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Adequate folate availability is necessary to sustain normal DNA synthesis and normal patterns of DNA methylation and these features of DNA can be modified by methylenetetrahydrofolate reductase (MTHFR) C677T genotype. This study investigated the effect of MTHFR C677T genotype and daily supplementation with 5 mg folic acid and 1.25 mg vitamin B-12 on uracil misincorporation into DNA and promoter methylation. Subjects (n = 86) with a history of colorectal adenoma and MTHFR CC or TT genotype were randomly assigned to receive folic acid plus vitamin B-12 or placebo for 6 mo. Uracil misincorporation and promoter methylation of 6 tumor suppressor and DNA repair genes were assessed in DNA from rectal biopsies at baseline and after the intervention. The biomarkers did not differ between the treated group and the placebo group after 6 mo compared with baseline. The uracil concentration of DNA increased in the treated group (5.37 fmol/[micro]g DNA, P = 0.02), whereas it did not change in the placebo group (P = 0.42). The change from baseline of 4.01 fmol uracil/[micro]g DNA tended to differ between the groups (P = 0.16). An increase in promoter methylation tended to occur more often in the intervention group than in the placebo group (OR = 1.67; P = 0.08). This study suggests that supplementation with high doses of folic acid and vitamin B-12 may not favorably influence uracil incorporation and promoter methylation in subjects with previous colorectal adenomas. Because such alterations may potentially increase the risk of neoplastic transformation, more research is needed to fully define the consequences of these molecular alterations.

The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair were studied at the B3LYP/DZP++ level of theory. It was found that the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage because the unpaired electrons in the carbon-centered radicals were mainly localized on the atom from which the hydrogen atom was removed.

Various modified oligonucleotides are used for investigating the mechanism of ribonolactane formation in 5'-(G/C)AA[super Br]UT-3' and 5]-(G/C)A[super Br]UT-3' (where [super Br]U is bromouracil). The results have shown that the hotspot sequence has electron-donating G/C base pair, the 5'-[super Br]UT-3' sequence as an acceptor, and appropriate number of A/T base pairs as a bridge for the charge-transfer process.

Bis- and trisuracil nucleosides with nucleobases anchored to isoxazoline ring-fused 11-, 12-, and 16-membered macrooxacycles are synthesized by nucelosidation of 1,2-isopropylidenefuranose ring-fused macrocycles. The nucleosides have displayed spherical and fiber-like morphologies in water and in one case, the morphology is changed by complementary base pairing.

Infrared laser spectroscopy is used to obtain the vibrational spectra of the diketo tautomers of uracil and thymine solvated in helium nanodroplets, in the N-H stretching region of the spectrum. The ambiguity found in the vibrational moment angle (VTMA) assignment of the N3H band for the uracil monomer can be described using dimer bands that are overlapped with the monomer band.

The density functional theory is employed to study and explain the various effects of the hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil, which depends on the nature of amino acid and binding orientation. The results show that such interactions decrease the gas-phase acidity of uracil, which also varies with the nature of the molecule bound, as well as the binding orientations and strengths.

The high-level CASPT2//CASSCF quantum chemical techniques and ANO-type basis sets are applied to analyze the low-lying singlet states of the three pyrimidine DNA and RNA nucleobases uracil, thymine and cytosine. The analysis attempts to present a single view to elucidate the main photochemical events in the three systems after light irradiation, such as the measured ultrafast sub-picosecond decay and the origin of the low quantum yield fluorescence.

A QM/MM method is developed by combining ONIOM quantum chemistry and molecular dynamics and applied to a step in the deamination of cytosine to uracil in yeast cytosine deaminase (yCD). It is observed that cleavage of the Zn-O4 bond occurs through a pentacoordinated Zn transition state complex and E64 has a significant role as a proton shuttle in the deamination reaction and also aids the cleavage of the zinc-oxygen bond between the catalytic zinc and the deamination product uracil so that the product can be released.

Free energy simulations were used to investigate the basis for an apparent discrepancy between theoretical predictions and subsequent experiments concerning the mechanism of the DNA repair protein uracil-DNA glycosylase. The calculations indicated that the terminal (+2) phosphate group of the ssDNA oligomers that were studied is fully solvated and that the resultant shielding is sufficient to reduce the catalytic contribution of this group.

Electrospray ionization mass spectrometry experiments (ESIMS) are performed on the pyrimidine nucleobases (B) uracil and thymine complexed with lead(II). The intermolecular proton transfers in uracil-[H.sub.2]O, uracil-O[H.sup.-] or uracil-uracil complexes have explained the experimentally detected [[Pb(U)-H].sup.+] ions.

