Stereoselective synthesis of alkynyl C-2-deoxy-beta-d-ribofuranosides via intramolecular nicholas reaction: A versatile building block for nonnatural C-nucleosides

The reaction of 3,5-di-O-benzyl-2-deoxy-d-ribofuranose with various alkynyllithium reagents afforded diastereomeric mixtures of the corresponding ring-opened alkynyldiols. The resulting diastereomeric mixtures were successively treated with Co(2)(CO)(8), a catalytic amount of TfOH, Et(3)N, and iodine in one pot to give alkynyl C-3,5-di-O-benzyl-2-deoxy-beta-d-ribofuranosides with high beta-selectivities. The cobalt-mediated cyclization (intramolecular Nicholas reaction) is reversible; thus, thermodynamically more stable beta-anomers were obtained preferentially. The alkynyl C-deoxyribofuranosides were converted to a variety of C-deoxyribofuranoside derivatives.     

DNA binding properties of oligodeoxynucleotides containing pyrrolidino C-nucleosides

We have incorporated pyrrolidino-C-nucleosides (pyrrolidino-pseudonucleosides) containing the base uracil and N-1-methyl uracil into oligodeoxynucleotides and compared their thermal duplex and triplex stabilities with unmodified or pseudouridine-containing oligodeoxynucleotides. We find relative destabilizations of triplex formation by ca. -13 to -1 degrees C per modification (relative to thymidine) in a strongly sequence dependent mode. Duplex formation is less destabilizing and more homogeneous with -4 to -2 degrees C per modification.     

Luminescent Ir(III) complex exclusively made of polypyridine ligands capable of intercalating into calf-thymus DNA

Efficient intercalation of a luminescent Ir(III) complex exclusively made of polypyridine ligands in natural and synthetic biopolymers is reported for the first time. The emission of the complex is largely enhanced in the presence of [poly(dA-dT)(2)] and strongly quenched in the presence of [poly(dG-dC)(2)]. By comparing the emission decays in DNA and in synthetic polynucleotides, it is proposed that the emission quenching of the title compound by guanine residues in DNA is no longer effective over a distance of four dA-dT base pairs.     

5-hydroxyuracil can form stable base pairs with all four bases in a DNA duplex

NMR studies, UV-monitored melting experiments, and ab initio calculations show that 5-hydroxyuracil, produced by the oxidative de-amination of cytosines by reactive oxygen species, can form stable base-pairs with dA, dG, dC and dT residues in a DNA duplex, providing a basis for the in-vivo incorporation of 5-hydroxyuracil during DNA replication.     

Synthesis and redox-active base-pairing properties of DNA incorporating mercapto C-nucleosides

Here, we describe the synthesis and incorporation of the nucleoside base analogue C-deoxyribonucleoside 3 carrying thiophenol into DNA. The 1′-β compound 3 was synthesized by Friedel-Crafts alkylation, followed by deprotection. The coupling reaction with 3,5-ditoluoyl-1-α/β-methoxy-2-deoxy-d-ribose and diphenyldisulfide in the presence of SnCl₄ afforded the α/β mixture 2 (β/α=2.8), and the β-form was separated by silica gel chromatography. After formation of the phosphoramidite derivative, the C-nucleoside 3 was incorporated into DNA. When the mercapto-bases were incorporated into complementary singled-stranded (ss) DNAs, the resulting duplex displayed high thermal stabilization on treatment with bubbling O₂ (T_m 73 °C), but was destabilized in the presence of mercaptoethanol (T_m 33 °C). CD spectra showed that the duplex had a right-handed double-stranded structure. Imino proton NMR studies of temperature stability suggested that the strength of hydrogen bonding around the mercapto C-nucleoside was larger when treated with bubbling O₂ than when in treated with reducing agent. Thus, formation of the base-to-base disulfide bond increased the stability of the duplex; correspondingly, reduction of the disulfide to two thiol bases destabilized the DNA reversibly. The duplex-forming disulfide base pair showed resistance to exonulease III. The present strategy could be used to introduce new functionalities into cells and novel biomaterials.     

