Barbara A. Messerle

Proximity extension of circular DNA aptamers with real-time protein detection

Multivalent circular aptamers or ‘captamers’ have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the ‘proximity extension’ assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer–thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier.

Three-dimensional structure of human [113Cd7]metallothionein-2 in solution determined by nuclear magnetic resonance spectroscopy.

The three-dimensional structure of human [113Cd7]metallothionein-2 was determined by nuclear magnetic resonance spectroscopy in solution. Sequence-specific 1H resonance assignments were obtained using the sequential assignment method. The input for the structure calculations consisted of the metal-cysteine co-ordinative bonds identified with heteronuclear correlation spectroscopy, 1H-1H distance constraints from nuclear Overhauser enhancement spectroscopy, and spin-spin coupling constants 3JHN alpha and 3J alpha beta. The molecule consists of two domains, the beta-domain including amino acid residues 1 to 30 and three metal ions, and the alpha-domain including residues 31 to 61 and four metal ions. The nuclear magnetic resonance data present no evidence for a preferred relative orientation of the two domains. The polypeptide-to-metal co-ordinative bonds in human metallothionein-2 are identical to those in the previously determined solution structures of rat metallothionein-2 and rabbit metallothionein-2a, and the polypeptide conformations in the three proteins are also closely similar.

A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy.

A new lanthanide tag was designed for site-specific labeling of proteins with paramagnetic lanthanide ions. The tag, 4-mercaptomethyl-dipicolinic acid, binds lanthanide ions with nanomolar affinity, is readily attached to proteins via a disulfide bond, and avoids the problems of diastereomer formation associated with most of the conventional lanthanide tags. The high lanthanide affinity of the tag opens the possibility to measure residual dipolar couplings in a single sample containing a mixture of paramagnetic and diamagnetic lanthanides. Using the DNA-binding domain of the E. coli arginine repressor as an example, it is demonstrated that the tag allows immobilization of the lanthanide ion in close proximity of the protein by additional coordination of the lanthanide by a carboxyl group of the protein. The close proximity of the lanthanide ion promotes accurate determinations of magnetic susceptibility anisotropy tensors. In addition, the small size of the tag makes it highly suitable for studies of intermolecular interactions.

Comparison of the solution conformations of human [Zn7]-metallothionein-2 and [Cd7]-metallothionein-2 using nuclear magnetic resonance spectroscopy

The solution structure of native human [Zn7]-metallothionein-2 has been compared with the previously determined structure of human [Cd7]-metallothionein-2. The comparison was based on complete sequence-specific 1H nuclear magnetic resonance assignments for human [Zn7]-metallothionein-2 obtained using the sequential assignment method. The secondary structure was found to be very similar in the [Zn7]- and [Cd7]- forms of the protein. Only seven amide protons in [Zn7]- metallothionein-2 were found to have exchange rates lower than approximately 0.2 min-1 at pH 7.0 and 10 degrees C, which corresponds closely to the results of amide proton exchange studies with the [Cd7]- form of the protein. Finally, the 1H-1H distance constraints determined from nuclear Overhauser enhancement spectroscopy for human [Zn7]-metallothionein-2 were checked for compatibility with the [Cd7]-metallothionein-2 structure. Overall, although no direct method is available for identifying the metal-polypeptide co-ordinative bonds in the Zn(2+)-containing protein, these measurements provided several independent lines of evidence showing that the [Zn7]- and [Cd7]- forms of human metallothionein-2 have the same molecular architecture.

Rhodium(I) and iridium(I) complexes containing bidentate phosphine-imidazolyl donor ligands as catalysts for the hydroamination and hydrothiolation of alkynes

A series of novel cationic and neutral rhodium and iridium complexes containing bidentate phosphine-imidazolyl donor ligands of the general formulae [M(ImP)(COD)]BPh(4) (M = Rh, ImP = ImP2, 3; ImP1a, 4a; ImP1b, 4b and M = Ir, ImP = ImP2, 5; ImP1a, 6a and ImP1b, 6b), [Ir(ImP)(CO)(2)]BPh(4) (ImP = ImP2, 7; ImP1a, 8a and ImP1b, 8b), [Rh(ImP1b)(CO)(2)]BPh(4) (10b) and [M(ImP)(CO)Cl] (M = Rh, ImP = ImP2, 11; ImP1b,12 and M = Ir, ImP = ImP2, 13; ImP1b, 14 ) where COD = 1,5-cyclooctadiene, ImP2 = 1-methyl-2-[(2-(diphenylphosphino)ethyl]imidazole, 1; ImP1a = 1-methyl-2-[(diphenylphosphino)methyl]imidazole, 2a and ImP1b = 2-[(diisopropylphosphino)methyl]-1-methylimidazole, 2b were successfully synthesised. The solid state structures of 3, 6a, 11 and 12 were determined by single crystal X-ray diffraction analysis. A number of these complexes are effective as catalysts for the intramolecular hydroamination of 4-pentyn-1-amine to 2-methyl-1-pyrroline. The cationic complexes are significantly more effective than analogous neutral complexes. The cationic iridium complex 8b , containing the phosphine-imidazolyl ligand with the bulky isopropyl groups on the phosphorus donor, is more efficient than analogous complexes with the phenyl substituents on the phosphorus donor atom, 7 and 8a. The complexes 7-8b are also moderately effective in catalysing the addition of thiophenol to a range of terminal alkynes. In contrast to the hydroamination reaction, placement of the isopropyl group on the phosphorus donor leads to a decrease in the reactivity of the resulting metal complexes as catalysts for the hydrothiolation reaction.

