Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs

Molecular dynamics simulations of double-helical DNA oligomers have been performed to investigate differences in the structure, dynamics, and hydration of F-F and T-T mispairs. Hexamers containing F-F pairs were found to be more dynamic, especially in the region of the mispair itself. This dynamic variability derives from greater flexibility of F-F pairs. The T-T mispairs, on the other hand, were found to be comparatively tightly bound as wobble pairs. The major and minor groove edges of the T-T pairs were observed to be solvated at exposed carbonyl positions by at least one water molecule, while F-F pairs lacked solvating waters. Stacking interactions were nearly identical for T-T and F-F pairs, leading to similar average structures, even though F stacking was more dynamically variable. Solvation differences between F-F and T-T therefore support the steric exclusion model for nucleotide incorporation in DNA replication. Large differences in the orientation of minor groove functional groups, in addition to differences in solvation, further rationalize why F bases present during DNA extension events induce stalls. Two novel nucleotides are proposed to further elucidate minor groove interactions of DNA with polymerase molecules.Electronic Supplementary Material This Material consists of equilibration protocol, plots of center-of-mass stacking, water radial distribution functions, helical parameter dynamics, and dynamics data for a control AT sequence. Supplementary material is available in the online version of this article at Contribution to the Jacopo Tomasi Honorary Issue     

Precursor-directed biosynthesis of epothilone in Escherichia coli

Engineered biosynthetic pathways provide a powerful method for generating complex molecules. Precursor-directed biosynthesis, which combines chemical synthesis and enzymatic transformations, allows non-native starting materials to be incorporated into biosynthetic pathways. Using this approach, we achieved the production of the anticancer agent epothilone C in Escherichia coli. An E. coli strain was engineered to express the last three modules of the epothilone biosynthetic pathway (epoD-M6, epoE, and epoF) and the substrate required to complement the biosynthetic enzymes was obtained by chemical synthesis. Under high-density cell culture conditions, the E. coli strain processed exogenously fed synthetic substrate into epothilone C at levels comparable to the native host (1 mg/L) and at higher levels than other heterologous hosts. Importantly, this precursor-directed approach will allow chemical modifications to be introduced into the polyketide backbone and may ultimately provide access to epothilone analogues with improved pharmacological properties in quantities sufficient for clinical development.     

The mechanisms of decomposition of the 1- and 2-phenyltetralin radical cations

Mechanisms for decomposition of 1- and 2-phenyltetralins were investigated using low resolution mass spectrometry and metastable ion techniques. Four primary decompositions were observed for 1-phenyltetralin radical cations: (1) the loss of C₆H₆ via a 1,4-elimination; (2) the elimination of ethene via competing losses from carbons 3 + 4 and carbons 2 + 3; (3) the loss of C₈H₈, probably through a stepwise Diels-Alder cycloreversion to expel styrene; and (4) the loss of methyl radical involving carbon 2 and possibly carbon 4. Three major decompositions were observed for 2-phenyltetralin radical cations: (1) the loss of C₈H₈, possibly through a Diels-Alder cycloreversion to expel styrene; (2) the loss of C₆H₆ via a 1,3 elimination; and (3) the loss of methyl radical from carbon 1. Various exchange reactions occur prior to these losses, but they proved to be incomplete even for metastable ions.     

The IINS, IR and DFT studies of hydrogen bonds in 6-Furfuryl and 6-Benzylaminopurines

FTIR and IINS spectra of 6-Furfurylaminopurine (6-FAP) and 6-Benzylaminopurine (6-BAP) taken at different temperatures have been analysed and compared with the spectra calculated by the ab initio DFT/B3LYP method and the semiempirical PM3 method in the isolated molecule approximation, for the tautomers N3-H, N7-H and N9-H, and dimers with hydrogen bonds. For 6-FAP the best agreement between the calculated and experimental (at 20 K) spectra has been found for the N9-H tautomer, whose structure was established by X-ray diffraction. For 6-BAP the analogous agreement for the N9-H tautomer structure has been poor and much better for the N7-H tautomer. The vibrational spectra calculated for dimers of the molecules studied involved in hydrogen bonds, permitted also an interpretation of the bands whose positions and FWHM in the FTIR spectra changed with temperature.     

Partition and binding constants in micelles and vesicles from fluorescence quenching data

A method of analysing steady-state fluorescence quenching in compartmentalized systems is proposed which allows the evaluation of partition and binding constants where both association processes occur simultaneosly. The number of binding sites is shown to be dependent on the nature of the quencher.     