Interaction of phenazine with water and DNA bases

The fluorescence spectrum of aqueous phenazine (PZ), an N-heterocyclic compound, shows some interesting features that indicate the formation of PZ-water complex in the excited state. Two types of complexes are postulated; Type I, formed by the association of water molecule with one of the nitrogen of PZ and Type II, formed by the association of water molecules with both the nitrogen of PZ. In addition, PZ also interacts with the DNA bases, adenine and thymine and the corresponding nucleosides, adenosine and thymidine. Fluorescence and laser flash photolysis studies indicate that the mode of interaction may be photoinduced electron transfer.     

Artificial molecular-level machines. Dethreading-rethreading of a pseudorotaxane powered exclusively by light energy

The reversible light-driven dethreading-rethreading of a pseudorotaxane is obtained in solution by exploiting the (E)-(Z) photoisomerisation of azobenzene, and monitored through fluorescence signals.     

Complexes of pyrimidine DNA bases with thallium(I)

The stability constants of complexes of a thallium(I) ion with cytosine and thymine were determined in aqueous solution at 25°C and 0.1 mol dm⁻³ ionic media, using a combination of potentiometric and spectrophotometric techniques. Sodium perchlorate was used to maintain the ionic strength. The composition of the formed complexes was determined and it was shown that thallium(I) forms two mononuclear 1:1 species with cytosine of the type TIHL⁺ and TIL, and a mononuclear 1:1 complex species with thymine in the form TIHL, in the pH range of study (1–11), where L represents the fully dissociated ligand. The cumulative stability constants, β _xyz, of the complexes, [(thallium)_x(H)_y(ligand)_z], were calculated by a nonlinear fitting method and their distributions were presented as a function of-log[H⁺]. This text was submitted by the authors in English.     

Structural characterisation of trimethylsilyl-protected DNA bases

The structures of the silylated DNA bases, bis(trimethylsilyl)thymine (1), bis(trimethylsilyl)cytosine (2), bis(trimethylsilyl)adenine (3) and tris(trimethylsilyl)guanine (4), have been determined. 1 is O-silylated and displays no intermolecular interactions. 2 is silylated at both exocylic O, N positions and forms a chain structure through intermolecular NH…O and NH…N hydrogen bonds. 3 contains two SiMe₃ groups, on the exocylic NH and endocyclic N⁹ position, respectively; of two independent molecules in the asymmetric unit, one dimerises through complementary NH…N hydrogen bonds, while the other forms a strained intramolecular hydrogen bond through the same pair of donor and acceptor centres. 4 incorporates N, N, O–SiMe₃ moieties and forms chains via bifurcated CH…O/N hydrogen bonds, while the NH function remains unexploited. The effects of silylation on these pyrimidine and purine ring structures are also discussed in comparison with the native bases.

The structures of the silylated DNA bases, bis-(trimethylsilyl)thymine (1), bis-(trimethylsilyl)cytosine (2), bis-(trimethylsilyl)adenine (3) and tris-(trimethylsilyl)guanine (4), have been determined. While 1 displays no intermolecular interactions. 2 forms a chain structure through intermolecular NH…O and NH…N hydrogen bonds, 3 incorporates two independent molecules in the asymmetric unit, one dimerises through complementary NH…N hydrogen bonds while the other forms a strained intramolecular hydrogen bond through the same pair of donor and acceptor centres and 4 forms chains via bifurcated CH…O/N hydrogen bonds while the NH function remains unexploited.     

