Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Diphosphine-phosphenium coordination complexes representing monocations with pendant donors and ligand tethered dications

Homoatomic P-P coordinate bonding is exploited to prepare the first examples of triphosphorus monocations and tetraphosphorus dications using dimethylphosphenium or diphenylphosphenium Lewis acceptors with diphosphinomethane, diphosphinoethane, diphosphinohexane, or diphosphinobenzene ligands. Solid-state structures and spectroscopic characterization data for complexes involving bis(diphenylphosphino)methane ligands show coordination of only one donor site of the diphosphine ligand in the monocations, and chelate complexation is not observed. Tetraphosphorus dications are observed with longer diphosphines, in which the ligand tethers two phosphenium acceptors. The structural preferences between monocations with pendant phosphines and tethered dications are dependent on intramolecular steric interactions and the flexibility of the tether.     

Gas-Phase cationization and protonation of neutrals generated by matrix-assisted laser desorption

The ionization mechanisms involved in matrix-assisted ultraviolet laser desorption/ionization (MALDI) were studied with a time-of-flight mass spectrometer. When protonated or cationized quasimolecular ions generated by MALDI are not extracted promptly, their abundance is a function of the delay time between laser irradiation and ion extraction, maximizing at an optimum delay time (DTM) of a few hundred nanoseconds. The ion abundance at DTM exceeds that of prompt extraction by a factor of 2 or more. Increasing the cation density near the sample surface reduces the DTM, whereas increasing the desorption laser irradiance has the opposite effect. The enhancement suggests extensive gas-phase ion-molecule reactions after irradiation by the desorption laser has ceased.     

Rapid transacylations of activated ester substrates bound to the primary side β-cyclodextrin-cyclen conjugate and its M2+ complexes

The ability of cyclodextrins to effect rapid transacylations of bound substrates has been well studied. One important difference between cyclodextrin and enzyme-mediated transacylation is the pH required. Because the pK _a of a cyclodextrin secondary-side hydroxyl group is about 12, transacylations are accelerated in the presence of cyclodextrin under basic conditions (pH > 10.5). In 1988, our group reported the synthesis of cyclodextrin with attached cyclen-Co(III) complexes; significant acceleration in the reaction withp-nitrophenyl acetate was observed only with the primary side derivative. Of course, metalloenzymes utilize M²⁺ and not M³⁺ catalytic centers; in addition, large rate accelerations in the transacylations of both activated and unactivated substrates have been observed previously in systems utilizing M²⁺ ions (e.g., Zn, Cu, Ni) as well as M³⁺ ions (e.g. Co, Ir, Cr). In this paper, we describe the ability of CD-cyclen-M²⁺ conjugates to transacylate activated esters, amides, and phosphates. In addition, the ability of the apoenzyme mimic to effect transacylations was examined.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

Adsorption of aspartic acid on kaolinite

The interaction of aspartic acid with kaolinite was studied by potentiometric titrations and by adsorption measurements both at constant aspartate concentration (but varying pH) and at a constant pH of 5.5. The temperature was 25 degrees C, and the ionic medium 5 mM KNO3. Aspartic acid dissociation constants estimated from titrations agreed with those from the literature. The adsorption of aspartic acid to kaolinite was weak and varied only slightly with pH; 10-18% of 100 microM aspartic acid adsorbed to kaolinite at 100 m(2)L(-1) between pH 3 and 10. Data from the titrations and adsorption experiments were fitted closely by an extended constant-capacitance surface complexation model, in which monodentate outer-sphere complexes formed between deprotonated aspartic acid molecules and protonated sites on the variable-charge edges of the kaolinite crystals. There appeared to be no adsorption to the permanently charged crystal faces.     

Aromatic foldamers as scaffolds for metal second coordination sphere design

As metalloproteins exemplify, the chemical and physical properties of metal centers depend not only on their first but also on their second coordination sphere. Installing arrays of functional groups around the first coordination sphere of synthetic metal complexes is thus highly desirable, but it remains a challenging objective. Here we introduce a novel approach to produce tailored second coordination spheres. We used bioinspired artificial architectures based on aromatic oligoamide foldamers to construct a rigid, modular and well-defined environment around a metal complex. Specifically, aza-aromatic monomers having a tethered [2Fe–2S] cluster have been synthesized and incorporated in conical helical foldamer sequences. Exploiting the modularity and predictability of aromatic oligoamide structures allowed for the straightforward design of a conical architecture able to sequester the metal complex in a confined environment. Even though no direct metal complex–foldamer interactions were purposely designed in this first generation model, crystallography, NMR and IR spectroscopy concurred to show that the aromatic oligoamide backbone alters the structure and fluxional processes of the metal cluster.

Wrapping a [2Fe–2S] metal complex in an aromatic foldamer helix is introduced as a new approach to tailor a second coordination sphere.     

Structural and Spectroscopic Studies of Halocuprate(I) and Haloargentate(I) Complexes [M2XnX′4−n]2−

The complexes [Cu₂Br₄]^2?, [Cu₂I₄]^2?, [Cu₂I₂Br₂]^2?, [Cu₂I₃Cl]^2?, [Ag₂Cl₄]^2? have been characterized as their isomorphous bis(triphenylphosphoranylidene)ammonium ([Ph₃PNPPh₃]⁺ = PNP⁺) salts by single crystal structural determinations. All anions show the centrosymmetric doubly halogen‐bridged forms [XM(μ‐X)₂MX]^2? with three‐coordinate metal atoms that have been observed in [M₂X₄]^2? complexes with other large organic cations. In [Cu₂I₂Br₂]^2? the iodide ligands occupy the bridging positions and the bromide the terminal positions, while in [Cu₂I₃Cl]^2?, obtained in an attempt to prepare [Cu₂I₂Cl₂]^2?, two of the iodide ligands occupy the bridging positions with the third iodide and the chloride ligand occupying two statistically disordered terminal positions. In [Ag₂Cl₄]^2? the distortion from ideal trigonal coordination of the metal atom is greater than in the copper complexes, but less than in other previously reported [Ag₂Cl₄]^2? complexes with organic cations. The ν(MX) bands have been assigned in the far‐IR spectra, and confirm previous observations regarding the unexpectedly simple IR spectra of [Cu₂X₄]^2? complexes.