Functional Analysis of an Acid Adaptive DNA Adenine Methyltransferase from Helicobacter pylori 26695

HP0593 DNA-(N-6-adenine)-methyltransferase (HP0593 MTase) is a member of a Type III restriction-modification system in Helicobacter pylori strain 26695. HP0593 MTase has been cloned, overexpressed and purified heterologously in Escherichia coli. The recognition sequence of the purified MTase was determined as 5'-GCAG-3' and the site of methylation was found to be adenine. The activity of HP0593 MTase was found to be optimal at pH 5.5. This is a unique property in context of natural adaptation of H. pylori in its acidic niche. Dot-blot assay using antibodies that react specifically with DNA containing m6A modification confirmed that HP0593 MTase is an adenine-specific MTase. HP0593 MTase occurred as both monomer and dimer in solution as determined by gel-filtration chromatography and chemical-crosslinking studies. The nonlinear dependence of methylation activity on enzyme concentration indicated that more than one molecule of enzyme was required for its activity. Analysis of initial velocity with AdoMet as a substrate showed that two molecules of AdoMet bind to HP0593 MTase, which is the first example in case of Type III MTases. Interestingly, metal ion cofactors such as Co2+, Mn2+, and also Mg2+ stimulated the HP0593 MTase activity. Preincubation and isotope partitioning analyses clearly indicated that HP0593 MTase-DNA complex is catalytically competent, and suggested that DNA binds to the MTase first followed by AdoMet. HP0593 MTase shows a distributive mechanism of methylation on DNA having more than one recognition site. Considering the occurrence of GCAG sequence in the potential promoter regions of physiologically important genes in H. pylori, our results provide impetus for exploring the role of this DNA MTase in the cellular processes of H. pylori.

Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography

Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin. Structural details of similar adenine binding were reported in only one legume lectin, Dolichos biflorus, before this study. Here, we present the structure of the galactose-binding D. lablab lectin at different pH values in the native form and in complex with galactose and adenine. This first structure report on this lectin also provides a high resolution atomic view of legume lectin-adenine interactions. The tetramer has two canonical and two DB58-like interfaces. The binding of adenine, a non-carbohydrate ligand, is found to occur at four hydrophobic sites at the core of the tetramer at the DB58-like dimeric interfaces and does not interfere with the carbohydrate-binding site. To support the crystallographic observations, the adenine binding was further quantified by carrying out isothermal calorimetric titration. By this method, we not only estimated the affinity of the lectin to adenine but also showed that adenine binds with negative cooperativity in solution.

Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N-6-adenine DNA methyltransferases of Neisseria meningitidis

Phase variation (random ON/OFF switching) of gene expression is a common feature of host-adapted pathogenic bacteria. Phase variably expressed N-6-adenine DNA methyltransferases (Mod) alter global methylation patterns resulting in changes in gene expression. These systems constitute phase variable regulons called phasevarions. Neisseria meningitidis phasevarions regulate genes including virulence factors and vaccine candidates, and alter phenotypes including antibiotic resistance. The target site recognized by these Type III N-6-adenine DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome analysis was used to identify the recognition site for three key N. meningitidis methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY(m6)AG-3'), ModA12 (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC(m6)ACC-3') and ModD1 (exemplified by M.Nme579I) (5'-CC(m6)AGC-3'). Restriction inhibition assays and mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and atypical and is dependent on the type of pyrimidine at the central position, in combination with the bases flanking the core recognition sequence 5'-CGY(m6)AG-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome ranged from 4.6% at 5'-GCGC(m6)AGG-3' sites, to 100% at 5'-ACGT(m6)AGG-3' sites. Analysis of the distribution of modified sites in the respective genomes shows many cases of association with intergenic regions of genes with altered expression due to phasevarion switching.

Superior Performance of a MoS2-RGO Composite and a Borocarbonitride in the Electrochemical Detection of Dopamine, Uric Acid and Adenine

A MoS2-RGO composite and borocarbonitride (BC5N) have been used as electrodes to selectively detect dopamine and uric acid in the presence of ascorbic acid. Both the electrodes show excellent eletrocatalytic activity towards the detection of dopamine, the detection limits being 0.55 mu M and 2.1 mu M in the case of MoS2-RGO and BCN respectively. MoS2-RGO shows a linear range of current over the 1-110 mu M concentrations of dopamine, while BCN shows over the 2.3-20 mu M range. BCN also exhibits satisfactory performance in the oxidation of uric acid with a detection limit of 3.8 mu M and the linear range from 4 to 40 mu M. The MoS2-RGO has also been used to detect adenine as well.