Selective pairing of polyfluorinated DNA bases

Novel selective non-hydrogen-bonding DNA base pairs utilizing fluorinated nucleoside analogues have been investigated. Melting studies of DNA duplexes containing 2,3,4,5-tetrafluorobenzene and 4,5,6,7-tetrafluoroindole bases on opposite strands show greater stabilization of the duplex compared with nonfluorinated hydrocarbon controls. Overall, these hydrophobic analogues are destabilizing compared with natural base pairs but are stabilizing compared with natural base mismatches. Such selective pairing may be due to solvent avoidance of these hydrophobic structures, burying their surfaces within the duplex. Our findings suggest that polyfluoroaromatic bases might be employed as a new, selective base-pairing system orthogonal to the natural genetic system.     

Single base interrogation by a fluorescent nucleotide: each of the four DNA bases identified by fluorescence spectroscopy

Nucleoside C, which contains a rigid nitroxide spin label, is effectively reduced in DNA by sodium sulfide to the corresponding amine, yielding a fluorescent probe (Cf) that can report the identity of its base-pairing partner in duplex DNA.     

Electron-transfer oxidation properties of DNA bases and DNA oligomers

Kinetics for the thermal and photoinduced electron-transfer oxidation of a series of DNA bases with various oxidants having the known one-electron reduction potentials (E(red)) in an aqueous solution at 298 K were examined, and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of DNA bases and the intrinsic barrier of the electron transfer. Although the E(ox) value of GMP at pH 7 is the lowest (1.07 V vs SCE) among the four DNA bases, the highest E(ox) value (CMP) is only 0.19 V higher than that of GMP. The selective oxidation of GMP in the thermal electron-transfer oxidation of GMP results from a significant decrease in the pH dependent oxidation potential due to the deprotonation of GMP*+. The one-electron reduced species of the photosensitizer produced by photoinduced electron transfer are observed as the transient absorption spectra when the free energy change of electron transfer is negative. The rate constants of electron-transfer oxidation of the guanine moieties in DNA oligomers with Fe(bpy)3(3+) and Ru(bpy)3(3+) were also determined using DNA oligomers containing different guanine (G) sequences from 1 to 10 G. The rate constants of electron-transfer oxidation of the guanine moieties in single- and double-stranded DNA oligomers with Fe(bpy)3(2+) and Ru(bpy)3(3+) are dependent on the number of sequential guanine molecules as well as on pH.     

Synthesis of C-nucleosides designed to participate in triplex formation with native DNA: specific recognition of an A:T base pair in DNA

[structure: see text] We have previously described a system of 2-aminoquinoline- and 2-aminoquinazoline-based C-deoxynucleosides (TRIPsides) that are designed to be incorporated into oligomers that can specifically bind in the major groove via Hoogsteen base pairing to any sequence of native DNA. The four TRIPsides are termed antiGC, antiCG, antiTA, and antiAT with respect to the Watson-Crick base pair targets that they bind. The first three TRIPsides have been prepared, characterized, and shown to form stable and sequence-specific triplexes. In the present study, we describe the preparation of two molecules, 2-amino-4-(2'-deoxy-beta-D-ribofuranosyl)quinazoline (7) and 2-amino-6-fluoro-4-(2'-deoxy-beta-D-ribofuranosyl)quinoline (14), that can serve as the remaining antiAT TRIPside. The phosphoramidites of 7 and 14 were prepared, but only the latter was successfully incorporated into DNA oligomers. It is demonstrated using UV-visible melting experiments that 14 forms sequence-specific intramolecular triplets with A:T base pairs at physiological pH.     

