Nucleic acid base properties

Even if It could be shown that RNA preceded both DNA and proteins in the march toward living things that doesn t automatically make RNA the first self replicating molecule Another possibility is that a self replicating polynucleotide based on some carbo hydrate other than o ribose was a precursor to RNA Over many generations natural selection could have led to the replacement of the other carbohydrate by D ribose giving RNA Recent research on unnatural polynucleotides by Professor Albert Eschenmoser of the Swiss Federal Institute of Technology (Zurich) has shown for example that nucleic acids based on L threose possess many of the properties of RNA and DNA... 

II. PROPERTIES OF DNA AND NATIVE NUCLEIC ACID-BASED NANOSTRUCTURES... 

To understand the extraordinary potential for DNA to be utilized as a material in construction processes, the general properties of this biomolecule will first be discussed. In addition, examples of naturally occurring nucleic acid-based nanostructures will be described that are of great importance both for cellular processes and conventional applications in molecular biotechnology. 

The refinement of other analytical methods, such as electrophoresis [34,36], the various techniques of optical spectroscopy [103-105], and nuclear magnetic resonance [201], is supplemented by the recent advances in real-time affinity measurements [152,202], contributing to the understanding of biomolecular reactivity. Taken together, the improvement of analytical methods will eventually allow a comprehensive characterization of the structure, topology, and properties of the nucleic acid-based supramolecular components under consideration for distinctive applications in nanobiotechnology. 

Maes BUW (2006) Transition-Metal-Based Carbon-Carbon and Carbon-Heteroatom Bond Formation for the Synthesis and Decoration of Heterocycles. 1 155-211 Maiti M, Kumar GS (2007) Protoberberine Alkaloids Physicochemical and Nucleic Acid Binding Properties. lO. 155-210... 

Santamaria, R., and A. Vasquez. 1994. Structural and Electronic Property Changes of the Nucleic Acid Bases upon Base Pair Formation. J. Comp. Chem. 15,981. 

Bakalarski, G., P. Grochowski, J. S. Kwiatkowski, B. Lesyng, and J. Leszczynski. 1996. Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory. Chem. Phys. 204, 301. 

The investigations directed at the synthesis of thymine-substituted polymers demonstrate that the type of functional groups displayed by nucleic acid bases are compatible with ROMP. Moreover, the application of MALDI-TOF mass spectrometry to the analysis of these polymers adds to the battery of tools available for the characterization of ROMP and its products. The utility of this approach for the creation of molecules with the desired biological properties, however, is still undetermined. It is unknown whether these thymine-substituted polymers can hybridize with nucleic acids. Moreover, ROMP does not provide a simple solution to the controlled synthesis of materials that display specific sequences composed of all five common nucleic acid bases. Nevertheless, the demonstration that metathesis reactions can be conducted with such substrates suggests that perhaps neobiopolymers that function as nucleic acid analogs can be synthesized by such processes. 

Table 3. Synthesis and properties of nucleic acid base substituted L-lysines...

A series of new amino acid derivatives having pendant nucleic acid bases was prepared by the reaction of L-lysine and L-glutamic acid with the nucleic acid bases. These amino acids were further polymerized by using the N-carboxyamino acid anhydride ( NCA ) method. Alternatively, the nucleic acid base substituted poly-L-lysines were also prepared by using polymer reactions which include the reaction of carboxyethyl derivatives of the bases onto poly-L-lysine. Physico-chemical properties of the polymers obtained were given. 

To avoid too fast an energy transfer and enhance the selectivity of the laser excitation of the chosen sites in large biomolecules, it seems very promising to use their chemical labeling. This is especially important in the mapping of the sequences of DNA nucleotide bases having very close spectral properties. The first experiments on the MPI of dye-labeled nucleic acid bases were quite a success [11]. 

The study of the reactivity of the nucleic acid bases utilizes indices based on the knowledge of the molecular electronic structure. There are two possible approaches to the prediction of the chemical properties of a molecule, the isolated and reacting-molecule models (or static and dynamic ones, respectively). Frequently, at least in the older publications, the chemical reactivity indices for heteroaromatic compounds were calculated in the -electron approximation, but in principle there is no difficulty to define similar quantities in the all-valence or allelectron methods. The subject is a very broad one, and we shall here mention only a new approach to chemical reactivity based on non-empirical calculations, namely the so-called molecular isopotential maps. 

Varying the side groups X in 27b affects both the stability and selectivity of the complexes (lateral discrimination), and allows the receptor-substrate interactions in biological systems to be modelled, for instance, the interaction between nicotinamide and tryptophan [2.109b]. One may attach to 27b amino acid residues (leading to parallel peptides [2.109] as in 27c), nucleic acid bases or nucleosides, saccharides, etc. The structural features of 27 and its remarkable binding properties make it an attractive unit for the construction of macropolycyclic multisite receptors, molecular catalysts, and carriers for membrane transport. Such extensions require sepa-... 

Written by international experts knowledgeable about many aspects of nucleic acid-based therapeutics, this book will be an essential guide to aspiring scientists interested in the various aspects of nucleic acid-based therapeutics as well as established scientists in the gene therapy field and related disciplines. This book presents a comprehensive account of the structures and physicochemical properties of gene delivery and expression systems, with emphasis on their in vivo applications for the production of therapeutic... 

The affinity towards a complementary RNA strand can be improved by using peptide nucleic acids (PNAs) [20]. These DNA mimics, in which the nucleic acid bases are linked to a polyamide backbone [21], usually exhibit improved binding properties with a complementary DNA or RNA strand [22]. The use of an excess PNA-DETA adduct 20 in a Tris-HCl buffer (pH 7), in the presence of NaCl and EDTA at 40 °C, resulted in a sequence-selective cleavage of the RNA strand 21... 

The structure of the DNA molecule is basically determined by nucleic acid base interactions. Although the three-dimensional double helix structure of DNA is influenced by various contributions, the hydrogen bonding in DNA base pairs is of particuar importance. Because it is difficult to obtain gas phase experimental data for isolated base pair characterisation (only a limited number of experimental studies are available [21]) quantum chemical calculations can represent a useful tool to obtain reference data on the structure, properties and interactions of nucleic acid pairs. Theoretical studies can help us to understand the properties of nucleic acids and they are fundamental for verification... 

When oxides of nitrogen come in contact with water, both nitrous and nitric acids are formed (18) (Table IV). Toxic reactions may result from pH decrease. Other toxic reactions may be a consequence of deamination reactions with amino acids and nucleic acid bases. Another consideration is the reactions of oxides of nitrogen with double bonds (Table IV). The cis-trans isomerization of oleic acid exposed to nitrous acid has been reported (19). Furthermore, the reaction of nitrogen dioxide with unsaturated compounds has resulted in the formation of both transient and stable free radical products (20, 21) (Table V). A further possibility has been raised in that nitrite can react with secondary amines to form nitrosamines which have carcinogenic properties (22). Thus, the possible modes of toxicity for oxides of nitrogen are numerous and are not exhausted by this short list. 

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