High negative ion production yield in 30 keV F2+ + adenine (C5H5N5) collisions

In collisions between slow F2+ ions (30 keV) and molecular targets, adenine, scattered particle production yields have been measured directly by simultaneous detection of neutrals, positive and negative ions. The relative cross-section for a negative ion formation channel was measured to be 1%. Despite a slight decrease compared to a larger target, the fullerene C-60, the measured negative ion formation cross section is still at least one order of magnitude larger than the yield in ion-atom interactions.

Small-molecule-directed assembly: A gold nanoparticle-based strategy for screening of homo-adenine DNA duplex binders

By using AuNP-modified homo-adenine DNA conjugate as a model system, simple colorimetric and resonance Rayleigh scattering assays have been developed for screening small molecules that trigger the formation of the non-Watson-Crick homo-adenine duplexes. The assay presented here is more simplified in format as it involves only one type of ssDNA modified Au-NP, and can be easily adapted to high-throughput screening.

Nucleobase-metal hybrid materials: Preparation of submicrometer-scale, spherical colloidal particles of adenine-gold(III) via a supramolecular hierarchical self-assembly approach

We report a simple and effective supramolecular route for facile synthesis of submicrometer-scale, hierarchically self-assembled spherical colloidal particles of adenine - gold(III) hybrid materials at room temperature. Simple mixture of the precursor aqueous solutions of adenine and HAuCl4 at room temperature could result in spontaneous formation of the hybrid colloidal particles. Optimization of the experimental conditions could yield uniform-sized, self-assembled products at 1:4 molar ration of adenine to HAuCl4. Transmission electron microscopy results reveal the formation of hierarchical self-assembled structure of the as-prepared colloidal particles. Concentration dependence, ratio dependence, time dependence, and kinetic measurements have been investigated. Moreover, spectroscopic evidence [i.e., Fourier transform infrared (FTIR) and UV-vis spectra and wide-angle X-ray scattering data] of the interaction motives causing the formation of the colloidal particles is also presented.

Silver nanoparticles coated with adenine: preparation, self-assembly and application in surface-enhanced Raman scattering

We describe herein the preparation of silver nanoparticles (AgNPs) using nucleobase adenine as protecting agent through the in situ chemical reduction of AgNO3 with NaBH4 in an aqueous medium at room temperature. As-prepared AgNPs were characterized by UV-visible spectra, transmission electron microscopy and x-ray photoelectron spectroscopy. All these data confirmed the formation of AgNPs. On the basis of electrostatic interactions between as-prepared AgNPs and anionic polyelectrolyte poly(sodium 4-styrenesulfonate) (PSS), we successfully fabricated (PSS/AgNP)n (n = 0-9) multilayers on a 3-mercaptopropyltrimethoxysilane/AgNP functionalized indium tin oxide (ITO) substrate via the layer-by-layer self-assembly technique and characterized as-formed multilayers with UV-visible spectra. Furthermore, these ITO substrates coated with multilayers of different thickness were investigated as surface-enhanced Raman scattering (SERS)-active substrates using p-aminothiophenol as a probe molecule, implying that these multilayers substrates may be promising for a new type of SERS-active substrate.

A COMPARATIVE-STUDY ON STM IMAGING AND ELECTROCATALYTIC ACTIVITY OF DIFFERENT SURFACES MODIFIED WITH FLAVIN ADENINE-DINUCLEOTIDE

Flavin adenine dinucleotide (FAD) was modified onto the highly oriented pyrolytic graphite (hopg) and glassy carbon electrode (gee) surfaces with three methods, respectively. Corresponding image analysis for FAD-modified hopg surfaces has been performed by scanning tunnelling microscope (STM) for the first time. The molecular resolution STM image of FAD adsorbed on the freshly-cleaved hopg was obtained, the quantitative size determination suggests that the FAD molecules adsorb side lying on the substrate surface. The anodization treatment of hopg surface yields many pits, which were clearly observed under STM. These pits provide active sites on the hopg surface for modification and the treated hopg can strongly adsorb FAD molecules, the latter exhibiting an irregular cluster structure on such a surface. When FAD was electrochemically deposited on the substrate surface, a chain structure was successfully observed. The adsorbed FAD on anodized glassy carbon electrode (gee) surface can effectively catalyze the reduction of glucose oxidase, hemoglobin and myoglobin, with a large decrease in the overvoltage, whereas the deposited FAD film exhibits excellent electrocatalysis towards dioxygen reduction.