Rhodium(I) and iridium(I) complexes with bidentate N,N and P,N ligands as catalysts for the hydrothiolation of alkynes

Cationic iridium(I), rhodium(I) complexes containing bis(1-methylimidazol-2-yl)methane, bim, [M(bim)(CO)2]BPh4 (M = Ir (1), Rh (2)); bis(pyrazol-1-yl)methane, bpm, [M(bpm)(CO)2]BPh4 (M = Ir (3), Rh (4)) have been shown to be effective in catalysing the regioselective addition of thiophenol to a series of alkynes. Analogous cationic and neutral Ir(I), Rh(I) complexes with the novel mixed P,N-donor bidentate ligand 1-(2-diphenylphosphino)ethylpyrazole, PyP (5), [M(PyP)(COD)]BPh4 (M = Ir (6), Rh (7), COD = 1,5-cyclooctadiene); [Rh(PyP)(COD)]BF4 (8); [Ir(PyP)(CO)2]BPh4 (9); [Rh(PyP)(CO)2]BF4 (10); [M(PyP)(CO)Cl] (M = Ir (11), Rh (12)) have also been synthesised, and characterised by NMR. The solid-state structures of (6), (7), (11) and (12) have been determined by single-crystal X-ray diffraction analysis. The metal complexes (9)–(12) with the mixed P,N-donor ligand, PyP are in most cases more effective in promoting the hydrothiolation of alkynes in comparison with the analogous complexes (1)–(4) with N,N-donor ligands. The iridium complexes were significantly more effective than their rhodium analogues in promoting the hydrothioloation of alkynes. The cationic complexes (9) and (10) are more effective as catalysts for the hydrothiolation of alkynes than their neutral analogues (11) and (12).

Cyclisation of acetylenic carboxylic acids and acetylenic alcohols to oxygen-containing heterocycles using cationic rhodium(I) complexes

Abstract Square planar cationic rhodium(I) dicarbonyl complexes [{Rh((mim) 2 CH 2 )(CO) 2 } + BPh 4 − ] ( 1 ) and [{Rh((mBnzim) 2 CH 2 )(CO) 2 } + BPh 4 − ] ( 2 ) [mim= N -methylimidazol-2-yl, mBnzim= N -methylbenzimidazol-2-yl] are catalysts for the cyclisation of alkynoic acids to lactones. The unsaturated acids, 4-pentynoic acid, 4-hexynoic acid and 5-hexynoic acid were cyclised to γ-methylene-γ-butyrolactone, E -5-ethylidenetetrahydro-2-furanone and 6-methylidenetetrahydo-2-pyrone, respectively. Cyclisation of 4-hexynoic acid proceeds stereoselectively with exclusive formation of the E -isomer of 5-ethylidenetetrahydro-2-furanone. Complexes 1 and 2 also catalyse cyclisation of acetylenic alcohols to oxygen-containing heterocycles.

3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site-specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide-binding tag, 3-mercapto-2,6-pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N-terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co(2+) were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Delta chi) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Delta chi tensor orientations compared to the previously studied 4-mercaptomethyl-DPA tag, making it a highly complementary and useful tool for protein NMR studies.

Highly efficient Rh(I) and Ir(I) single and dual metal catalysed dihydroalkoxylation reactions of alkyne diols.

A highly efficient rhodium(I) and iridium(I) catalysed dihydroalkoxylation reaction of alkyne diols is employed here for the synthesis of spiroketals and a fused bicyclic ketal. The two metal catalysts show differential selectivity and efficiency for either the cyclisation of the 5-exo or 6-endo-membered rings. For the first time, a dual metal (Rh and Ir) catalyst system is effectively utilised for the formation of the 5,6-spiroketals, more efficiently than the single metal catalysts. The two different metals create a dual activation pathway to enhance the 5- and 6-membered ring closure as compared with the equivalent single catalysts.

Rh(I) and Ir(I) catalysed intermolecular hydroamination with substituted hydrazines

The catalysed intermolecular hydroamination of a series of terminal alkynes with substituted hydrazines was achieved using Rh(I) and Ir(I) complexes.