Programmable and autonomous computing machine made of biomolecules.

Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine, which stimulated work leading to the development of modern computers. The Turing machine and its special cases, including finite automata, operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers. Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated, but the realization of computing devices operating autonomously on the molecular scale remains rare. Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton's hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton's final state, and thus the computational result. In our implementation 1012 automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 microl solution at room temperature at a combined rate of 109 transitions per second with a transition fidelity greater than 99.8%, consuming less than 10-10 W.

A new class of antiarrhythmic-defibrillatory agents.

Novel dibenzoazepine and 11-oxo-dibenzodiazepine derivatives are shown to be effective ventricular defibrillating drug candidates. They exhibit significant in vivo defibrillatory activity with no observed changes in ECG either before or after the VF event. These compounds also exhibit antifibrillatory activity by elevating the fibrillation threshold potential, all suggesting that such drugs could be used to treat VF either by themselves or together with electrical defibrillators.

Catalysis of the kemp elimination by natural coals

Commercially available coals were found to be efficient heterogeneous catalysts of the Kemp elimination reaction in aqueous solutions. A pH-rate profile study suggests that catalysis originates from specific catalytic groups and not simply from the large graphitic surface area. The low-quality lignite coals, which exhibit similar catalytic efficiency per weight to that of molecularly imprinted polymers, are better catalysts for this reaction in comparison with the bituminous coals.

Highly sensitive and rapid detection of antibody catalysis by luminescent bacteria.

A highly sensitive, inexpensive, and facile bioluminescent assay for the detection of catalytic antibodies has been developed. This assay may be used for the early detection of antibody catalysis. The efficiency of this technique was exemplified by the use of the luminescent bacterium VhM42 for monitoring an antibody-catalyzed retroaldol fragmentation reaction with aldolase antibodies 38C2 and 24H6.

Total synthesis of asimicin and bullatacin.

The efficient total synthesis of asimicin, 1, and bullatacin, 2, has demonstrated the advantages of three different strategies for the synthesis of the tricyclic intermediates 6 and 7, which represent the key fragment of the bis-THF Annonaceous acetogenins. The naked carbon skeleton strategy is based on the production of all asymmetric centers by selective placement of the oxygen functions onto an unsaturated, nonfunctionalized carbon skeleton. Diversity in this approach arises from the relative timing of highly stereoselective reactions, such as the Sharpless asymmetric dihydroxylation (AD) reaction, the Kennedy oxidative cyclization (OC) with rhenium(VII) oxide, the Mitsunobu-type alcohol epimerization reaction, and the Williamson etherification reaction. The convergent strategy, which is based on the combinatorial coupling of two series of diastereomeric fragments, to produce intermediates such as 11 and 12, enjoys the advantages of both efficiency and versatility. The third approach, which is based on partially functionalized intermediates, such as 13, combines the advantages of both the linear and the convergent strategies-synthetic efficiency and diversity.

Protein synthesis by solid-phase chemical ligation using a safety catch linker.

The native chemical ligation reaction has been used extensively for the synthesis of the large polypeptides that correspond to folded proteins and domains. The efficiency of the synthesis of the target protein is highly dependent on the number of peptide segments in the synthesis. Assembly of proteins from multiple components requires repeated purification and lyophilization steps that give rise to considerable handling losses. In principle, performing the ligation reactions on a solid support would eliminate these inefficient steps and increase the yield of the protein assembly. A new strategy is described for the assembly of large polypeptides on a solid support that utilizes a highly stable safety catch acid-labile linker. This amide generating linker is compatible with a wide range of N-terminal protecting groups and ligation chemistries. The utility of the methodology is demonstrated by a three-segment synthesis of vMIP I, a chemokine that contains all 20 natural amino acids and has two disulfide bonds. The crude polypeptide product was recovered quantitatively from the solid support and purified in 20%-recovered yield. This strategy should facilitate the synthesis of large polypeptides and should find useful applications in the assembly of protein libraries.

Opsin shift in an aldolase antibody.

An antibody-retinal assembly that mimics the opsin shift (OS) of the naturally occurring visual pigments is reported. Both experiments and calculations show that the aldolase antibody 33F12 covalently binds all-trans retinal via a protonated Schiff base with a lysine residue. This chromophore, which exhibits a remarkable opsin red shift (140 nm), represents a useful model system for studying the factors that contribute to the OS.

Substrate-selective mechanisms in biocatalysis demonstrated with a versatile and efficient aldolase antibody.

A structure-activity relationship study with a series of aldol substrates shows that the mechanism of the antibody 38C2-catalyzed retrograde aldol reaction depends on the nature of the substrate With electron-deficient substrates an early deprotonation precedes the C-C bond cleavage while with electron-rich substrates the catalytic mechanism involves an initial C-C bond cleavage leading to a positively charged intermediate.

Asymmetric organic synthesis with catalytic antibodies.

