Synthesis of the TT pyrimidine (6-4) pyrimidone photoproduct-thio analogue phosphoramidite building block

The phosphoramidite building block synthesis of the thio analogue at the 5,6-dihydropyrimidine C5 position of the thymidylyl(3'-5')thymidine (6-4) photoproduct 1 is presented. This compound was readily obtained from the appropriately protected dinucleotide P-methyl-5'-O-dimethoxytritylthymidilyl(3' --> 5')-4-thiothymidine 2 after irradiation at 366 nm, then S-sulfenylmethylation of the thiol function of the resulting (6-4) adduct, and phosphitylation of the 3'-hydroxyl group.     

Further insight in the photochemistry of DNA: structure of a 2-imidazolone (5-4) pyrimidone adduct derived from the mutagenic pyrimidine (6-4) pyrimidone photolesion by UV irradiation

Pyrimidine (6-4) pyrimidone photoproducts represent one of the major mutagenic and carcinogenic class of DNA damage produced by UV exposure. At present, besides their conversion to their Dewar valence isomer, (6-4) photoproducts are generally believed to be photostable, and the observed biological properties of Paterno-Büchi-derived photoproducts are, thus far, exclusively attributed to these two types of compounds. Using a model system (2) relevant to DNA photochemistry, we have observed that the 5'-base moiety of the (6-4) thymine dimer 3, under far-UV radiation, is able to undergo a ring contraction leading to a 2-oxoimidazoline, 1. This unprecedented secondary photochemical reaction constitutes the first report of a major photomodification affecting (6-4) photoproducts and strongly questions the biological stability of the (6-4) adducts under UV light with 2-imidazolone (5-4) pyrimidone adducts being possibly another source of endogenous DNA damage.     

The sugar conformation governs (6-4) photoproduct formation at the dinucleotide level

The LNA dinucleotide mimic of TpT whose two-sugar puckers are locked in the C3'-endo conformation selectively produces the corresponding cyclobutane pyrimidine dimer under 254 nm irradiation. In the natural series (TpT) the sugar puckers are in a major C2'-endo sugar conformation and the (6-4) photoproduct is also produced. Consequently, this study demonstrates that the C2'-endo conformation of the sugar pucker is necessary for (6-4) photoproduct formation.     

Decreased levels of (6-4) photoproduct excision repair in hybrid fish of the genus Xiphophorus

Selected hybridization in the fish genus Xiphophorus has been used for many years to study the genetics of malignant melanoma. Because DNA damage caused by ultraviolet radiation is implicated in the etiology of sunlight-induced melanoma, the heritability of mechanisms that mitigate DNA damage is a matter of some interest. We examined nucleotide excision repair of the two major types of DNA-damage induced by sunlight; the cyclobutane pyrimidine dimer (CPD) and the pyrimidine(6-4)pyrimidone dimer [(6-4)PD]. In most cases, removal of the (6-4)PD was more rapid than the CPD, and in many cases, the F1 hybrid showed reduced repair efficiency compared with the parental species. These data demonstrate reduced function in multienzyme hybrid systems and provide molecular support for potential reduced fitness in hybrid fish under conditions of environmental stress.     

Effects of a high-affinity antibody fragment on DNA polymerase reactions near a (6-4) photoproduct site

Pyrimidine (6-4) pyrimidone photodimers are major photoproducts that have mutagenic and carcinogenic consequences. One major reason for these biological effects of (6-4) photoproducts may be base mispairing/DNA replication errors due to hydrogen bonding to bases opposite these damaged sites. We synthesized a modified 41-mer DNA containing a (6-4) photoproduct using a preformed building block, then employed it as a template for primer extension reactions catalyzed by Klenow fragment and DNA polymerases alpha, beta and delta (pol alpha, pol beta and pol delta). None of these DNA polymerases were able to bypass the (6-4) photoproduct and elongation terminated at or near the 3'-pyrimidone of the photoproduct, depending on the dNTP concentration. When a single-chain Fv (scFv) with high affinity for the (6-4) photoproduct was included in the polymerization reaction, DNA synthesis was inhibited at base positions four, six, eight or eight nucleotides prior to the 3'-pyrimidone by Klenow fragment, pol alpha, pol beta or pol delta, respectively. These results suggest that the scFv can bind to the template DNA containing a (6-4) photoproduct and inhibit extension reactions by polymerases.     

