syn-planar with Pd[dot dot dot]Pd separations of 3.0878(13) A. The Pd...Ag distances are 3.0879(14) A in (isosceles triangle). In solution (D2O), the two ampy- ligand in are non-equivalent as concluded from a detailed 1H NMR spectroscopic study and confirmed by a 13C NMR spectrum. Removal of Ag+ from, as achieved by addition of Cl-, causes cluster degradation and linkage isomerization of PdII(tmeda) from the exocyclic N2 to the endocyclic N1 position.

Cyclic trimer versus head-tail dimer in metal-nucleobase complexes: importance of relative orientation (syn, anti) of the metal entities and relevance as a metallaazacrown compound.

The formation and crystal structure analysis of a cyclic trinuclear Pd complex with bridging 1-methylcytosinato model nucleobases is reported: [[(tmeda)Pd(1-MeC(-)-N3,N4)]3] (ClO4)3.5.5H2O (tmeda = N,N,N',N'-tetramethylethylenediamine; 1-MeC- = 1-methylcytosine deprotonated at exocyclic amino group) is obtained, among others, from the hydroxo-bridged dinuclear species [[(tmeda)Pd(OH)]2](ClO4)2, which likewise has been characterized by X-ray crystallography, and 1-MeC (1-MeC = neutral 1-methylcytosine) in aqueous solution. The usual head-tail dimer (HT1) appears not to be formed presumably because of the steric bulk of the tmeda ligand, which prevents a close approach of two tmeda ligands. There is also no evidence for formation of an alternative head-tail dimer structure (HT2) which, in principle, would not lead to any steric clash of ligands, but would require an orientation of the metal at N4 that is almost perpendicular to the nucleobase plane. In the Pd3 compound, the bridging metals are approximately in an anti arrangement, thereby leading to Pd...Pd separations within the Pd3 triangle close to 5.2 angstroms. This arrangement is reflected in the 1H NMR spectrum by a strongly deshielded H5 resonance of the nucleobase, occurring at 6.56 ppm (D2O). The overall structure of the Pd3 is that of a double cone, with ClO4- counterions approaching the cavities from either side. The trinuclear structure is also maintained in Me2SO-d6. In this solvent, Pd3 acts as a fluoride anion receptor, with F- binding to the N4H protons, as evident from large downfield shifts of these protons. The compound is compared with cyclic adeninato complexes of hexacoordinated metal ions, and a conceptional analogy with [12]metallacrown-3 species is outlined.