Metal ion-induced site-selective RNA hydrolysis by use of acridine-bearing oligonucleotide as cofactor

New types of noncovalent ribozyme-mimics for site-selective RNA scission are prepared by combining metal ions with oligonucleotides bearing an acridine. Lanthanide(III) ions and various divalent metal ions (Zn(II), Mn(II), Cu(II), Ni(II), Co(II), Mg(II), and Ca(II)) are employed without being bound to any sequence-recognizing moiety. The modified oligonucleotide forms a heteroduplex with the substrate RNA, and selectively activates the phosphodiester linkages in front of the acridine. As a result, these linkages are preferentially hydrolyzed over the others, even though the metal ions are not fixed anywhere. The scission is efficient under physiological conditions, irrespective of the sequence at the target site. Site-selective RNA scission is also successful with the combination of an oligonucleotide bearing an acridine at its terminus, another unmodified oligonucleotide, and the metal ion. In a proposed mechanism, the acridine pushes the unpaired ribonucleotide out of the heteroduplex and changes the conformation of RNA at the target site for the sequence-selective activation.     

Molybdenum cofactor biosynthesis in plants and humans

The transition element molybdenum (Mo) needs to be complexed by a special cofactor in order to gain catalytic activity. With the exception of bacterial Mo-nitrogenase, where Mo is a constituent of the FeMo-cofactor, Mo is bound to a pterin, thus forming the molybdenum cofactor Moco, which in different variants is the active compound at the catalytic site of all other Mo-containing enzymes. The biosynthesis of Moco involves the complex interaction of six proteins and is a process of four steps, which also requires reducing equivalents, iron, ATP and probably copper. After its synthesis, Moco is distributed to the apoproteins of Mo-enzymes by Moco–carrier/binding proteins that also participate in Moco-insertion into the cognate apoproteins. A deficiency in the biosynthesis of Moco has lethal consequences for the respective organisms. In humans, Moco deficiency is a severe inherited inborn error in metabolism resulting in severe neurodegeneration in newborns and causing early childhood death. Due to our better understanding of the chemistry of Moco synthesis, a first therapy has been brought to the clinic.     

Transmembrane signal transduction by cofactor transport

Information processing and cell signalling in biological systems relies on passing chemical signals across lipid bilayer membranes, but examples of synthetic systems that can achieve this process are rare. A synthetic transducer has been developed that triggers catalytic hydrolysis of an ester substrate inside lipid vesicles in response to addition of metal ions to the external vesicle solution. The output signal generated in the internal compartment of the vesicles is produced by binding of a metal ion cofactor to a head group on the transducer to form a catalytically competent complex. The mechanism of signal transduction is based on transport of the metal ion cofactor across the bilayer by the transducer, and the system can be reversibly switched between on and off states by adding cadmium(ii) and ethylene diamine tetracarboxylic acid input signals respectively. The transducer is also equipped with a hydrazide moiety, which allows modulation of activity through covalent conjugation with aldehydes. Conjugation with a sugar derivative abolished activity, because the resulting hydrazone is too polar to cross the bilayer, whereas conjugation with a pyridine derivative increased activity. Coupling transport with catalysis provides a straightforward mechanism for generating complex systems using simple components.

Synthetic transducers transport externally added metal ion cofactors across the lipid bilayer membrane of vesicles to trigger catalysis of ester hydrolysis in the inner compartment. Signal transduction activity is modulated by hydrazone formation.     

Comparative study of folate cofactor models

The structures of a type of tetrahydrofolate cofactor models, asymmetric substituted imidazolinium, have been studied theoretically, and the relation of reactivities to the electronic structures of these compounds has been analyzed. It is found that the reactivity of one‐carbon unit transfer of this type of tetrahydrofolate cofactor models has a tight relation to properties of the two nitrogen atoms that link to the transferring carbon atom. The followed regularity is obtained. With the group on the para‐position of benzenesulfonyl changing from an electronic acceptor to an electronic donor, the difference between N3 and N6 is smaller step by step, and the model becomes more active to transfer one‐carbon unit gradually. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Efficient synthesis of azide-bearing cofactor mimics

8-Azido-5'-aziridino-5'-deoxyadenosine (6), a novel cofactor mimic, was synthesized in nine steps from commercially available 2',3'-isopropylideneadenosine in approximately 4% overall yield. Crucial to this success was a very unorthodox phthalimide cleavage procedure, C8 azidation prior to aziridination and late stage alkylation of the 5' amino group with iodoethanol necessitated by the high degree of lability endowed by the aryl azide moiety. Aziridine 6 is envisioned as a useful biochemical tool by which to probe DNA and protein methylation patterns.     