The science of catalytic antibodies has undergone a rapid maturation process within its first nine years of existence. From initial 'proof of concept' and demonstration of fundamental, enzyme-like characteristics, antibodies have been shown to catalyze a remarkably broad scope of organic transformations, including difficult and unfavorable chemical reactions. Yet, the ultimate testing ground for new concepts in organic chemistry has always been the synthesis of natural products. Here we focus on several issues related to the applicability of antibody catalysis in organic synthesis. We show that (a) in the hydrophobic environment of the antibody active site, short-lived intermediates can be formed and reacted in a controlled way, thus allowing antibodies to catalyze reactions that are normally incompatible with aqueous media, (b) the intrinsic order of reactivity (chemoselectivity) in a series of structurally related enol ethers and ketals can be inverted from 1:10 in the uncatalyzed hydrolysis reaction to 1000:1 under antibody catalysis, and (c) an efficient total synthesis of alpha-multistriatin, an important, biologically active natural product can be achieved via antibody catalysis.

Using antibodies to perturb the coordination sphere of a transition metal complex.

Metal ions in the active sites of many metalloenzymes exhibit distinctive spectral and chemical features which are different from those of small inorganic complexes. These features are the result of the unusual geometric and electronic constraints that are imposed on the metal ion within the protein environment. Much effort has been invested to try to mimic this feature of metalloenzymes in synthetic systems, but this remains a formidable task. Here we show that one of the key lessons learned from the science of catalytic antibodies--that binding energy can be converted into chemical energy--can be exploited to 'fine-tune' the physicochemical properties of a metal complex. We show that an antibody's binding site can reversibly perturb the coordination geometry of a metal ion, and can stabilize a high-energy coordinated species. Specifically, antibodies designed to bind the organosilicon compound 1 also bind the geometrically similar Cu(I) complex 2. However, the antibody binds a slightly compressed form of 2, which is closer in size to 1. This distortion is manifested by a spectral shift--an 'immunochromic' effect.

Antibody catalysis of a reaction otherwise strongly disfavoured in water.

Several examples have been reported recently of antibody catalysis of reactions that are strongly disfavoured because of the high free energy of the transition state. Here we show that catalytic antibodies can be used to promote a particularly useful kind of reaction from a synthetic point of view: one involving an intermediate that is highly unstable in water. We show that an antibody elicited against the quaternary ammonium ion 4a (Fig. 1) catalyses the protonation of the enol ether 1 to form, with complete enantioselectivity, an oxocarbonium intermediate. This species is highly reactive in water, and would normally react with a water molecule to give the corresponding ketone 2. But the antibody provides a hydrophobic environment that allows the oxocarbonium ion instead to undergo an intramolecular reaction to form an enantiomerically pure ketal 3. This result shows that catalytic antibodies can exclude solvent molecules entirely from crucial steps on the reaction pathway.

Antibody-catalyzed reversal of chemoselectivity.

A monoclonal antibody, 14D9, which has been elicited against a cationic hapten, N-alkyl-N-methyl-3-glutarylamidomethyl piperidinium, in which alkyl = [4-(2-hydroxyethylamido)carbonyl]phenylmethyl, is capable of inverting the intrinsic order of reactivity in a series of structurally related enol ethers and ketals towards hydrolysis. The order of reactivity of compounds 2 (1-methoxy-2-alkylcyclopent-1-ene), 3 (1-methoxy-5-alkylcylopent-1-ene), and 4 (1,1-dimethoxy-2-alkylcyclopentane) has changed from 0.09:0.17:1 in the uncatalyzed reaction to 1100:25:1 under antibody catalysis. Also, the order of reactivity of the three chemically similar ketals, 6a (1-alkyl-2,2-dimethoxypropane), 6b (1-alkyl-1-methyl-2,2-dimethoxypropane), and 4, has changed from 0.23:0.38:1 in the uncatalyzed hydrolysis to 100:9:1 within the antibody active site. As all compounds bind the antibody with very similar affinities, these effects cannot be simply attributed to selective binding by the antibody. In fact, ketal 4, which shows no measurable catalysis, acts as a competitive inhibitor of 14D9-catalyzed hydrolysis of 6a. Both the solution and the antibody-catalyzed hydrolysis of the ketal substrates are shown to be specific acid catalyzed, involving the unimolecular cleavage of the protonated substrate or antibody-substrate complex in the rate-determining step. Reactivity effects from the acid catalyst itself on ketal hydrolysis (reagent-controlled reactivity) are ruled out under this mechanistic scheme.

Stereospecificity of hydrogen transfer by the NADP-linked alcohol dehydrogenase from the thermophilic bacterium Thermoanaerobium brockii.

Class A and class B NAD(H)/NADP(H) coenzyme-dependent dehydrogenases distinguish between the diastereotopic hydrogens pro-R and pro-S at position 4 of the cofactor. We investigated the stereochemistry of hydride transfer in reactions catalyzed by an unusual thermophilic, zinc-containing, NADP-linked enzyme Thermoanaerobium brockii alcohol dehydrogenase (TBAD). Using proton NMR spectroscopy of monodeuterated alcohols and coenzymes we found that TBAD is a class A enzyme that transfers the pro-R hydrogen from the pyridine 4 position of the reduced coenzyme. This stereospecificity is stable over (a) a broad range of temperatures up to 70 degrees C, (b) different concentrations of the coenzyme (catalytic or stoichiometric) and (c) a wide scope of substrates. Although NAD+ is not an effective coenzyme for TBAD, NADP+ and its synthetic analogs, 3-acetylpyridine-ADP+ and thio-NADP+, can be used successfully.