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.     

Intermolecular alkyne hydroaminations involving 1,1-disubstituted hydrazines

[reaction: see text] Two readily prepared catalysts have been developed for the hydroamination of alkynes by 1,1-disubstituted hydrazines. The catalyses are facile with terminal alkynes and some internal alkynes. If the hydrazine bears an aryl group, Fischer cyclization can occur in a one-pot procedure. In addition, reactions with acetylene to produce a plethora of hydrazones are described. Catalytic reactions involving acetylene and substituted hydrazines are complete in less than 2 h at room temperature and 1 atm of pressure.     

Synthesis, characterization, and adsorption properties of nanocrystalline ZSM-5

Nanocrystalline ZSM-5 with a Si/Al ratio of 20 was synthesized using clear solutions and a hydrothermal synthesis procedure. The resulting ZSM-5 materials were characterized by powder X-ray diffraction, scanning electron microscopy (SEM), nitrogen adsorption isotherms, solid-state nuclear magnetic resonance, and toluene adsorption. A commercial ZSM-5 sample was similarly characterized for comparison with the synthesized materials. The particle sizes of the synthesized ZSM-5 samples were calculated using the measured external surface areas and were determined to be 15 and 60 nm. SEM images indicated that the ZSM-5 samples consist of agglomerated and possibly intergrown particles. Toluene adsorption measurements showed that the ZSM-5 sample with a particle size of 15 nm adsorbed approximately 50% more toluene than the other ZSM-5 samples, most likely due to the adsorption of toluene on the external surface. For the toluene adsorbed on the internal zeolite surface, approximately one toluene molecule was adsorbed per channel intersection for each of the ZSM-5 samples.     

Mediation of ultrafast light-harvesting by a central dimer in phycoerythrin 545 studied by transient absorption and global analysis

We report ultrafast femtosecond transient absorption measurements of energy-transfer dynamics for the antenna protein phycoerythrin 545, PE545, isolated from a unicellular cryptophyte Rhodomonas CS24. The phycoerythrobilins are excited at both 485 and 530 nm, and the spectral response is probed between 400 and 700 nm. Room-temperature measurements are contrasted with measurements at 77 K. An evolution-associated difference spectra (EADS) analysis is combined with estimations of bilin spectral positions and energy-transfer rates to obtain a detailed kinetic model for PE545. It is found that sub pulse-width dynamics include relaxation between the exciton states of a chromophore dimer (beta 50/60) located in the core of the protein. Energy transfer from the lowest exciton state of the phycoerythrobilin (PEB) dimer to one of the periphery 15,16-dihydrobiliverdin (DBV) bilins is found to occur on a time scale of 250 fs at room temperature and 960 fs at 77 K. A host of energy-transfer dynamics involving the beta 158, beta 82, and alpha 19 bilins occur on a time scale of 2 ps at room temperature and 3 ps at 77 K. A final energy transfer occurs between the red-most DBV bilins with a time scale estimated to be approximately 30 ps. The role of the centrally located phycoerythrobilin dimer is seen as crucial-spectrally as it expands the cross-section of absorption of the protein; structurally as it sits in the middle of the protein acting as an intermediary trap; and kinetically, as the internal conversion and subsequent red-shift of the excitation is extremely fast.     

Report on three aliphatic dimethylarsinoyl compounds as common minor constituents in marine samples. An investigation using high-performance liquid chromatography/inductively coupled plasma mass spectrometry and electrospray ionisation tandem mass spectrometry

Three water-soluble aliphatic arsenicals, dimethylarsinoyl acetate (DMAA), dimethylarsinoyl ethanol (DMAE), and dimethylarsinoyl propionate (DMAP), were identified in marine biological samples. Sample extracts in methanol/water (1 + 1) were analysed by cation-exchange high-performance liquid chromatography/inductively coupled plasma mass spectrometry (HPLC/ICPMS). Eluate fractions from the HPLC/ICPMS analyses containing the compounds in question were collected and subjected to analysis by electrospray ionisation tandem mass spectrometry (ESI-MS/MS), which provided supportive evidence for the structures of the three compounds. The concentrations of the three arsenicals were determined in 37 marine organisms comprising algae, crustaceans, bivalves, fish and mammals by HPLC/ICPMS. The three arsenicals DMAA, DMAE and DMAP, which occurred at microg kg(-1) concentrations, were detected in 25, 23 and 17 of the 37 samples analysed, respectively. The limits of detection were 2-3 microg kg(-1) dry mass. The data illustrate that the three compounds are common minor constituents in marine samples. This is the first report on DMAE and DMAP as naturally occurring species in marine samples. The presence of DMAA and DMAE supports a proposed biosynthesis of arsenobetaine (AB) from dimethylarsinoylribosides. Alternative proposals, which explain the presence of the compounds in marine samples, are addressed briefly in the paper.     

