Unraveling the aflatoxin-FAPY conundrum: structural basis for differential replicative processing of isomeric forms of the formamidopyrimidine-type DNA adduct of aflatoxin B1

Aflatoxin B1 (AFB) epoxide forms an unstable N7 guanine adduct in DNA. The adduct undergoes base-catalyzed ring opening to give a highly persistent formamidopyrimidine (FAPY) adduct which exists as a mixture of forms. Acid hydrolysis of the FAPY adduct gives the FAPY base which exists in two separable but interconvertible forms that have been assigned by various workers as functional, positional, or conformational isomers. Recently, this structural question became important when one of the two major FAPY species in DNA was found to be potently mutagenic and the other a block to replication [Smela, M. E.; Hamm, M. L.; Henderson, P. T.; Harris, C. M.; Harris, T. M.; Essigmann, J. M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6655-6660]. NMR studies carried out on the AFB-FAPY bases and deoxynucleoside 3',5'-dibutyrates now establish that the separable FAPY bases and nucleosides are diastereomeric N5 formyl derivatives involving axial asymmetry around the congested pyrimidine C5-N5 bond. Anomerization of the protected beta-deoxyriboside was not observed, but in the absence of acyl protection, both anomerization and furanosyl --> pyranosyl ring expansion occurred. In oligodeoxynucleotides, two equilibrating FAPY species, separable by HPLC, are assigned as anomers. The form normally present in duplex DNA is the mutagenic species. It has previously been assigned as the beta anomer by NMR (Mao, H.; Deng, Z. W.; Wang, F.; Harris, T. M.; Stone, M. P. Biochemistry 1998, 37, 4374-4387). In single-stranded environments the dominant species is the beta anomer; it is a block to replication.     

Performance of cryogenic probes as a function of ionic strength and sample tube geometry

The pursuit for more sensitive NMR probes culminated with development of the cryogenic cooled NMR probe. A key factor for the sensitivity is the overall resistance of RF circuitry and sample. Lowering the coil temperature to approximately 25 K and the use of superconducting coil material has greatly reduced the resistance contribution of the hardware. However, the resistance of a salty sample remains the same and evolves as the major factor determining the signal-to-noise ratio. Several approaches have been proposed to reduce the resistance contribution of the sample. These range from encapsulating proteins in a water cavity formed by reverse micelles in low viscosity fluids to the optimal selection of low mobility, low conductivity buffer ions. Here we demonstrate that changing the sample diameter has a pronounced effect on the sample resistance and this results in dramatic improvements of the signal-to-noise ratio and shorter pi/2 pulses. We determined these parameters for common 5 mm NMR tubes under different experimental conditions and compared them to the 2, 3 and 4 mm tubes, in addition, 5mm Shigemi tubes were included since these are widely used. We demonstrate benefits and applicability of studying NMR samples with up to 4M salt concentrations in cryogenic probes. Under high salt conditions, best results in terms of short pi/2 pulses and high signal-to-noise ratios are obtained using 2 or 3mm NMR tubes, especially when limited sample is available. The 4 mm tube is preferred when sample amounts are abundant at intermediate salt conditions.     

Selective Homogeneous Palladium(0)-Catalyzed Hydrogenation of Alkynes to (Z)-Alkenes

Zero-valent palladium precatalysts containing rigid bidentate bis(arylimino)acenaphthene ligands (shown schematically) facilitate the highly stereoselective homogeneous catalytic hydrogenation of alkynes to (Z)-alkenes. Internal, terminal, aryl-substituted, and cyclic alkynes are suitable substrates, as are some enynes, which are chemoselectively hydrogenated to dienes. E=CO(2)Me; R(1), R(2)=4-OCH(3), 4-CH(3), 2,6-(CH(3))(2).     

Detection of an interchain carbinolamine cross-link formed in a CpG sequence by the acrolein DNA adduct gamma-OH-1,N( 2)-propano-2'-deoxyguanosine

Spectroscopic evidence is presented for the formation of a carbinolamine interchain cross-link in 5'-CpG-3' sequences, arising from the acrolein adduct gamma-OH-PdG. This may be important in understanding biological processing of acrolein-induced DNA damage in CpG sequences.     