Preparation of (R)- and (S)-4-chloro-3-acetoxybutyronitrile using microbial resolution

A new preparation of optically active 4-chloro-3-acetoxybutyronitrile (AcBN) was developed using the resting cells of bacteria. The resolution was based on enantioselective hydrolysis of the ester function of the substrate. (R)-AcBN was prepared using Pseudomonas sp. DS-K-717, and the resulting (R)-AcBN was obtained with high enantiomeric excess of >98% with a yield of 36% during the microbial resolution step. (S)-AcBN was prepared in the same manner using the resting cells of Pseudomonas sp. DS-K-19 and showed a high enantiomeric excess of >98% with a yield of 32%. The enzyme activity was enhanced and induced by the addition of AcBN, particularly the (R)-ester hydrolysis, which was enhanced 20-fold.     

Ab initio study of the (5R)- and (5S)-TT pyrimidine h5(6-4) pyrimidone photoproducts. Implications on the design of new biologically relevant analogues

A computational study of a series of N(1)- and/or C(6)-alkyl-5,6-dihydrothymine diastereomers at theory levels up to MP4(SDTQ)/6-31G//HF/6-31G and MP2/6-311G//HF/6-31G has demonstrated the respective importance of the substituents at positions 1, 5, and 6 on the energetically favored conformation of each isomer. Results obtained both in the gas and condensed phase indicate that unsubstitution of the N(1)-position favors a half-chair conformation with the C(5) -and C(6)-substituents in the equatorial position. On the other hand, in the case of the (6S)-1,6-dimethyl-5,6-dihydrothymine, the C(6)-substituent adopts the axial position to minimize its van der Waals interactions with the N(1)-substituent. Furthermore, if the configuration at the C(5)-dihydrothymine position has no resultant influence on the total molecular free energy, when a pyrimidone substituent is introduced at the dihydrothymine C(6)-position, additional repulsive forces between the C(5)- and C(6)-substituents make the diaxially substituted half-chair conformation the most energetically favorable one. These results indicate that the observed C(6)-axially substituted conformation of the thymine-thymine pyrimidine h(5)(6-4) pyrimidone photoproducts is not necessarily induced by the macrocyclic structure. They also nicely explain the formation mechanism of these photoproduct derivatives, and allow the prediction of the conformation of new analogues.     

In search of benzene-like Sn6(6-): synthesis of Na4CaSn6 with interconnected cyclohexane-like Sn6(6-)

The title compound was synthesized in an attempt to produce stacked benzene-like Sn6(6-) rings separated by alkaline-earth cations in analogy with the recently reported stacks of aromatic cyclopentadienyl-like Sn5(6-) in Na8BaSn6 (in addition to isolated Sn4- anions). The resulting compound, synthesized from a stoichiometric mixture of the elements at high temperature, has the "correct" stoichiometry with six tin atoms and six positive charges. However, the rings of Sn6(6-) are puckered into chair-type cyclohexanes that are interconnected into isolated cylindrical tubes stuffed with Ca2+ between the rings. Such tubes, if fused to each other, form the hexagonal diamond structure. The new compound is electronically balanced according to magnetic and four-probe resistivity measurements. Reported are also the synthesis and properties of Na10EuSn12 and Na10YbSn12 which are isostructural with the known Na10CaSn12.     

Functionalization of 2-Amino-3-benzyl-6-(benzylthio)pyrimidin-4(3H)-one: An Efficient Access to the Synthesis of Polycyclic Pyrimidine Scaffolds

Russian Journal of General Chemistry - 2-Aminouracil is used in the synthesis of a new series of tri- and tetracyclic pyrimidine scaffolds as the precursor. Thiazolo[5,4-d]triazolo[4,3-a]pyrimidine...     

Spectrophotometric determination of iron(III)-dimethyldithiocarbamate (ferbam) using 9-(4-carboxyphenyl)-2,3,7-trihydroxyl-6-fluorone

A spectrophotometric method was developed for the determination of iron(III)-dimethyldithiocarbamate (ferbam) by concerting it into an iron(III)-9-(4-carboxyphenyl)-2,3,7-trihydroxyl-6-fluorone complex. In NH₃-HAc buffer solution (pH 6.5), the reagent reacts with ferbam to form a blue complex with a maximum absorption peak at 640 nm. The reaction can be completed rapidly at room temperature and the absorbance is stable for at least 24 h. The apparent molar absorption coefficient, Sandell’s sensitivity of the complex, the detection limit and the relative standard deviation were found to be 1.06×10⁵ l mol⁻¹ cm⁻¹, 3.9 ng cm⁻², 2.2 ng ml⁻¹ and 1.06%, respectively. From 0 to 75 μg of ferbam in 25 ml solution the absorbance obeyed Beer’s law. The effect of foreign ions and other dithiocarbamates were also studied in detail. The results indicated that all coexisting ions examined can be tolerated in considerable amounts, especially other dithiocarbamates such as ziram and zineb, which always interfere with the determination of ferbam in the literature. The proposed method is very sensitive, selective and simple, it has been applied to determine ferbam in commercial samples.     

