Retention Behavior of Nucleic Acid Bases and Purine Derivatives on Titania

The retention of nucleic acid bases and purine derivatives on titania was studied using a 0.4 mM acetic acid–sodium acetate buffer (pH 6.0) and 70% aqueous methanol as mobile phases. We observed that the retention strength of tested analytes on titania was dependent on the structural differences between pyrimidine and purine skeletons and the variety and number of substituents. The retention order was purine derivatives with methyl groups, pyrimidine bases and purine derivatives with hydrophilic functional groups, which were retained most strongly on titania. We concluded that the retention of each analyte was caused by the analyte’s hydrophobicity in the case of purine derivatives with methyl groups and pyrimidine bases. In the case of purine and its derivatives with hydrophilic functional groups, it was considered that the retention was dependent on the analyte’s ability to form chelates, and the variety and number of functional groups on C6 and C2.     

Syntheses of polyfluoroalkyl aryl ether

The reactions of methoxyphenol and dihydroxybenzene with hexafluoropropene were studied. Eight new compounds 2-9 were separated from the reaction mixture of catechol and hexafluoropropene. The formation of these products was explained through nucleophilic attack of the aryloxy anion on hexafluoropropene, followed by elimination and addition (Scheme 1). However, the reaction of resorcinol and hydroquinone with C₃F₄ only gave the simple addition products 10 and addition-elimination products Z, E-11, 12. All new compounds were characterized by ¹H and ¹⁹F NMR, IR, MS and elemental analyses. The ¹⁹F NMR of seven membered ring compounds 4 and 5 were discussed in detail.     

Chemical Investigations of the Molecular Origin of Biological Radiation Damage

The radiation damage observed when UV and ionizing radiations react on biological objects is caused in many cases by changes in the nucleic acids. Exposure of these compounds to UV radiation in vitro and in vivo leads, inter alia, to dimerization of the pyrimidine bases with formation of cyclobutane derivatives, and to addition of water to the 5,6-double bond of the pyrimidine bases to form derivatives of the 6-hydroxyhydropyrimidine system. The structure of the irradiation products has been established. The dimerization prevents the reduplication of the DNA, and the addition of water appears to be the cause of UV mutations. Ionizing radiation in aqueous solution results e.g. in addition of H and/or HO radicals to the 5,6-double bond of the pyrimidine bases and cleavage of the imidazole ring of the purine bases. The mutations caused by ionizing radiation are probably also due, in part, to the formation of 6-hydroxydihydropyrimidine derivatives.     

PHOTOCHEMICAL REACTION BETWEEN PROTEIN AND NUCLEIC ACIDS: PHOTOADDITION OF TRYPTOPHAN TO PYRIMIDINE BASES*1

Abstract— The photochemical interactions between tryptophan and nucleic acid bases were studied. When aqueous solutions of tryptophan were irradiated (Λ > 260 nm) at neutral pH in the presence of each of the nucleic acid bases, pyrimidine bases but not purine bases were altered. Air was found to decrease the rate of reaction. Two classes of photoproducts were isolated by thin layer and ion-exchange chromatography and partially characterized. One was the dihydro-pyrimidine forms of the base (see Reeve and Hopkins, 1979) and the other consisted of tryptophan-pyrimidine photoadducts. Four tryptophan-uracil and two tryptophan-thymine adducts each with a 1:1 molecular stochiometry were found. Spectroscopic measurements and a positive reaction with Ehrlich's reagent indicate that the indole nucleus remained intact, but that the pyrimidine base was reduced at the 5, 6 double bond. The absence of a positive ninhydrin reaction and the effect of pH on the quantum yield of the photoadduct formation indicated that the ionized a-amino acid group of tryptophan was involved in photoadduct formation. Indole derivatives lacking an a-amino group were also found to form photoadducts with pyrimidine bases. The experimental results are consistent with a reaction mechanism involving tryptophan excitation to the first excited singlet state as the initial event. Radical scavenging experiments indicate that tryptophan free radicals, formed by electron dissociation from the excited state, react with the ground state pyrimidine.     

Oxidative amination of cuprated pyrimidine and purine derivatives

Using regioselective cuprations (via magnesiations), various primary, secondary and tertiary aminated pyrimidine and purine derivatives were prepared by the oxidative coupling of lithium amidocuprates using chloranil. DNA and RNA units such as aminated uracil or thymine, and adenine, as well as a CDK inhibitor, purvalanol A, were all obtained under mild conditions and satisfactory yields.     