ELECTROCATALYTIC REDUCTION OF DIOXYGEN BY AN ELECTROCHEMICALLY POLYMERIZED FLAVIN ADENINE-DINUCLEOTIDE FILM

An electrochemically polymerized flavin adenine dinucleotide (FAD) film electrode is reported for the first time. The polymerized film was prepared by a two-step method. The electrocatalytic reduction of dioxygen at a glassy carbon electrode (GCE) modifie

Riboflavin, Flavin Mononucleotide and Flavin Adenine Dinucleotide in Human Plasma and Erythrocytes at Baseline and after Low-Dose Riboflavin Supplementation.

Background: Vitamin B2 exists in blood as riboflavin and its cofactors, flavin mononucleotide (FMN) and FAD. The erythrocyte glutathione reductase activation coefficient (EGRAC) has traditionally been used to assess vitamin B2 status in humans. We investigated the relationships of EGRAC and plasma and erythrocyte concentrations of riboflavin, FMN, and FAD in elderly volunteers and their responses to riboflavin administration. Methods: EGRAC and plasma and erythrocyte concentrations of riboflavin, FMN, and FAD were determined in 124 healthy individuals with a mean age of 69 years. The same measurements were made in a subgroup of 46 individuals with EGRAC 1.20 who participated in a randomized double-blind 12-week intervention study and received riboflavin (1.6 mg/day; n = 23) or placebo (n = 23). Results: Median plasma concentrations were 10.5 nmol/L for riboflavin, 6.6 nmol/L for FMN, and 74 nmol/L for FAD. In erythrocytes, there were only trace amounts of riboflavin, whereas median FMN and FAD concentrations were 44 and 469 nmol/L, respectively. Erythrocyte FMN and FAD correlated with each other and with EGRAC and plasma riboflavin (P

Novel nicotinamide adenine dinucleotide analogues as selective inhibitors of NAD-dependent enzymes

Three novel dinucleotide analogues of nicotinamide adenine dinucleotide (NAD+) have been synthesised from -ribonolactone. These compounds incorporate a thiophene moiety in place of nicotinamide and are hydrolytically stable. They have been evaluated as inhibitors of adenosine diphosphate ribosyl cyclase, glutamate dehydrogenase and Sir2 acyltransferase activities. Enzyme specificity and a high level of inhibition was observed for the dehydrogenase.

High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications.

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine–adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3'-5')-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554–1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis–syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield.

The electrochemical reduction of the purines guanine and adenine at platinum electrodes in several room temperature ionic liquids

The reduction of guanine was studied by microelectrode voltammetry in the room temperature ionic liquids (RTILs) N-hexyltriethylammonium his (trifluoromethanesulfonyl) imide [N-6.2.2.2][N(Tf)(2)], 1-butyl-3-methylimidazolium hexafluorosphosphate [C(4)mim] [PF6], N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide [C(4)mpyrr][N(Tf)(2)], 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C-4mim][N(TF)(2)], N-butyl-N-methyl-pyrrolidinium dicyanamide [C(4)mpyrr][N(NC)(2)] and tris(P-hexyl)-tetradecylphosphonium trifluorotris(pentafluoroethyl)phosphate [P-14,P-6,(6,6)][FAP] on a platinum microelectrode. In [N-6,N-2,N-2,N-2][NTf2] and [P-14,P-6,P-6.6][FAP], but not in the other ionic liquids studied, guanine reduction involves a one-electron, diffusion-controlled process at very negative potential to produce an unstable radical anion. which is thought to undergo a dimerization reaction, probably after proton abstraction from the cation of the ionic liquid. The rate of this subsequent reaction depends on the nature of the ionic liquid, and it is faster in the ionic liquid [P-14,P-6,P-6.6[FAP], in which the formation of the resulting dimer can be voltammetrically monitored at less negative potentials than required for the reduction of the parent molecule. Adenine showed similar behaviour to guanine but the pyrimidines thymine and cytosine did not; thymine was not reduced at potentials less negative than required for solvent (RTIL) decomposition while only a poorly defined wave was seen for cytosine. The possibility for proton abstraction from the cation in [N-6,N-2,N-2,N-2],[NTF2] and [P-14,P-6,P-6.6][FAP] is noted and this is thought to aid the electrochemical dimerization process. The resulting rapid reaction is thought to shift the reduction potentials for guanine and adenine to lower values than observed in RTILs where the scope for proton abstraction is not present. Such shifts are characteristic of so-called EC processes where reversible electron transfer is followed by a chemical reaction. (C) 2009 Elsevier B.V. All rights reserved.