Chlorobiphenyls in sewage sludge; comparison of extraction methods

Six extraction methods for the analysis of PCBs (CB-28, CB-52, CB-101, CB-118, CB-138, CB-153 and CB-180) in sewage sludge were tested. A certified reference material (CRM 392) was used for the evaluation of the performance of the methods. Soxhlet-Dean-Starch with toluene as solvent, Soxhlet with hexane:acetone (2:3), cold digestion/saponification with 2 mol/L KOH in methanol followed by partition with hexane, and sonicated liquid-solid extraction with hexane:acetone (1:1) produced accurate results (97%, 93%, 104%, and 88%, respectively) with acceptable precisions (6.2%, 6.8%, 15% and 12%, respectively). Results in close agreement with the certified value for all congeners were obtained by treatment with BF₃-methanol prior to partition with dichloromethane. However, this is a tedious procedure and involves the use of hazardous compounds. Cyclic steam distillation produced results with an accuracy of around 80% and a good precision (5.2%). The very low consumption of solvents and other expensive chemicals by this technique and the possibility of analyzing the extract directly without clean-up make it an interesting alternative to the more sophisticated methods. Column elution with dichloromethane was found to be less efficient (61%), but it is a rapid, direct method with a low consumption of solvents and it may therefore serve as screening method. Received: 29 April 1997 / Revised: 30 July 1997 / Accepted: 6 August 1997     

Using spin dynamics of covalently linked radical ion pairs to probe the impact of structural and energetic changes on charge recombination

We have synthesized a series of structurally related, covalently linked electron donor-acceptor triads having highly restricted conformations to study the effects of radical ion pair (RP) structure, energetics, and solvation on charge recombination. The chromophoric electron acceptor in these triads is a 4-aminonaphthalene-1,8-dicarboximide (6ANI), in which the 4-amine nitrogen atom is part of a piperazine ring. The second nitrogen atom of the piperazine ring is part of a para-substituted aniline donor, where the para substituents are X = H, OMe, and NMe(2). The imide group of 6ANI is linked to a naphthalene-1,8:4,5-bis(dicarboximide) (NI) electron acceptor across a phenyl spacer in a meta relationship. The triads undergo two-step photoinduced electron transfer to yield their respective XAn(*)(+)-6ANI-Ph-NI(*)(-) RP states, which undergo radical pair intersystem crossing followed by charge recombination to yield (3)NI. Time-resolved electron paramagnetic resonance experiments on the spin-polarized RPs and triplet states carried out in toluene and in E-7, a mixture of nematic liquid crystals (LCs), show that for all three triads, the XAn(*)(+)-6ANI-Ph-NI(*)(-) RPs are correlated radical pairs and directly yield values of the spin-spin exchange interaction, J, and the dipolar interaction, D. The values of J are all about -1 mT and show that the LC environment most likely enforces the chair conformation at the piperazine ring, for which the RP distance is larger than that for the corresponding boat conformation. The values of D yield effective RP distances that agree well with those calculated earlier from the spin distributions of the radical ions. Within the LC, changing the temperature shows that the CR mechanism can be changed significantly as the energy levels of the RPs change relative to that of the recombination triplet.     

Sample preparation for high throughput accurate mass analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

An automated sample preparation for high throughput accurate mass determinations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been developed. Sample preparation was performed with an automated workstation and automated mass analyses were performed with a commercial MALDI-TOF mass spectrometer. The method was tested with a 41-sample library. MALDI-TOFMS was found to give the needed sensitivity, accurate mass measurement, and soft ionization necessary for structure confirmation, even of mixtures. A mass accuracy of 5 ppm or less was obtained in over 80% of known compound measurements. A mass accuracy better than 10 ppm was obtained for all measurements of known compounds. Analyses of parallel synthesis products resulted in 77% of the measurements with a mass accuracy of 5 ppm or better.