A procedure involving the one-pot reaction of the key synthon was used to prepare a new ferrocenyl uracil peptide nucleic acid (PNA) monomer, tert-butyl-2-(N-(2-(((9H-floren-9-yl)-methoxy)carbonylamino)ethyl)2-(5-(N-ferrocenylmethylbenzamido)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetate. Electrochemical measurement showed that the monomer exhibits a single and reversible one-electron wave with a diffusion coefficient that is slightly larger than that observed for similar ferrocenyl PNA monomers.

Five dinucleating ligands and one trinucleating ligand incorporating two and three 1,5,9-triazacyclododecan-3-yloxy groups are synthesized and studied in [Zn.sup.2} ion. UV spectrophotometric and [sup.1.H] nuclear magnetic resonance spectroscopic studies with dinucleating ligands verify binding to the bases of two uracil basis andadenylyl-3',5'-uridine at less than millimolar concentrations, while no interaction with base moieties of adenylyl-3',5'-adenosine is observed.

Two families of bicyclic fluorinated uracils are prepared starting from a gem-difluorinated unsaturated nitrile by means of a ring-closing metathesis reaction to form the new ring, which is fused at the C-5/C-6 or N-1/C-6 positions of the uracil moiety. The selective formation of olefin regioisomers in the metathesis process could be controlled according to the reaction conditions.

The laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy was used to investigate the jet-cooled rotational spectrum of uracil. The approach provides a definitive method to establish the pyrrolic or pyrimidinic nature of the N nuclei and indicates that the observed tautomer of uracil in the gas phase is the diketo form.

X-ray crystallographic study results for the methylene linked Ferrocene-bis(thymine/uracil) conjugates Fc[(T:T).sub.M] and Fc[(U:U).sub.M] are reported. The base dependent 2-D supramolecular assemblies generated via wobble self-pairing for bis-thymine and reverse wobble self-pairing for bis-uracil conjugates are observed to differ in architecture from the corresponding butylene spacer linked conjugates.

One-pot, three-component cyclocondensation of aromatic aldehydes, [beta]-oxodithioesters, and urea/6-amino-1,3-dimethyluracil in the presence of recyclable Si[O.sub.2]-[H.sub.2]S[O.sub.4] is performed to develop an efficient and highly convergent route to dihydropyrimidinones (DHPMs) and hitherto unreported dihydropyridopyrimidinones. The newly developed strategy could find useful application in diversity-oriented synthesis (DOS) to prepare three important bioactive heterocyclic frameworks from the same [beta]-oxodithioester under the similar reaction conditions.

The concept of the mechanical adaptation of relatively simple hosts within dynamic media to determine the optimum conformation for molecular recognition was applied for discriminating thymine from uracil. The concept of mechanical tuning of a host structure for optimization of molecular recognition offers a new methodology in host-guest chemistry as an alternative to the more traditional molecular design strategies.

The synthesis of 6-substituted 2,4-dimethoxypyrimidines with different nucleophiles is achieved through [S.sub.RN]1 reactions, starting from 6-chloro-2,4-dimethoxypyrimidine. The preparation of uracils from 6-chloro-2,4-dimethoxypyrimidine without the isolation of 2,4-dimethoxypyrimidine derivatives has produced a rapid access to the compounds in excellent purity by avoiding unnecessary step of purification.

A unique and efficient copper bromide mediated pallado-catalyzed coupling of protecting group-free 2-thiouracil derivatives with organostannanes is described. The nature of the copper is shown to be very important for successful cross coupling.

The presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches were detected by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand. The results demonstrated the energy landscape of the bound ligand with intricate details and the elastic nature of the ligand recognition mode by the purine-sensing riboswitches exhibing dynamic balance between hydrogen bonding and base stacking interactions.

A new pyrimidine catabolic pathway (the Rut pathway) is discovered in Escherichia coli K12, where uracil is converted to 3-hydroxypropionate, ammonia and carbon dioxide with the help of the seven-gene Rut operon. The flavoenzyme RutA has catalyzed the initial uracil ring-opening reaction to produce 3-ureidoacrylate.

The synthesis of the stable, water-soluble receptor contains a 2,6-bis(glycylamino)pyridine group as a structural mimic of the active site in uracil DNA glycosylase (UDG) understand the functional role of UDG which pulls unwanted uracil into it active site through hydrogen bonding and [pi]-[pi] stacking interactions. The obtained results provide insight into the binding mechanism of uracil and its derivatives in DNA, by DNA repair enzymes through hydrogen bonding and [pi]-[pi] stacking interactions.

