Biological polynucleotides

Besides the MDL Molfile formal, other file formats are often used in chemistry SMILES has already been mentioned in Section 2.3.3. Another one, the PDB file format, is primarily used for storing 3D structure information on biological macromolecules such as proteins and polynucleotides (Tutorial, Section 2.9.7) [52, 53). GIF (Crystallographic Information File) [54, 55] is also a 3D structure information file format with more than three incompatible file versions and is used in crystallography. GIF should not be confused with the Chiron Interchange Formal, which is also extended with. cif. In spectroscopy, JCAMP is apphed as a spectroscopic exchange file format [56]. Here, two modifications can be... 

The interest in this area may be seen to stem from the biological area where the phenomenon is well known and accounts for the regularity in the structure of natural proteins and polynucleotides. Such polymers are efficiently synthesized by enzymes which arc capable of organizing monomer units within regularly structured molecular-scale spaces and exploiting weak forces such as hydrogen bonds and Van der Waal forces to control the polymerization process.. 

A biologically formed protein or polynucleotide, while exhibiting some limited heterogeneity in length or microheterogeneity in the main chain sequence or in pendant prosthetic groups, has an essentially unique sequence. Different forms of a protein or polynucleotide often can be... 

Polymeric drugs are macromolecules that elicit biological activity (7). Many synthetic polymers are biologically inert. However, some exhibit toxicity, while others exhibit a wide range of therapeutic activities. There are three kinds of polymer drugs polycations, polyanions, and polynucleotides. 

Polyanionic polymers can enter into biological functions by distribution throughout the host and they behave similar to proteins, glycoproteins and polynucleotides which modulate a number of biological responses related to the host defense mechanism. These are enhanced immune responses, and activation of the reticuloendothelial system (RES) macrophages. 

A detailed discussion of the modes of occurrence and biological importance of the polynucleotides is outside the scope of this article. However, in examining the structures of polynucleotides, it is necessary to take into consideration the origins of the materials studied. The pioneer researches of Caspersson114 indicated that deoxyribonucleic acids are present exclusively in the nucleus, whereas ribonucleic acids are found chiefly in the cytoplasm and only to a small extent in the nucleus. This general outline of the distribution of nucleic acids within the cell has been confirmed and extended by more recent work,116 and it has been possible to isolate both types of nucleic acid from different cellular fractions of the same tissue.116... 

Based on its nature (aqueous solutions, physiological conditions, well-investigated labeling, and staining reactions) and the historical transition from slab-gel electrophoresis to CE, the main targets are biological and bioequivalent samples such as proteins, peptides, polynucleotides, oligonucleotides, and carbohydrates. 

Azaguanine was the first purine analogue shown to be incorporated into polynucleotides [337] and, since its primary metabolic effect is on protein synthesis, the incorporation into RNA is considered the basis for its biologic activity [338]. In microbial systems 8-aza-adenine, 8-azahypoxanthine, 8-azaxanthine, and 5(4)-amino-l/f-l, 2, 3-triazole-4(5)-carboxamide are all incorporated into RNA as 8-azaguanylic acid [336]. 

The techniques called mobility shift or gel shift assay can be considered a first step in this direction. These are widely used in molecular biology to detect interactions between regulatory proteins for gene expression and specific sequences of polynucleotides (21-23). 

A particular dimer of thymine was the first heat-stable photoproduct isolated from photolysis of nucleic acid derivatives, and still appears to be the principal isolable product from photolysis of most examples of biologically active DNA.8,10 Investigation of this product has drawn much attention in recent years. Most of this work has been carried out on polynucleotides and nucleic acids and will be dealt with in those sections. The remaining work has been largely carried out with... 

The photodynamic action of these dyes was first observed in terms of inactivation of biological activity, and of changes in the physical properties of polynucleotides. For example, the infectivity of viral RNA is destroyed by the photodynamic action of acridine orange129 and the transforming ability of DNA (see Glossary) is similarly destroyed by the similar action of a variety of dyes.130... 

Since drugs interact with optically active, asymmetric biological macromolecules such as proteins, polynucleotides, or glycolipids acting as receptors, many of them exhibit stereochemical specificity. This means that there is a difference in action between stereoisomers of the same compound, with one isomer showing pharmacological activity while the other is more or less inactive. In 1860, Louis Pasteur was the first to demonstrate that molds and yeasts can differentiate between (+)- and (-)-tartarates, utilizing only one of the two isomers. 

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