Highly selective adenine recognition by a macrocyclic host molecule employing multiple hydrogen bonding and π-π stacking interactions

A new macrocyclic host, which contains a 2,6-bis(oxazol-2-yl)pyridine unit and a 2,7-dialkoxynaphthalene unit tethered by the appropriate length of alkyl side chains is prepared. This host undergoes highly selective complex formation with an adenine nucleobase, accompanied by a fluorescence response in CHCl₃ by a combination of multiple hydrogen bonding and π-π stacking interactions.     

Binary and ternary chromium(III) complexes with cellular reductants and DNA components isolated from redox type systems. Part 2. Chromium(VI)—glutathione—adenine (adenosine,ATP)

The reduction of CrO₃ with an excess of glutathione and its interaction with DNA fragments (adenine, adenosine) and the ATP nucleotide was studied by analysis of the isolated solid products. The precipitates were characterised by elemental analyses, FAB-mass spectral data, spectroscopic methods (u.v.–vis., i.r., f.i.r.) and magnetic measurements. The Cr^III complexes obtained from ternary systems appeared to be [Cr^III—glutathione] and [Cr^III—glutathione—adenine (adenosine, ATP)] species. The structure of the complexes has been proposed assuming hydrogen bonding between the Cr^III GSH complex and the DNA fragment.     

Gas-phase hydrogen/deuterium exchange of adenine nucleotides

Gas-phase hydrogen/deuterium exchange reactions of (de)protonated (sodiated) adenosine-5'-mono-, di- and triphosphate ions with CD(3)OD, CD(3)CO(2)D and ND(3) were achieved using a combination of electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry. The reaction kinetics are dependent on factors such as the charge state, the phosphate chain length, the properties of the exchange reactants and the sodium content. The results indicate that the overall H/D exchange may involve specific sites even if endowed with high energetic barriers. The enhanced reactivity exhibited by adenosine polyphosphate ions compared with adenosine-5'-monophosphate suggests a critical role of the polyphosphate chain in rendering conformationally accessible remote H-donor sites. Low-energy collision-induced dissociation of (sodiated) adenine nucleotides anions supports the aptitude of the (poly)phosphate chain in probing distant sites via the intermediacy of a cyclic structure.     

Adenine ribbon with Watson-crick and Hoogsteen motifs as the "double-sided adhesive tape" in the supramolecular structure of adenine and metal carboxylate

The cocrystals of adenine and metal (II) quinoline-2-carboxylates (M = Mn2+, Fe2+, Co2+) have been obtained by self-assembly. The complexes are composed of adenine ribbons with the AA22 pairing pattern involving both Watson-Crick and Hoogsteen faces in hydrogen bonding and the neutral molecules of carboxylate positioned in inorganic layers. The very compact supramolecular structure is made by the extensive system of hydrogen bonds and face-to-face pi-pi interactions.     

Measurement of adenine nucleotide levels with an adenine analyser as an index of freshness of porgy

In a prototype of an adenine analyser, adenosine and adenine nucleotides were derivatized with a fluorescent reagent, bromoacetaldehyde, after separation on a Hitachi gel No. 3012-N column by high-performance liquid chromatography. The previous analyser was improved by using a shorter reaction coil and by introduction of a Hitachi gel No. 3013-N with 5-microns particles of porous polystyrene-divinylbenzene, and applied to estimate the freshness of porgy. Total amounts of ATP, ADP and AMP in an isolated muscle just after death gradually decreased to 60% of the original amount after 5 h, and the ATP content rapidly decreased to 20% after 1 h. A good correlation was found between the levels of total adenine compounds and the energy charge values obtained from nineteen porgies frozen at a prerigour state. On the other hand, there existed no relationship between total adenine levels and the K values, which were indices for estimating freshness of fish. The analyser will be useful to evaluate the freshness of tissues and cells based on the higher contents of total adenine compounds, especially ATP.     

Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution

Rebek imides (3), formed from Kemp's triacid, were developed in the mid-1980's as model receptors for adenine derivatives. We report here the first account of their hydrogen-bonding preferences upon binding 9-ethyladenine (1a) in the solid state. Structural analysis begins with simple imides 3a-e that form discrete dimers, while bis-imide 4 forms ribbon-like structures in the crystalline phase. The hydrogen-bonding interface within each of the representative assemblies features short intermolecular N(3)imide...O(8*)imide* distances (ca. 2.95 A), indicative of two-point hydrogen bonding. Imides 3f-h could be co-crystallized with 1a; single-crystal X-ray analysis of the resulting complexes reveals hydrogen-bonding geometries nearly identical to those observed in nucleobase complexes of adenine and pyrimidine derivatives. Imides 3f and 3g form 2:1 ternary assemblies with 1a; the complex of the former, (3f)2 x 1a, displays both Watson-Crick- and Hoogsteen-type hydrogen bonding, whereas the complex of the latter, (3g)2 x 1a, shows the Hoogsteen motif and imide hydrogen bonding to N(3) of the purine base (N(3)adenine...N(3')imide = 3.07(1) A). Imide 3h forms a 1:1 complex with 1a (3h x 1a x CHCl3) and displays Hoogsteen binding exclusively. All of the 3 x 1a assemblies show C(adenine)...O(imide) distances (3.38-3.75 A) that are consistent with C-H...O hydrogen bonding. Base-pairing preferences for the Rebek imides are further explored in solution by 1H NMR one-dimensional NOE experiments and by computational means; in all cases the Hoogsteen motif is modestly favored relative to its Watson-Crick counterpart.     