Preparation of (R)- and (S)-6-hydroxybuspirone by enzymatic resolution or hydroxylation

6-Hydroxybuspirone is an active metabolite of the antianxiety drug buspirone. The (R)- and (S)-enantiomers of 6-hydroxybuspirone were prepared using an enzymatic resolution process. l-Amino acid acylase from Aspergillus melleus (Amano Acylase 30000) was used to hydrolyze racemic 6-acetoxybuspirone to (S)-6-hydroxybuspirone in 95% ee after 45% conversion. The remaining (R)-6-acetoxybuspirone with 88% ee was converted to (R)-6-hydroxybuspirone by acid hydrolysis. The ee of both enantiomers could be improved to 99% by crystallization as a metastable polymorph. (S)-6-Hydroxybuspirone was also obtained in 88% ee and 14.5% yield by hydroxylation of buspirone using Streptomyces antibioticus ATCC 14890.     

Model studies of the (6-4) photoproduct photoreactivation: efficient photosensitized splitting of thymine oxetane units by covalently linked tryptophan in high polarity solvents

Three covalently linked tryptophan-thymine oxetane compounds used as a model of the (6-4) photolyase-substrate complex have been prepared. Under 290 nm light, efficient splitting of the thymine oxetane with aromatic carbonyl compounds gives the thymine monomer and the corresponding carbonyl compounds by the covalently linked tryptophan via an intramolecular electron transfer, and exhibits a strong solvent dependence: the quantum yield (Phi) is ca. 0.1 in dioxane, and near 0.3 in water. Electron transfer from the excited tryptophan residue to the oxetane unit is the origin of fluorescence quenching of the tryptophan residue, and is more efficient in strong polar solvents. The splitting efficiency of the oxetane radical anion within the tryptophan.+-oxetane.- species is also solvent-dependent, ranging from ca. 0.2 in dioxane to near 0.35 in water. Thus, the back electron transfer reaction in the charge-separated species would be suppressed in water, but is still a main factor causing low splitting efficiencies in the tryptophan-oxetane systems. In contrast to the tryptophan-oxetane system, fast nonradiation processes are the main causes of low efficiency in the flavin-oxetane system. Hence, nonradiative processes of the excited FADH-, rather than electron transfer to oxetane, may be an important factor for the low repair efficiency of (6-4) photolyase.     

Crystal structure of 4-(4'-diethylaminophenyl)-6-(4-methoxyphenyl)-(2-pyrrolidin-1-yl)-pyridine-3-carbonitrile.

4-(4'-Diethylaminophenyl)-6-(4-methoxyphenyl)-(2-pyrrolidin-1-yl)-pyridine-3-carbonitrile (DMPPC) was studied by X-ray diffraction methods due to its non-linear optical properties. The pyrrolidine and pyridine rings adopt half-chair and planar conformations, respectively. The molecules in the crystal are stabilized by C-H...O and C-H...N types of intermolecular interactions in addition to van der Waals forces.     

Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.     

Kinetic resolution of sec-alcohols using a new class of readily assembled (S)-proline-derived 4-(pyrrolidino)-pyridine analogues

We report the development of a new class of readily prepared chiral 4-(pyrrolidino)-pyridine catalysts capable of exploiting both van der Waals (pi) and H-bonding interactions, thus allowing remote chiral information to stereochemically control the kinetic resolution of sec-alcohols.     

Bromo derivatives of 1-(4-hydroxyphenyl)dihydrouracil and 1-(4-hydroxyphenyl)-5- or -6-metehyldihydrouracils

Bromination of 1-(4-hydroxyphenyl)dihydrouracil and its 6-methyl derivative with bromine in refluxing acetic acid gave 1-(3,5-dibromo-4-hydroxyphenyl)-5-bromo-, 1-(3,5-dibromo-4-hydroxyphenyl)-5-bromo-, and 1-(3,5-dibromo-4-hydroxyphenyl)-5-bromo-6-methyldihydrouracils and 1-(3,5-dibromo-4-hydroxyphenyl)-5-methyluracil. 5-Bromo- and 5,5-dibromodihydrouracils were dehydrobrominated, and the same compounds undergo decomposition to 3,5-dibromo-4-hydroxyphenylurea upon alkaline hydrolysis.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1251–1254, September, 1982.