7-Benz[c] acridinemethanols as tetracyclic analogs of the 2-phenyl-4-quinolinemethanol antimalarials

A series of new 7-benz[c]acridinemethanols and 5,6-dihydro-7-benz[c]acridinemethanols was prepared as rigid, tetracyclic analogs of the antimalarial 2-phenyl-4-quinolinemethanols. Condensation of 5,7-dichloroisatin with 6-chloro-, 7-chloro-, and 6,7-dichloro-1-tetralone furnished halogenated 5,6-dihydro-7-benz[c]acridinecarboxylic acids, which were transformed into the corresponding acid chlorides, acyl malonates, α-bromomethyl ketones, and epoxides. Fully aromatic members of the series obtained via dehydrogenation of the 5,6-dihydro acids were likewise converted into epoxides via the acylmalonate route. Although all the epoxides studied proved to be exceptionally resistant to ring-opening by di-n-butylamine, probably on account of steric effects, they could be cleaved readily with piperidine or morpholine. Nmr spectra of the resulting amino alcohols suggest that these compounds exist in a single preferred conformation stabilized by internal O-H····N hydrogen bonding, and that free rotation about the side chain C-C bond does not occur at room temperature.     

Formamidino and carbamoyl-formamidino complexes of manganese and rhenium carbonyls

Lithio-1,3-diarylformamidines undergo reaction with the monomeric and dimeric carbonyl chlorides of manganese and rhenium, [M(CO)₅Cl] and [M(CO)₄Cl₂] to yield respectively the carbamoyl-formamidino [M(CO)₄-CON(R)CHNR] and the formamidino [M(CO)₄RNCHNR] types of complex. The carbamoyl complexes undergo decarbonylation to produce the formamidino complexes in low yield.     

A mathematical analysis of the bjerrum function for the stepwise equilibrium model

A mathematical analysis of the Bjerrum function is carried out. This function arises from the Stepwise Equilibrium Model, which is used to describe successive complex formation in systems consisting of free metal ion, free ligand, and all theML _i complexes that can form in solution. The appropriate root of the Bjerrum polynomial allows the determination of the concentrations of all species present in solution, given the initial concentrations of metal and of ligand, and the equilibrium constants governing the system. It is proved that there is only one positive root of the Bjerrum polynomial, and thus that only a single equilibrium state can exist. It is also shown that the positive root of the Bjerrum polynomial can be reliably obtained by Newton's method, but only if the initialization point is properly chosen, and that the initial concentrationL of ligand is the optimum such point. Finding this root is a calculation that typically must be carried out at each iteration in nonlinear least squares procedures for determining equilibrium constants. Finally, the necessary mathematical analysis is carried out to determine the optimum initial concentrations of metal and lgand which maximize the resulting concentration of a particularML _i complex.     

Some reactions of 1-alkyl-1,2,3,4-tetrahydropyridines with organic azides. Synthesis of 1-alkylpiperidylidene-2-sulfonamides

The 1,3-dipolar cycloaddition reaction of 1-substituted-1,2,3,4-tetrahydropyridines 4a-d with organic azides 5 afforded the respective 1-substituted-piperidylidene-2-sulfonamides 6 . In contrast, the reaction of (E)-1-(1-propenyl)-1,2,3,4-tetrahydropyridine ( 4e ) with 4-chlorobenzenesulfonyl azide yielded 6m as well as 1-(4-chlorophenyl)sulfonimine-1,2,3,4-tetrahydropyridine ( 7 ) arising from addition of the azide to the (E)-1-(1-propenyl) substituent of 4e .     

Light-emitting diode-induced fluorescence detection of native proteins in capillary electrophoresis

A continuous-wave 280 nm light-emitting diode (LED) was used as the excitation source for native fluorescence detection of proteins in CE. The operating current and temperature of the LED were optimized in order to achieve high luminescence power. It was found that a forward current of 30 mA and a temperature of approximately 5 degrees C gave the best S/N. By using a set of two ball lenses to focus light from the LED, we achieved a spot of approximately 200 mum with a power of 0.1-0.2 mW on the detection window. Fluorescence was collected with a ball lens at 90 degrees angle through a bandpass filter onto a photomultiplier tube. In CZE an LOD of 20 nM for conalbumin was reached. In capillary gel electrophoresis all eight proteins from a commercial standard kit were detected with high S/N. For a 10 microg/mL total protein mixture, S/N was better than 3 for all proteins in solution. Further improvement in LOD should be possible on utilization of an LED with higher luminescence power.