Hydrogen bonding of adenine with benzoic acids in the solid state. An FTIR study

Complex formation by hydrogen bonding, in the solid-state, between adenine and benzoic acid derivatives, was studied by IR spectroscopy.     

A Biomimetic Heteroditopic Receptor for Zwitterions in Protic Media

The efficient synthesis of calix[6]cryptothiourea 6 was achieved through a two‐step sequence that involves a key [1+1] macrocyclization step. It was shown by NMR spectroscopy that this heteroditopic receptor can bind zwitterions in protic media with an outstanding selectivity for β‐alanine betaine G5 , which is likely due to a high complementarity between the two partners. This result constitutes a rare example of cavity complexation of a zwitterion by a calix[6]arene. In comparison with the parent urea‐based receptors, 6 behaves as a much more efficient host for betaines. This strengthening of the binding properties is due to the better preorganization of the tripodal hydrogen‐bonding cap as well as to the higher acidity of the thiourea groups and their poor ability to self‐associate. Remarkably, host 6 is able to perform solid–liquid as well as liquid–liquid extraction of G5 . Finally, 6 provides an excellent structural model for the binding site of glycine betaine G4 encountered in natural systems.     

Structure effects of the protonated lincomycin molecule on the mechanism of its complexation with organic compounds

The mechanism of complexation of the protonated lincomycin molecule with para-substituted nitrobenzenes in the gas phase is analyzed by quantum chemical methods. The regioselectivity of lincomycin protonation is treated in a B3LYP/6-31G(d′, p) approximation; the geometrical structure and conformation of the molecule are analyzed. The lincomycin molecule is protonated at the nitrogen atom of the pyrrolidine cycle. In stable conformers, a pseudovoid is formed and stabilized by intramolecular hydrogen bonding. The cross section of the pseudovoid (1.77–2.62 Å) is too small for the protonated lincomycin molecule to participate in host guest complexation with organic compounds. According to B3LYP/6-31G(d′, p) calculations, complexation of the protonated lincomycin molecule with nitrobenzenes occurs through hydrogen bonding.     

New Upper Rim Pyridine-Bridged Calix[4]arenes: Synthesis and Complexation Properties toward Neutral Molecules and Ammonium Ions in Organic Media

A new series of calix[4]arenes, diametrically bridged at the upper rim with pyridino systems, has been synthesized. The shape, rigidity, and chemical structure of the bridge influence the host-guest complexation properties of these systems in solution toward several neutral molecules having acidic C-H bonds. Additionally, selective complexation of methylammonium tosylate in comparison with other ammonium salts has been observed and the strength of this complexation enhanced by electron-donor ability of the p-substituent on the pyridine moiety of the calixarene host. X-ray crystal structures of endo complexes of host 5with malononitrile and nitromethane have been resolved, verifying specific C-H bonding with the hard oxygen and nitrogen atoms of the bridge and the soft aromatic ring of the calixarene.     

Homopairing possibilities of the DNA base adenine

Using calculations based on the ab initio density functional theory, we for the first time report all possible planar DNA base adenine homodimers. Two density functionals and both localized and plane wave basis sets were used, and the results are compared with previous quantum chemical and semiempirical calculations available for a few pairs. We find that there are 21 possible planar adenine pairs with variable binding energies ranging from -0.03 to -0.86 eV. More stable pairs are associated with two strong hydrogen bonds formed between the monomers, while the least stable pairs are characterized by two or one relatively weak bonds. We find that stable hydrogen bonds can be characterized by the difference charge density that shows well-developed regions of alternating excess and depletion of the electron charge similar to a "kebab" structure. The presented detailed information on all planar adenine pairs can be utilized, for example, in considering possible adenine monolayers seen on various surfaces.     

Quadracyclic adenine: a non-perturbing fluorescent adenine analogue

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300?nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456?nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.     

