Nucleobase nucleic acid chains

Hydrolytic cleavage of N,0-acetals due to enzymatic processes leads to nucleic acid chain elements without a nucleobase. Such positions are potential mutation sites. To study such mechanisms and to induce directed mutagenesis, oligonucleotides have been synthesized containing tetrahydrofuran building blocks introduced via corresponding phosphoramidites [310,311] (Fig. 35). 

It is assumed that tholins also played an important role in the PAH world hypothesis. The PAH world could have existed as a pre-RNA world on the primeval Earth. It is suggested that PAHs can undergo stacking, thus forming structures to which nucleobases are chemically bound (to OH functions which are formed by photochemical derivatisation of the PAHs). The PAH stacks replace the more complex phosphate-D-ribose-phosphate chains in the nucleic acids (Ehrenfreund et al., 2006). 

DyNAs, dynamic analogs of nucleic acids, were obtained as cationic main-chain dynamers bearing nucleobase groups and were shown to interact with polyanionic species displaying a marked increase in size with the negative charge of the substrate, thus demonstrating their adaptive character (Fig. 9) [69]. 

Fig. 9 DyNAs dynamic analogs of nucleic acids built on a main-chain cationic reversible polymer chain bearing nucleobase groups...

When two nucleic acid strands have complementary nucleic acid sequence, they can undergo hybridization to form double-stranded duplex structures. DNA forms a double-stranded helix composed of two complementary helical polynucleotide chains, aligned antiparallel, which are coiled around a common axis. In helix form, the anionic backbone lies on the outside of the structure with the nucleobases in the core, perpendicular to the axis and separated by a distance of 3.4 A. This B-form helix (Figure 2a) has a right-handed coil that repeats itself every 34 A with a turn every... 

Abstract Mixed-quantum classical dynamics simulations have recently become an important tool for investigations of time-dependent properties of electronically excited molecules, including non-adiabatic effects occurring during internal conversion processes. The high computational costs involved in such simulations have often led to simulation of model compounds instead of the full biochemical system. This chapter reviews recent dynamics results obtained for models of three classes of biologically relevant systems protonated Schiff base chains as models for the chromophore of rhodopsin proteins nucleobases and heteroaromatic rings as models for UV-excited nucleic acids and formamide as a model for photoexcited peptide bonds. 

---