Kinetics and mechanism of the general-acid-catalyzed ring-closure of the malondialdehyde-DNA adduct, N2-(3-oxo-1-propenyl)deoxyguanosine (N2OPdG-), to 3-(2'-Deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin- 10(3H)-one (M1dG)

3-(2'-Deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10(3H)-one (M1dG) is the major product of the reaction of deoxyguanosine with malondialdehyde (MDA). M1dG blocks replication by DNA polymerases in vitro and is mutagenic in vivo. M1dG reacts with hydroxide to form the N2-(3-oxo-1-propenyl)deoxyguanosine anion (N2OPdG-). This reaction is pH-dependent and reverses under neutral and acidic conditions to form M1dG. Here we describe the kinetics and mechanism of the ring-closure reaction in both the nucleoside and oligonucleotides. Kinetic analysis of absorbance and fluorescence changes demonstrates that ring-closure is biphasic, leading to the rapid formation of an intermediate that slowly converts to M1dG in a general-acid-catalyzed reaction. The dependence of the rate of the rapid phase on pH reveals the pKa for protonated N2OPdG is 6.9. One-dimensional 1H NMR and DQF-COSY experiments identified two distinct intermediates, N2OPdG-H and 8-hydroxy-6,7-propenodeoxyguanosine (HO-Prene-dG), that are formed upon acidification of N2OPdG-. Characterization of ring-closure in single-stranded and in melted duplex oligonucleotides shows M1dG formation is also acid-catalyzed in single-stranded oligonucleotides and that the denaturation of an oligonucleotide duplex enhances ring-closure. This work details the complexity of ring-closure in the nucleoside and oligonucleotides and provides new insight into the role of duplex DNA in catalyzing ring-opening and ring-closing of M1dG and N2OPdG.     

A critical investigation of the effects of the radio frequency potential on the trapping of externally injected ions in ion trap mass spectrometry

The sensitivity of all ion trap mass spectrometry (ITMS) methods is dependent on the trapping efficiency of the instrument. For ITMS instruments utilizing external ion sources, such as laser desorption, trapping efficiency is known to depend on the phase and amplitude of the radio frequency (RF) potential applied to the ring electrode at the time of ion introduction. It is remarkable that, in a considerable body of literature, no consensus exists regarding the effects of these parameters on the efficacy of trapping externally generated ions. In this paper, a summary of the literature is presented in order to highlight significant discrepancies. New laser desorption ion trap mass spectrometry (LD-ITMS) data are also presented, from which conclusions are drawn in our effort to clarify some of the confusion. Copyright 1999 John Wiley & Sons, Ltd.     

Photoelastic determination of stresses in multiple-pin connectors

The design, fabrication, and testing of photoelastic models of double-lap, multiple-pin connectors are discussed. Interest is in the stresses in the inner laps. These stresses are determined by constructing models with photoelastic inner laps and transparent-acrylic outer laps. The connectors have two pins, in tandem, parallel to the load direction. A photoelastic-isotropic point is shown to permit the evaluation of load sharing between the two pins. A numerical scheme, utilizing the isochromatic- and isoclinic-photoelastic data and a finite-difference representation of the planestress equilibrium equations, is used to compute the stresses around the two pins. Representative stress distributions and stress-concentration factors are shown.     

Convergent oxygenation of arachidonic acid by 5-lipoxygenase and cyclooxygenase-2

5-Lipoxygenase and cyclooxygenase-2 (COX-2) initiate the biosynthesis of distinct families of mediators from arachidonic acid (leukotrienes and prostaglandins, respectively) and are each the target of anti-inflammatory medications. Here we show that the product of 5-lipoxygenase, 5S-hydroxyeicosatetraenoic acid, is selectively and efficiently triply oxygenated by COX-2, implicating a cross-pathway interaction. The product is a unique diendoperoxide, potentially representing the parent compound of a novel group of lipid mediators.     