Binary and ternary chromium(III) complexes with cellular reductants and DNA components isolated from redox type systems. Part 3. Chromium(VI) – <Emphasis Type="SmallCaps">L</Emphasis>-ascorbic acid – adenine (adenosine,ATP)

The reduction of CrO3 with an excess of L-ascorbic acid and its interaction with DNA fragments (adenine, adenosine) and the ATP nucleotide was studied by the analysis of the isolated solid products. The precipitates were characterised by elemental analyses, FAB-mass spectral data, spectroscopic methods (u.v.–vis., i.r) and magnetic measurements. The Cr^III complexes obtained from ternary systems appeared to be [Cr^III–L-ascorbic acid] and [Cr^III–L-ascorbic acid–adenine (adenosine, ATP)] species. The structure of ternary complexes has been proposed assuming hydrogen bond formation between the [Cr^III–ascorbic acid] complex and the DNA components. The effect of main cellular reductants: cysteine, glutathione and L-ascorbic acid on the composition and structure of isolated products has been discussed.     

Highly selective imine-linked fluorescent chemosensor for adenine employing multiple hydrogen bonding

We investigated an imine-linked fluorescent receptor bearing both the hydrogen bond donor and the hydrogen bond acceptor motifs as recognition sites in the design of the receptor. The recognition behavior of the receptor toward various nucleobases was evaluated in CH₃CN/H₂O (95:5, v/v) solution. The receptor showed significant changes in fluorescent intensity with adenine, but it showed no such changes on the addition of other nucleobases.     

Density functional theory study on hydrogen‐bonded complexes of adenine with polyformamide molecules

The structures of hydrogen‐bonded complexes A–F_n (n = 2–7) of adenine with polyformamide molecules have been fully optimized at B3LYP/6‐31G(d) basis set level. All the formamide molecules prefer to be N? H proton donor rather than C? H proton donor and are favorably bound to the five‐numbered moiety of adenine. A displacement of formamide molecules to one side of adenine mean plane has happened with an increasing number of formamide molecules. An obvious effect of hydrogen‐bonding cooperativity can be seen during the complex process. The most interesting geometrical change of adenine upon the complex is the shortening of the bond C4? N6 resulting from the strengthening of the conjugation between the π system of the adenine ring and the lone pair of the nitrogen atom. An existence of weak N? H···π bonding interaction between the π system of adenine and N? H bond of F7 is found and further conformed by an natural bond orbital analysis specially carried out on A–F₇. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Multiple hydrogen bonding for reversible polymer surface adhesion

Specific and reversible adhesion of a terminal thymine-functionalized polystyrene (PS-thymine) was demonstrated for a silicon surface with complementary adenine recognition sites. A novel adenine-containing triethoxysilane (ADPTES), which was suitable for covalent attachment to silanol containing surfaces, was synthesized in one step from adenine and 3-isocyanatopropyl triethoxysilane (IPTES). 1H and 13C NMR spectroscopy and fast atom bombardment mass spectroscopy confirmed the chemical structure, and 29Si NMR spectroscopy indicated the absence of any premature hydrolysis of the alkoxysilane derivative. X-ray photoelectron spectroscopy (XPS) and water contact angle measurements indicated the attachment of PS-thymine to silicon surfaces that were modified with a mixture of ADPTES and 3-mercaptopropyl triethoxysilane (MPTES). PS-thymine attachment to surfaces that were modified with only MPTES was not observed. The exclusive attachment of PS-thymine to an ADPTES/MPTES-modified surface confirmed hydrogen bonding-mediated adenine-thymine association to silicon surfaces containing a sufficiently low concentration of adenine recognition sites. Although PS-thymine attachment to the ADPTES/MPTES-modified surfaces was insensitive to THF rinsing, the PS-thymine was completely removed from the surface upon DMSO rinsing because of the disruption of adenine-thymine hydrogen bonding with a more polar aprotic solvent. PS-thymine was successfully reattached to the ADPTES/MPTES-modified surface following the DMSO rinse, demonstrating the solvato-reversible nature of the adenine-thymine association.     

Nucleotide recognition by macrocyclic receptors

It is shown that complementary positioning of recognition sites (particularly hydrogen bonding, stacking and hydrophobic groups) into a macrocyclic structure can lead to very strong and specific complexation of uncharged organic molecules.     

Binary and ternary chromium(III) complexes with cellular reductants and DNA components isolated from redox type systems. Part 1. Chromium(VI)–cysteine–adenine (adenosine,ATP)

The reduction of CrO₃ with an excess of L-cysteine and its interaction with DNA fragments (adenine, adenosine) and ATP nucleotide was studied by analysis of the isolated solid products. The precipitates were characterised by elemental analyses, FAB mass spectral data, spectroscopic methods (u.v.–vis., f.i.r., i.r.) and magnetic measurements. The Cr^III complexes obtained appear to be various Cr^III cysteinate and adenine or ATP (but not adenosine) ternary species of the addition type bound through the hydrogen bonding network.