Photoionization of DNA and RNA bases,nucleosides and nucleotides through a combination of one- and two-photon pathways upon 266 nm nanosecond laser excitation

The 266 nm nanosecond laser photolysis of various purine and pyrimidine derivatives results in their photoionization (PI) as one of the primary photochemical pathways. Electron photoejection occurs through a combination of one- and two-photon mechanisms. The PI values depend on the substituents attached to the chromophore of the base. The net PI of the purine bases at 266 nm are of the same order of magnitude (10(-2)) as those of the pyrimidine bases under similar experimental conditions. The monophotonic component is approximately one-third of the net PI yield of the bases. A nonrelaxed singlet excited state intermediate is tentatively proposed for this pathway. It is proposed that this state is significantly stabilized by water solvation, transforming it into a charge transfer to solvent state from which the hydrated electron evolves.     

Computational design of ring-expanded pyrimidine-based DNA motifs with improved conductivity

Motivated by a promising expansion of the genetic alphabet and a successful design of conductive DNA bases justified from the hetero-ring-expanded purine base (G and A) analogs, we extend our hetero-ring expansion scheme to the pyrimidine bases (C and T) to examine the ring-expansion effects on various properties of these single-ring bases with a comparison with those in the double-ring purine case. Four kinds of the hetero-rings are considered to expand C and T, forming the C and T analogs (nC and nT), respectively. The relevant structures and properties were investigated by means of quantum calculations and molecular dynamics simulations. The results reveal that all the modified bases can form base pairs specifically with their natural counterparts and assemble duplex helices which have comparable stability to native ones. The HOMO-LUMO gaps of G-nC and A-nT are smaller than those of the natural pairs, and the assembled duplex helices ((G-nC)(12) and (A-nT)(12)) are diameter-enlarged but with smaller rise and twist, both of which favor DNA-conduction, as confirmed by ionization potentials and spin density distributions. In addition, the hetero-ring expansion can lower the activation barriers and reduce the reaction heats of the inter-base double proton transfers. In particular, as evidenced by NMR parameters and the excited states, the hetero-ring expansion leads to an enhancement of the transverse electronic communication between two pairing bases, clearly facilitating the conduction along the helices. Furthermore, the hetero-ring expansion effect on the pyrimidine bases is larger than that on the purine bases. In summary, this work presents clear theoretical evidence for the possibility of hetero-ring expanded pyrimidine bases as promising candidates for the motifs of the genetic alphabet and DNA nanowires.     

Practical Synthesis of Sugar Monophosphonucleotides

A reliable procedure for the preparation of sugar nucleoside monophosphates is presented, which involves condensation of an activated glycosyl‐1‐H‐phosphonate with an appropriately protected nucleoside and simple end‐product isolation via lithium perchlorate–induced precipitation. The utility of these methods is demonstrated by the preparation of a number of purine‐ and pyrimidine‐based sugar nucleoside monophosphate derivatives.     

Synthesis and antiviral evaluation of 2'-deoxy-2'-C-trifiuoromethyl beta-D-ribonucleoside analogues bearing the five naturally occurring nucleic acid bases

2'-Deoxy-2'-C-trifluoromethyl-beta-D-ribonucleoside derivatives bearing the five naturally occurring acid bases have been synthesized. All these derivatives were prepared by glycosylation reactions of purine and pyrimidine bases with a suitable peracylated 2-deoxy-2-C-trifluoromethyl sugar precursor to afford anomeric mixtures of protected nucleosides. After separation and deprotection, the resulting beta-nucleoside analogues were tested for their activity against HIV, HBV and several RNA viruses. However, none of these compounds showed significant antiviral activity nor cytotoxicity.     

Synthesis and structures of platinum(II) mixed ligand complexes with purine or piyrimidine bases of DNA and imidazole derivatives. Part 2

Summary Platinum(II) mixed ligand complexes with either purine or pyrimidine and imidazole derivatives were prepared and characterized by i.r., Raman and electronic spectroscopy. The compounds had the general formula [PtL¹L²Cl₂], where L¹ = adenine, guanine, hypoxanthine, cytosine, 2-aminopyrimidine; L² =N-methylimidazole,N-ethyl-imidazole orN-propylimidazole. The platinum(II) complexes had a square planar structure withcis-halogens. Purine or pyrimidine and imidazole derivatived bases acted as monodentate ligands coordinated via the N(7) of purine and N(3) of pyrimidine and imidazole derivatives.     

PHOTOCHEMICAL REACTIONS OF AROMATIC KETONES WITH NUCLEIC ACIDS AND THEIR COMPONENTS I—. PURINE AND PYRIMIDINE BASES AND NUCLEOSIDES*.

