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Upon exposure to UVA light, psoralens can induce DNA interstrand cross-links (ICLs), which can block DNA replication and transcription. Among the psoralen derivatives, 8-methoxypsoralen (8-MOP) is conventionally applied for psoriasis therapy, and amotosalen S59 is used to inactivate bacterial and viral pathogens in blood components. In addition to the ICL formation, psoralens also readily form various monoadducts (MAs) with thymidine residues in DNA when exposed to UVA light, and the biological implications for these monoadducts remain unclear. Here, we reported a method that encompassed digestion with a single enzyme (nuclease P1) and LC-MS/ MS, for the simultaneous quantification of ICL and MAs induced in human cells exposed with 8-MOP or S59 and UVA light. Our results showed that the yield of ICL induced by S59, which increased from 3.9 to 12.8 lesions/[10.sup.3] nucleotides as the dose of UVA light increased from 0.5 to 10.0 J/[cm.sup.2], was ~100 fold more than that induced by 8-MOP. In addition, three and five products were identified as 8-MOP- and S59-MAs, respectively, and the yields of MAs were significantly lower than that for ICL. The yields of the three 8-MOP-MAs were 7.6-2.2, 1.9-9.9, and 7.2-51 per [10.sup.6] nucleotides and those of the five S59-MAs were 215-19, 106-39, 25-21, 32-146, and 22-26 per [10.sup.6] nucleotides as the dose of UVA light increased from 0.5 to 10.0 J/[cm.sup.2]. Although the yields of MAs induced by 8-MOP and S59 were lower than those of the respective ICLs under the same exposure conditions, the formation of appreciable amounts of MAs might account for some of the mutations induced by psoralens.

A novel DNA sequencing methodology was developed through a series of addition, detection, and deprotection steps. First step involved the construction of nucleoside triphosphates I with labile and fluorescent 3'-protecting group, followed by the removal of the 3,4-dimethoxy-6-nitrobenzyloxycarbonyl (NVOC) protecting group, resulting in an intermediate.

The two crystal structures of modified analogs of of the Dickerson-Drew dodecamer which contains 6'-a-methyl or 6'-a-hydroxy carboxylic thymidines have been reported. Isomorphism of both structures conforms with small geometrical deviation. The 6'-a-substituted carbocyclic thymidines of modified duplexes adopt either C2'-endo or C1'-exo B-DNA type puckers. DNA duplexes which contain 6'-a-hydroxy-substituted nucleotide have a higher thermodynamic stabilities than those which contain 6'-a-methyl carbocyclic modification.

The vibrational spectra of the (2'S)=[2'-2H]thymidine stereoisotopomer were analyzed by infrared and Raman spectroscopy to determine the vibrational modes of thymidine. The vibrational spectra of the thymidine stereoisotopomer indicated the presence of vibrational coupling between the thymidine base residue and the deoxyribose moiety. The C2 methylene group of the attached sugar in the thymidine stereoisotopomer also exhibited significant vibrational coupling.

Two oxidative pathways for the reaction of a high valent chromium(V) species with thymidine nucleotides are observed by the identification and quantitation of specific degradation products. The first is an oxygen-dependent mechanism which involves the abstraction of the C-4'-hydrogen atom. A second mechanism, which is oxygen-independent, is shown by the release of the free base thymine. These two pathways involve chromium(IV), and not chromium(V) itself, as the reactive high valent species in these sugar oxidation mechanisms.

An automated beta-cyanoethyl phosphoramidite method helps synthesize modified oligothymidylates d(T)12 having 5-(o-carboran-1-yl)-2-deoxyuridine (CDU). The position of the carboranyl nucleotide influences duplex stability duplex and conformation of single- and double-stranded structures. Melting temperature studies and molecular modeling help analyze the influence of CDU on duplex stability. Half-life measurements reveal that some 3'- and 3',5'-CDU-modified oligonucleotides resist toward 5'-exonuclease activity.

Use of antibodies which are specific to acetylated H4 facilitates the immunoprecipitation of newly duplicated or newly formed nucleosomes. When duplication occurs along with histone preparation, majority of new H3 and at least 60-65% of new H2A/H2B become complexes with H4 which is acetylated. Duplication of chromatin in the absence of butyrate leads to decreased immunoprecipitation of old and new chromatin.

The borophosphonylating agent, methyl(o-carboran-1-ylmethyl)phosphonate, is the main intermediate for the synthesis of thymidine (3',5')thymidine (o-carboran-1-ylmethyl)phosphonate and 5'-O-(monomethoxytrityl)thymidine 3'-O-(methyl(o-carboran-1-ylmethyl)phosphonate) monomer. The thymidine phohsphonate has a corboran internucleotide linkage instead of a phosphodiester residue. The borophosphonylating agent synthesis procedure has three steps and includes a Michaelis-Arbuzov reaction on propragyl bromide with trimethyl phosphite.