The gas-phase substitution reactions of methyl chloride and 1,3-dimethyluracil are investigated. The leaving group ability of the N1-deprotonated 3-methyluracil anion relative to the N1-deprotonated 3-methylthymine anion is examined in the context of an enzymatic reaction that has cleaved uracil but not thymine from DNA.

The dynamics of electron injection and quantum yields for photoinduced dehalogenation are examined in a series of DNA hairpins possessing an aminopyrene capping group. Dehalogenation has occurred via a multistep mechanisms consisting of electron injection, electron transport to the halouracil, loss of halide, and trapping of the uracilyl radical and the quantum yields for product formation have decreased by a factor of 2 for each additional A-T base pair interposed between the aminopyrene and bromouracil.

A series of kinetic and photo-cross-linking studies were conducted to gain insight into the roles of each subunit in DNA binding and primer synthesis for the helicase-primase complex from herpes simplex virus-1 contains three subunits, UL5, UL52, and UL8. Photo-cross-linking of a RNA primer-template, the product of primer synthesis, containing 5-iodouracil in the template were shown to generate the same apparent cross-linked species.

The copying of longer, mixed-sequence RNA templates and a series of nucleic acid templates were explored to assess the sequence-general copying ability of 2'-amino-2',3'-dideoxynucleotide-5'-phosphorimidazolides. The results showed that more efficiently copied sequences could be generated by replacing the adenine nucleobase with diaminopurine, and uracil with C5-(1-propynyl)uracil.

Oligonucleotides containing 5-chlorouracil (ClU), one of the known inflammation damage products were constructed to examine the thermodynamic stability, base pairing configuration, and duplex conformation of oligonucleotides containing ClU paired opposite adenine. The sufficiently stable fraudulent, pseudo-Watson-Crick ClU-A base pair is able to avoid glycosylase removal and hence might constitute a persistent form of cellular DNA damage.

The first three steps of base excision repair (BER) in zebrafish extracts from unfertilized eggs, embryos at different developmental stages, and adults were characterized to gain insight into (BER) pathway involved in recognition and repairs of most nonbulky lesions, uracil and abasic (AP) sites in DNA during embryogenesis. The results indicated that switch to normal, adult BER occured fully when the embryos hatched from the chorionic membrane and encountered normal oxidative stress.

The additive Pummerer reaction between 3,5-O-(di-tert-butyl)silylene-4-thiofuranoid glycal S-oxide and [Ac.sub.2]O/TMSOAc/B[F.sub.3].O[Et.sub.2] in C[H.sub.2][Cl.sub.2] to obtain the corresponding 1,2-di-O-acetyl-4-thioribofuranose is described. The newly obtained 1,2-di-O-acetyl-4-thioribofuranose could also be extended to the [beta]-selective synthesis of 4'-thio-C-ribonucleosides.

The structure of isolated biomolecules, uracil and guanine, is described, which has shown the capability of the electron diffraction apparatus augmented with surface-assisted infrared (IR) laser desorption. The structures of uracil and guanine are refined at the vibrational temperature, which is lower than the translational temperature of the plume.

The first competitive inhibitor of uracil DNA glycosylase (UDG) that is incorporated into DNA by the Klenow fragment of DNA polymerase I, a replicative polymerase, is described. The presence of the molecule within the DNA scaffold has contributed to its potency and nucleosides are often useful as therapeutic agents.

A linear DNA of the Saccharomyces cerevisiae ScURA3 gene is used to isolate and transform a uracil auxotroph and develop a Kluyveromyces marxianus DMKU3-1042 derivative strain suitable for genetic engineering. The results obtained demonstrated that K. marxianus DMKU3-1042 could be an alternative cost-effective bioethanol producer and a host for transformation with linear DNA by use of S. cerevisiae-based molecular genetic tools.

A novel archaeal family B DNA polymerase from Nanoarchaeum equitans that could successfully utilize deaminated bases, such as uracil and hypoxanthine, and its application to PCR is reported. The Neq DNA polymerase and Neq plus DNA polymerase are found to be useful in DNA amplification and PCR-based applications such as clinical diagnoses using uracil-DNA glycosylase.

An approach toward enantiomerically pure (S)-methanocarba nucleosides based on functional group transformation on a sensitive bicyclo[3.1.0]hexane system is developed. These derivatives are suitable for detailed studies in biological systems.