Metal nitrosyl reactivity: Acetonitrile-promoted insertion of an alkylidene into a nitrosyl ligand with fission of the NO bond

Treatment of the complexes [Re(NO)2(PR3)2][BAr(F)4] (R = Cy, 1 a; R = iPr, 1 b) with phenyldiazomethane gave the cationic benzylidene species [Re{CH(C6H5)}(NO)2(PR3)2][BAr(F)4] (2 a and 2 b) in good yields. Upon reaction of 2 a and 2 b with acetonitrile, the consecutive formation of [Re(N[triple bond]CCH3)(N[triple bond]CPh)(NO)(OC(CH3)=NH)(PR3)][BAr(F)4] (3 a and 3 b) and [Re(NCCH3)(OC{CH3}NH{C6H5})(NO)(PR3)2][BAr(F)4] (4 a and 4 b) was observed. The proposed reaction sequence involves the coupling of coordinated NO, carbene and acetonitrile molecules to yield the (1Z)-N-[imino(phenyl)methyl]ethanimidate ligand. The coupling of the nitrosyl and the benzylidene is anticipated to occur first, forming an oximate species. The subsequent acetonitrile addition can be envisaged as a heteroene reaction of the oximate and the acetonitrile ligand yielding 3 a and 3 b, which in turn can cyclise and undergo a prototropic shift initiated by an internal attack of the ethaneimidate ligand on the benzonitrile moiety to afford 4 a and 4 b.     

Pterin chemistry and its relationship to the molybdenum cofactor

The molybdenum cofactor is composed of a molybdenum coordinated by one or two rather complicated ligands known as either molybdopterin or pyranopterin. Pterin is one of a large family of bicyclic N-heterocycles called pteridines. Such molecules are widely found in Nature, having various forms to perform a variety of biological functions. This article describes the basic nomenclature of pterin, their biological roles, structure, chemical synthesis and redox reactivity. In addition, the biosynthesis of pterins and current models of the molybdenum cofactor are discussed.     

Enzymatic biofuel cells utilizing a biomimetic cofactor

The performance of immobilized enzyme systems is often limited by cofactor diffusion and regeneration. Here, we demonstrate an engineered enzyme capable of utilizing the minimal cofactor nicotinamide mononucleotide (NMN(+)) to address these limitations. Significant gains in performance are observed with NMN(+) in immobilized systems, despite a decreased turnover rate with the minimal cofactor.     

Coimmobilization of a redox enzyme and a cofactor regeneration system

The coimmobilization of nitrobenzene nitroreductase and glucose-6-phosphate dehydrogenase in silica particles enables the continuous conversion of nitrobenzene to hydroxylaminobenzene with NADPH recycling.     

Purification of heparin cofactor II from human plasma

Heparin cofactor II (HCII) is an inhibitor of thrombin in human plasma whose activity is enhanced by heparin and dermatan sulphate. HCII was purified to homogeneity from normal human plasma with an overall yield of 7.5%. After treatment with barium chloride, precipitation with 50% saturated ammonium sulphate and dialysis of the resuspended precipitate against 0.02 M Tris-HCl (pH 7.4), the sample was chromatographed on a heparin-Sepharose CL 6B affinity column, DEAE-Sepharose CL 6B ion-exchange gel and an AcA 34 gel permeation column. For the final steps, a high-performance liquid chromatographic system was used which included ion-exchange chromatography on a Mono-Q column and gel permeation using a Superose column. The purified protein was homogeneous by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The specific activity of purified HCII was 12.2 U/mg. The HCII activity was evaluated as antithrombin dermatan sulphate cofactor activity. A specific antiserum against HCII was raised in the rabbit.     

Manipulating reduction potentials in an artificial safranin cofactor

Safranines hold great promise as artificial flavin-like electron transfer cofactors with tunable properties. We report the design and chemical synthesis of the p-methoxy derivative of safranine O using a new synthetic route based on the Ulmann condensation. Spectroelectrochemical comparison of the purified parent safranine and this derivative demonstrates that the modification increases its two-electron reduction potential by 125 mV, or 5.75 kcal/mol. This modification also causes redshifts in the absorbance and fluorescence spectra of the cofactor, suggesting that it may find future utility in arrayed sensor applications.     

Activation and protonation of dinitrogen at the FeMo cofactor of nitrogenase

The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode with open sulfur bridge is less reactive by 30 kJ/mol and the energetic ordering of the axial and bridged binding modes is reversed in favor of the bridging dinitrogen during the first protonation. Protonation of the central ligand is thermodynamically favorable but kinetically hindered. If the central ligand is protonated, the proton is transferred to dinitrogen following the second protonation. Protonation of dinitrogen at the Mo site does not lead to low-energy intermediates.     