Ionizing radiation and thymidine react in hypoxic surroundings to generate chemically, 5,6-Dihydro-5-hydroxythymidine. Both cis-diastereomers of 5,6-dihydro-5,6-dihydroxythymidine can be availed easily be this preparation. The use of concentrated ammonium hydroxide is removed by insulating units and solid phase supports which can synthesize chemically prepared oligonucleotides with the nucleosides. Biopolymer geometry is influenced by the product obtained when oligonucleotides accept both the compounds site specifically.

2-deoxy-D-ribose is treated with HCl in methanol to synthesize methyl 2-deoxy-3, 5-di-O-p-toluoyl-D-erythro-pentofuranoside. It is also treated with p-toluoyl chloride in pyridine to produce the same compound. Arylaldehydes are condensed with hydantoin piperidine to synthesize 5-Arylidenehydantoins, while 5-ethylidene-2-thiohydantoin is desulfurized by aqueous chloroacetic acid to synthesize 5-ethylidenehydantoin. 1,1,1,3,3,3-hexamethyldisilazane is used to silylate hydantoins when a quantity of ammonium sulfate required for catalysis occurs.

Arenesulfonyl azole condensing agent interacts with guanosine or thymidine at the O6 or O4 location to produce sulfonates in the process of preparing oligonucleotides via a phospotriester method. Azoles are used to dislocate sulfonates, resulting in the relative azolyl by products. The highly nucleophilic oxygen atoms reveal changes at the base during the preparation by using phosphoramidite process. The unfavorable side interactions are eliminated by employing insulating groups. The insulators are eliminated by powerful bases which cleave internucleotide linkages.

Acis-syn thymidine dimer-based linkage is susceptible to photochemical and photoenzymatic cleavage. The 22-mer with a central dimer is derived by a six-step process from 5'-O-DMT-thymidine and 3'-TBDMS-thymidine. The 22-mer is photolyzed by direct 254 nm light and provides cleavage products. The use of a camera flash induces 20% cleavage by photolyase.

A method for the straightforward synthesis of furocoumarin-thymidine furan-side adduct was developed based on the selective placement a furocoumarin-thymidine adduct in sequences that permit multiple sites of adduction. The synthetic approach was characterized by a shortened synthetic scheme that eliminates all but one reaction with a saturated pyrimidine. Furthermore, the photoproduct exhibited a circular dichroism spectrum that was similar to an isolated psoralen-thymidine photoproduct.

The possibility that human thymine DNA glycosylase (hTDG) specificity depends on the stability of the scissile base-sugar bond is examined by determining the maximal activity [K.sub.max] against a series of nucleobases with varying leaving-group ability. It is found that hTDG removes 5-fluorouracil 78-fold faster than uracil, and 5-chlorouracil, 572-fold faster than thymine, differences that can be attributed predominantly to leaving-group ability.

The design, preparation, and properties of two key building blocks of a size-expanded genetic system is described. The nucleoside analogues of the natural nucleosides dA and dT are reported in which the fusion of a benzo ring increases their size.

The role of thymidine's hydrogen-bonding groups on the fidelity of deoxyribonucleic acid (DNA) polymerase during DNA replication was analyzed by utilizing difluorotoluene nucleoside. Difluorotoluene nucleoside acted as a good template for the analysis of DNA polymerase activity during DNA replication. The analog also promoted the efficiency of nucleoside insertion in a level that is similar to the activity of natural thymidine. Furthermore, the analog successfully promoted the fidelity of nucleoside insertion by retaining the steric shape and conformation of the natural nucleoside.

5'-O-(4, 4-dimethoxytrityl)thymidine facilitated stereoselective preparation of the novel 3'-C-(hydroxymethyl)thymidine in four stages. Destabilization of the resultant DNA:DNA duplex does not result or occurs marginally from incorporation of this nucleoside into oligodeoxynucleotides. A phospharamidite synthon was used in the incorporation.

The complex Ru(bpy)2-(dmap)OH(sub 2)(super 2+) (bpy = 2,2'-bypyridine, dmap = 4-(dimethylamino)pyridine) was synthesized to exclude specific recognition by the ethylguanine ligand as the process of thymide specificity. This was observed during investigations of the stoichiometric and electrocatalytic oxidation of DNA by oxopolypyridylruthemium(IV) complexes.

The structure of thymidylate synthase (TS) from Lactobacillus casei in complex with the nonsubstrate analogue phenolphthalein was used in designing inhibitors that can take advantage of the bacterial enzyme's features different from those of the human enzyme. Synthesis and testing of the inhibitors showed that they were more selective for the bacterial enzyme over the human enzyme. It was also found out that the analogues bind to the enzyme in substantially different orientations, although chemical similarities were the same in the inhibitors.