The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti or...

Described here are mechanistic details of the chemical reactivities of two modified/saturated pyrimidine residues that represent naturally occurring forms of DNA damage: 5-thyminyl-5,6-dihydrothymine, commonly referred to as the "spore photoproduct" (SP), and 5,6-dihydro-2'-deoxyuridine (dHdU), formed via ionizing radiation damage to cytosine under anoxic conditions and also serving as a genera...

Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebio...

Nucleotide de novo synthesis is highly conserved among organisms and represents an essential biochemical pathway. In plants, the two initial enzymatic reactions of de novo pyrimidine synthesis occur in the plastids. By use of green fluorescent protein fusions, clear support is provided for a localization of the remaining reactions in the cytosol and mitochondria. This implies that carbamoyl asp...

Recent studies concerning properties of oligonucleotides (ONs) with aminoalkyl side chains at the nucleobase and sugar moieties have been comprehensively reviewed in relation to the antisense, antigene, ribozyme, aptamer, decoy, and siRNA strategies. Thermal stabilities of ONs incorporating nucleoside analogs with a wide variety of aminoalkyl side chains at the 5and 4-positions of pyrimidine ba...

Although not yet identified in the interstellar medium (ISM), N-heterocycles including nucleobases-the information subunits of DNA and RNA-are present in carbonaceous chondrites, which indicates that molecules of biological interest can be formed in non-terrestrial environments via abiotic pathways. Recent laboratory experiments and ab initio calculations have already shown that the irradiation...

Despite the paramount importance of protein-nucleic acid interactions in different cellular processes, our understanding of such interactions at the atomistic level remains incomplete. We have used molecular dynamics (MD) simulations and 15 μs of sampling time to study the behavior of amino acids and amino-acid sidechain analogs in aqueous solutions of different mimetics of naturally occurring ...

Many critical processes in the cell involve direct binding between RNAs and proteins, making it imperative to fully understand the physicochemical principles behind such interactions at the atomistic level. Here, we use molecular dynamics simulations and 15 μs of sampling to study the behavior of amino acids and amino acid sidechain analogs in high-concentration aqueous solutions of standard RN...

Laser photodissociation spectroscopy of the I-·thymine (I-·T) and I-·cytosine (I-·C) nucleobase clusters has been conducted for the first time across the regions above the electron detachment thresholds to explore the excited states and photodissociation channels. Although photodepletion is strong, only weak ionic photofragment signals are observed, indicating that the clusters decay predominan...

The paramagnetic gadolinium(III) ion is used as contrast agent in magnetic resonance (MR) imaging to improve the lesion detection and characterization. It generates a signal by changing relaxivity of protons from associated water molecules creates clearer physical distinction between molecule surrounding tissues. New gadolinium-based agents displaying larger values specifically targeted might p...