Abstract— The photochemical reactions of benzophenone and acetophenone with purine and pyrimidine derivatives in aqueous solutions have been investigated by flash photolysis and steady-state experiments. Upon excitation of these two ketones in aqueous solutions, two transient species are observed: molecules in their triplet state and ketyl radicals. The triplet state lifetimes are 65 μsec for benzophenone and 125 μsec for acetophenone. The ketyl radicals disappear by a second order reaction, controlled by diffusion. In the presence of pyrimidine derivatives, the triplet state is quenched and the ketyl radical concentration is decreased without any change in its kinetics of disappearance. Ketone molecules in their triplet state react with purine derivatives leading to an increase in the yield of ketyl radicals due to H-atom abstraction from the purines. Steady-state experiments show that benzophenone and acetophenone irradiated in aqueous solution at wavelengths longer than 290 nm undergo photochemical reactions. The rate of these photochemical reactions is increased in the presence of pyrimidine derivatives and even more in the presence of purine derivatives. Following energy transfer from the triplet state of benzophenone to diketopyrimidines, cyclobutane dimers are formed. The energy transfer rate decreases in the order orotic acid > thymine > uracil. Benzophenone molecules in their triplet state can also react chemically with pyrimidine derivatives to give addition photoproducts. All these results are discussed with respect to photosensitized reactions in nucleic acids involving ketones as sensitizers.     

A new route for the synthesis of 4,5-diamino-6-arylsulfanylpyrimidine derivatives and also purines on their basis

5-Acylamino-4-amino-6-arylsulfanylpyrimidines were formed by the reaction 3-arylsulfanyl-2-acylami- no-3-chloroacrylonitriles with benzamidine. The products were converted into new derivatives of 6-aryl- sulfanyl-substituted purine bases by treatment with polyphosphoric acid.     

Stability of the chlorinated derivatives of the DNA/RNA nucleobases,purine and pyrimidine toward radical formation via homolytic CCl bond dissociation

The chlorinated derivatives of nucleobases (and nucleosides), as well as those of purine, have well‐established anticancer activity, and in some cases, are also shown to be involved in the link between chronic inflammatory conditions and the development of cancer. In this investigation, the stability of all of the isomeric forms of the chlorinated nucleobases, purine and pyrimidine are investigated from the perspective of their homolytic C?Cl bond dissociation energies (BDEs). The products of these reactions, namely chlorine atom and the corresponding carbon‐centered radicals, may be of importance in terms of potentiating biological damage. Initially, the performance of a wide range of contemporary theoretical procedures were evaluated for their ability to afford accurate C?Cl BDEs, using a recently reported set of 28 highly accurate C?Cl BDEs obtained by means of W1w theory. Subsequent to this analysis, the G3X(MP2)‐RAD procedure (which achieves a mean absolute deviation of merely 1.3 kJ mol^?1, with a maximum deviation of 5.0 kJ mol^?1) was employed to obtain accurate gas‐phase homolytic C?Cl bond dissociation energies for a wide range of chlorinated isomers of the DNA/RNA nucleobases, purine and pyrimidine.     

Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents,and Beyond

Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.     

Synthesis and characterization of phosphorylated polystyrene derivatives for use in chromatography: DNA-like and phospholipid-like behavior

New functional crosslinked polystyrene derivatives have been synthesized. These polymers are substituted with chemical groups such as phosphate, purine, and pyrimidine bases, choline, serine, and nucleotides in order to mimic DNA and phospholipids. For this purpose, hydroxylated polystyrene beads were prepared, where monomer units were substituted via spacers. Then, phosphomonoester groups at various substitution ratios were grafted onto hydroxylated resins by using a phosphorus oxychloride method. Nucleosides and nucleic acid bases derivatives were coupled with dicyclohexylcarbodiimide on phosphorylated polymers whereas nucleotides, phosphorylcholine, and phosphorylserine were grafted on to hydroxylated polystyrene. The synthesis and characterization of these DNA-like and phospholipid-like polystyrene resins are described here extensively.     

Synthesis of novel 9-aryl and heteroarylpurine derivatives via copper mediated coupling reaction

A series of 9-(hetero)arylpurine derivatives has been prepared through N-arylation of 6-chloropurine with boronic acids in the presence of copper(II) acetate. Screening reaction conditions in terms of bases and solvents led to the successful coupling of a series of sterically demanding (hetero)arylboronic acids, never described so far. The coupling products were next readily converted into the target adenine derivatives. The described procedure provides easy access to original fragments for screening applications. Moreover these 9-aryl-6-chloropurine derivatives might be useful as intermediates for the preparation of purine derivatives with potential biological properties.     