Spectroscopic characterization of interstrand carbinolamine cross-links formed in the 5'-CpG-3' sequence by the acrolein-derived gamma-OH-1,N2-propano-2'-deoxyguanosine DNA adduct

The interstrand N2,N2-dG DNA cross-linking chemistry of the acrolein-derived gamma-OH-1,N2-propanodeoxyguanosine (gamma-OH-PdG) adduct in the 5'-CpG-3' sequence was monitored within a dodecamer duplex by NMR spectroscopy, in situ, using a series of site-specific 13C- and 15N-edited experiments. At equilibrium 40% of the DNA was cross-linked, with the carbinolamine form of the cross-link predominating. The cross-link existed in equilibrium with the non-crosslinked N2-(3-oxo-propyl)-dG aldehyde and its geminal diol hydrate. The ratio of aldehyde/diol increased at higher temperatures. The 1,N2-dG cyclic adduct was not detected. Molecular modeling suggested that the carbinolamine linkage should be capable of maintaining Watson-Crick hydrogen bonding at both of the tandem C x G base pairs. In contrast, dehydration of the carbinolamine cross-link to an imine (Schiff base) cross-link, or cyclization of the latter to form a pyrimidopurinone cross-link, was predicted to require disruption of Watson-Crick hydrogen bonding at one or both of the tandem cross-linked C x G base pairs. When the gamma-OH-PdG adduct contained within the 5'-CpG-3' sequence was instead annealed into duplex DNA opposite T, a mixture of the 1,N2-dG cyclic adduct, the aldehyde, and the diol, but no cross-link, was observed. With this mismatched duplex, reaction with the tetrapeptide KWKK formed DNA-peptide cross-links efficiently. When annealed opposite dA, gamma-OH-PdG remained as the 1,N2-dG cyclic adduct although transient epimerization was detected by trapping with the peptide KWKK. The results provide a rationale for the stability of interstrand cross-links formed by acrolein and perhaps other alpha,beta-unsaturated aldehydes. These sequence-specific carbinolamine cross-links are anticipated to interfere with DNA replication and contribute to acrolein-mediated genotoxicity.     

Trimethylsilylated allyl complexes of nickel. The stabilized bis(pi-allyl)nickel complex [eta3-1,3-(SiMe3)2C3H3]2Ni and its mono(pi-allyl)NiX (X=Br, I) derivatives

Reaction of 2 equiv of K[1,3-(SiMe3)2C3H3] with NiBr2(dme) in THF at -78 degrees C produces the orange pi-allyl complex [1,3-(SiMe3)2C3H3]2Ni (1). Unlike the pyrophoric (C3H5)2Ni, the trimethylsilylated derivative only slowly decomposes in air (from hours to days). Both eclipsed (1a) and staggered (1b) conformations are found in solution; the eclipsed form irreversibly converts to the thermodynamically more stable staggered conformation when heated above 85 degrees C. Single-crystal X-ray structures obtained for both 1a and 1b confirm that the allyl ligands are bound in a trihapto manner to the metals and that trimethylsilyl substituents are in syn, anti arrangements. Density functional theory calculations performed on the bis(allyl)nickel complexes indicate that the substituents exert little effect on the basic metal-ligand geometries. Trimethylphosphine is converted to tetramethyltetraphosphane, (MeP)4, on reaction with 1. In toluene, 3-bromo-1,3-bis(trimethylsilyl)propene reacts with (COD)2Ni to produce the dimeric purple complex {[1,3-(SiMe3)2C3H3]NiBr}2 (2a). Both NMR and X-ray crystallographic data establish that the allyl ligands are staggered and that the trimethylsilyl substituents are in a syn, syn conformation. NMR data indicate that the reaction of one equivalent of 1 with Br2 in benzene produces an analogous complex (2b) with the allyl ligand substituents in a syn, anti configuration. When 1 equiv of 1 is treated with I2 in hexanes, the dark red dimeric complex {[1,3-(SiMe3)2C3H3]NiI}2 (3) is formed. Its X-ray crystal structure demonstrates that both eclipsed (3a) and staggered (3b) allyl conformation are present. The trimethylsilyl groups on the allyl ligands are in syn, anti arrangements in the two forms.