Preparation of stilbene-tethered nonnatural nucleosides for use with blue-fluorescent antibodies

The synthesis of the first examples of stilbene-tethered hydrophobic C-nucleosides is described. Compounds of this type are targeted for use with our recently reported "blue-fluorescent antibodies" with the aim of probing native and nonnatural DNA. The nucleophilic addition of aryl Grignard reagents to either a protected 2'-deoxy-1'-chloro-ribofuranose or a protected 2'-deoxy-ribonolactone was the key synthetic step and afforded C-nucleosides in good yields. Both routes resulted in a final product that was >/=90% of the beta-anomer. Amide- and ether-based linkers for attachment of trans-stilbene to the nucleobase were assessed for utility during synthesis and in binding of the ligands to a blue-fluorescent monoclonal antibody. X-ray structures of each complex were obtained and serve as a guideline for second-generation stilbene-tethered C-nucleosides. The development of these hydrophobic nucleosides will be useful in current native and nonnatural DNA studies and invaluable for investigations regarding novel, nonnatural genomes in the future.     

Reversible logic circuits made of DNA

We report reversible logic circuits made of DNA. The circuits are based on an AND gate that is designed to be thermodynamically and kinetically reversible and to respond nonlinearly to the concentrations of its input molecules. The circuits continuously recompute their outputs, allowing them to respond to changing inputs. They are robust to imperfections in their inputs.     

Ab initio study of naphtho-homologated DNA bases

Naphtho-homologated DNA bases have been recently used to build a new type of size-expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naphtho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like forms of naphtho-thymine (yyT) and naphtho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naphtho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.     

Syntheses and crystal structures of four new organotin complexes with Schiff bases containing triazole

Four new organotin complexes, namely [(Bu₂Sn)₂O(EtO)(L1)]₂ (1), [(Bu₂Sn)₂O(EtO)(L2)]₂ (2), [(Bu₂Sn)₂O(EtO)(L3)]₂ (3) and [Ph₃Sn(L4)] · 0.5H₂O (4), were obtained by reactions of Bu₂SnO and Ph₃SnOH with 4-phenylideneamino-3-methyl-1,2,4-triazole-5-thione (HL1), 4-furfuralideneamino-3-methyl-1,2,4-triazole-5-thione (HL2), 4-(2-thienylideneamino)-3-ethyl-1,2,4 -triazole-5-thione (HL3) and 4-(3,5-di-t-butylsalicylideneamino)-3-ethyl-1,2,4-triazole-5-thione (HL4). Compounds 1-4 were characterized by elemental analysis, IR spectra and their structures were determined by single-crystal X-ray diffraction methods. Complexes 1-3 show similar structures containing a Sn₄O₄ ladder skeleton in which each of the exo tin atoms is bonded to the N atom of a corresponding thione-form deprotonated ligand. Complex 4 shows a mononuclear structure in which the tin atom of triphenyltin group is coordinated by the S atom of a thiol-form L4⁻ anion.     

Interaction of low-energy electrons with the pyrimidine bases and nucleosides of DNA

We report computed cross sections for the elastic scattering of slow electrons by the pyrimidine bases of DNA, thymine and cytosine, and by the associated nucleosides, deoxythymidine and deoxycytidine. For the isolated bases, we carried out calculations both with and without the inclusion of polarization effects. For the nucleosides, we neglect polarization effects but estimate their influence on resonance positions by comparison with the results for the corresponding bases. Where possible, we compare our results with experiment and previous calculations.     

Analysis of DNA adducts bases by capillary electrophoresis with amperometric detection.

We have developed a method for the detection of DNA adducts by combining capillary electrophoresis (CE) with the specificity of amperometric detection. Guanine is the most easily damaged base of the four normal DNA bases and many adducts of guanine have been found in DNA. These guanine adducts are often electrochemically active, while the normal bases with the exception of guanine are not. Therefore, CE with amperometric detection will be a promising method to study DNA damage. The four normal deoxynucleosides and two damaged deoxnucleosides N2-ethyldeoxyguanosine (N2-ethyl-dG) and 8-hydroxydeoxyguanosine (8-OH-dG), were completely separated by micellar electrokinetic chromatography (MEKC). Deoxyguanosine and the two damaged deoxynucleosides were identified using amperometric detection. The sensitivity of our system was comparable to that of UV detection. Analysis of DNA hydrolysis products was also performed briefly using this method.