An improved synthesis of 1-phenylpentafluoropropenes

1-Phenylpentafluoropropene and a number of its para- and ortho-substituted derivatives were prepared in high yields by reaction of hexafluoropropene with etheral solutions of corresponding phenylmagnesium bromides in sealed glass tubes under autogenous pressure. The products were obtained as mixtures of the Z and E isomers, which ratios varied from 1/2 to 1/6 in favour of the E forms. ¹⁹F n.m.r. and i.r. spectra and b.p. of the 1-phenylpentafluoropropenes are reported.     

Synthesis and structure of palladium(II) mixed complexes with DNA purine or pyrimidine bases and imidazole derivatives. Part I

Summary Palladium(II) mixed ligand complexes with purine or pyrimidine and imidazole derivatives were prepared and characterized by i.r., Raman and electronic spectroscopy. The compounds have the general formula [Pd(L₁)(L₂)(X₂)]; where L₁ = adenine, guanine, hypoxanthine, cytosine, 2-aminopyrimidine, 4(6)-hydroxypyrimidine; L₂ = N-methylimidazole, N-ethylimidazole or N-propylimidazole; X = Cl or Br. The complexes are square planar with cis-halogens. The purine, pyrimidine and imidazole bases act as monodentate ligands coordinated via the N(7) of purine and N(3) of pyrimidine and imidazole.     

Synthesis of Novel Nucleic Acid Mimics via the Stereoselective Intermolecular Radical Coupling of 3'-Iodo Nucleosides and Formaldoximes(1)

A highly convergent free radical coupling of alkyl iodides and oximes, mediated by bis(trimethylstannyl) benzopinacolate (8), has been utilized to prepare a series of dimeric nucleosides as mimics of natural nucleic acids. The systematic optimization of the reaction conditions allowed for the single-step conversion of the appropriate iodides and oximes into the 2'-deoxy dimers 9 in moderate to excellent yields. For example, the reaction of 3'-deoxy-3'-iodo-5'-(triphenylmethyl)thymidine (6a) with 3'-O-(tert-butyldiphenylsilyl)-5'-O-(methyleneimino)thymidine (7a) in the presence of 8 in degassed benzene gave an 81% yield of 3'-de(oxyphosphinico)-3'-(methyleneimino)-5'-O-(triphenylmethyl)thymidylyl-(3'-->5')-3'-O-(tert-butyldiphenylsilyl)thymidine (9a). Similarly prepared were dimers containing both pyrimidine (thymine, 5-methylcytosine) and purine (adenine, guanine) bases. The reaction was highly stereoselective, giving only a single dimeric species having the ribo-configuration of the newly introduced C-3'-branched methylene moiety. Also prepared were dimers 16, incorporating 2'-O-methyl ribonucleosides in both halves of the dimer. This required the synthesis of 3'-deoxy-3'-iodo-2'-O-methyl nucleosides 12 as well as 2'-O-methyl-5'-O-methyleneimino nucleosides 15. For example, 5'-O-(tert-butyldiphenylsilyl)-3'-deoxy-3'-iodo-2'-O-methyl-5-methyluridine (12e) was prepared in 80% yield by displacement of the corresponding triflate with Bu(4)NI. Also prepared were the suitably protected 3'-deoxy-3'-iodo adenosine and guanosine derivatives. Compounds 15 were prepared in high yield by a regioselective Mitsunobu reaction to give the corresponding 5'-O-phthalimido nucleosides 13, which were subsequently converted to the requisite oximes 15. In the 2'-O-methyl series, the pinacolate coupling reaction proceeded with efficiency equal to that observed for the 2'-deoxy series 9, but with slightly less stereoselectivity, giving predominantly the C-3'ribo products 16, contaminated with 5-25% of the epimeric material. Mixed base dimers containing both pyrimidine and purine bases at all possible positions, including purine-purine dimers were prepared. The hydroxylamine or methyleneimino (MI) backbone of several representative dimers so prepared was converted via methylation to give the corresponding methylenemethylimino (MMI)-linked compounds, which are novel phosphate surrogates for use in antisense oligonucleotides.     

New approaches to β-trifluoromethylated enone derivatives

β-Trifluoromethylated enaminones 1 were prepared stereospecifically or high stercoselectively in 31-92% yields from the reaction of Weinreb amides with trifluoropropynyl lithium, followed by quenching with H₂O in the presence of amine derivatives. β-Trifluoromethylated enaminone 1a was reacted with aryl or alkynyl Grignard reagents to give Michael addition products 5 at 0 °C, whereas addition-elimination adducts, β-aryl (or alkynyl)-β-trifluoromethylated enones 6, were obtained stereospecifically in 50-92% yields after stirring at room temperature for several hours.