Infrared spectrum and absorption coefficient of the cofactor flavin in water

Flavins play a key role as redox cofactors of enzymes involved in important metabolic processes. Moreover, they undergo photochemical reactions as chromophores in sensors of blue light or magnetic field in many organisms. The reaction mechanisms of flavoproteins have been investigated by infrared spectroscopy and theoretical studies. However, basic information on flavins in the infrared spectral range has been missing, such as absorption spectra in water and absorption coefficients. Here, the cofactors flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) were investigated in aqueous medium by Fourier transform infrared spectroscopy. Transmission and attenuated total reflection (ATR) configuration were employed in direct comparison. Absorption spectra in the range of 920–1800 cm⁻¹ were determined after accurate subtraction of the contributions from the water vibrations. The important carbonyl vibrations were resolved at 1661 and 1712 cm⁻¹. The absorption spectra may serve as a reference for theoretical and experimental studies on the effect of the microenvironment on the flavin cofactor. Furthermore, the molar absorption coefficient of FAD at 1547 cm⁻¹ was determined to 2200 L mol⁻¹ cm⁻¹ with an integral absorption coefficient of ∼50,000 L mol⁻¹ cm⁻². These values are prerequisite for the determination of reaction yields in flavoproteins from reaction-induced difference spectra.     

Uncommon carbene insertion reactions

Transition-metal-catalysed carbene insertion reaction is a straightforward and efficient protocol for the construction of carbon–carbon or carbon–heteroatom bonds. Compared to the intensively studied and well-established “common” carbene insertion reactions, including carbene insertion into C–H, Si–H, N–H, O–H, and S–H bonds, several “uncommon” carbene insertion reactions, including carbene insertion into B–H, Sn–H, Ge–H, P–H, F–H, C–C, and M–M bonds, have been neglected for a long time. However, more and more studies on uncommon carbene insertion reactions have been disclosed recently, and clearly demonstrate the great synthetic potential of these reactions. The current perspective reviews the history and the newest advances of uncommon carbene insertion reactions, discusses their potential applications and challenges, and also presents an outlook of this promising field.

Transition-metal-catalysed carbene insertion reaction is a straightforward and efficient protocol for the construction of carbon–carbon or carbon–heteroatom bonds.     

One-Pot Synthesis of High-Strained Metal Vinylidene and Metal Carbyne

A novel one-pot reaction producing a metal vinylidene structure in a five-membered ring by cyclization of a multiyne has been achieved. The ring strain and the high stability of the cyclic metal vinylidene complexes have been analyzed experimentally and computationally. The metal vinylidene unit in a fused-ring complex is unreactive to both nucleophiles and electrophiles. It reacts however at the nearby carbonyl group achieving the unprecedented conversion of metal tributing factors for the aromaticity-driven process has been studied by DFT calculations.     

Controllable stereoinversion in DNA-catalyzed olefin cyclopropanation via cofactor modification

The assembly of DNA with metal-complex cofactors can form promising biocatalysts for asymmetric reactions, although catalytic performance is typically limited by low enantioselectivities and stereo-control remains a challenge. Here, we engineer G-quadruplex-based DNA biocatalysts for an asymmetric cyclopropanation reaction, achieving enantiomeric excess (ee_trans) values of up to +91% with controllable stereoinversion, where the enantioselectivity switches to −72% ee_trans through modification of the Fe-porphyrin cofactor. Complementary circular dichroism, nuclear magnetic resonance, and fluorescence titration experiments show that the porphyrin ligand of the cofactor participates in the regulation of the catalytic enantioselectivity via a synergetic effect with DNA residues at the active site. These findings underline the important role of cofactor modification in DNA catalysis and thus pave the way for the rational engineering of DNA-based biocatalysts.

Cofactor modification in a DNA-catalyzed olefin cyclopropanation reaction enables controllable stereoinversion and achieves enantioselectivities of up to +91% and −72% ee_trans.     

Modeling a central ligand in the nitrogenase FeMo cofactor

In very recent work by Einsle et al. (Science 2002, 297, 1696), a new X-ray crystallographic structure of the FeMo cofactor of nitrogenase with a central ligand was presented. The central ligand is a light atom (N, O, or C), and Einsle et al. suggest that it is nitrogen. We present density functional calculations on the FeMo cofactor, and we investigate N, O, and C as central ligands. We show that both N and O lead to energetically stable FeMo cofactor structures, whereas C is energetically unfavorable. By comparison of bond geometries with the crystallographically determined values, we show that the central ligand is most likely nitrogen.