Nucleic acids properties

Chemists and biochemists And it convenient to divide the principal organic substances present m cells into four mam groups carbohydrates proteins nucleic acids and lipids Structural differences separate carbo hydrates from proteins and both of these are structurally distinct from nucleic acids Lipids on the other hand are characterized by a physical property their solubility m nonpolar solvents rather than by their structure In this chapter we have examined lipid molecules that share a common biosynthetic origin m that all their carbons are derived from acetic acid (acetate) The form m which acetate occurs m many of these processes is a thioester called acetyl coenzyme A... 

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... 

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

Plasmid DNAs. Plasmids are nucleic acid molecules capable of intracellular extrachromosomal repHcation. Usually plasmids are circular DNA species, but linear and RNA plasmids are known. In nature, plasmids can assume a variety of lifestyles. Plasmids can recombine into the host chromosome, be packaged into vims particles, and repHcate at high or low copy number relative to the host chromosome. Additionally, their information can affect the host phenotype. Whereas no single plasmid is usually capable of all these behaviors, the properties of various plasmids have been used to constmct vectors for a variety of purposes. 

Liquid Crystalline Structures. In certain ceUular organeUes, deoxyribonucleic acid (DNA) occurs in a concentrated form. Striking similarities between the optical properties derived from the underlying supramolecular organization of the concentrated DNA phases and those observed in chiral nematic textures have been described (36). Concentrated aqueous solutions of nucleic acids exhibit a chiral nematic texture in vitro (29,37). 

Essential for MD simulations of nucleic acids is a proper representation of the solvent environment. This typically requires the use of an explicit solvent representation that includes counterions. Examples exist of DNA simulations performed in the absence of counterions [24], but these are rare. In most cases neutralizing salt concentrations, in which only the number of counterions required to create an electrically neutral system are included, are used. In other cases excess salt is used, and both counterions and co-ions are included [30]. Though this approach should allow for systematic smdies of the influence of salt concentration on the properties of oligonucleotides, calculations have indicated that the time required for ion distributions around DNA to properly converge are on the order of 5 ns or more [31]. This requires that preparation of nucleic acid MD simulation systems include careful consideration of both solvent placement and the addition of ions. 

Centrifugation can be used either as a preparative technique for separating and purifying macromolecules and cellular components or as an analytical technique to characterize the hydrodynamic properties of macromolecules such as proteins and nucleic acids. 

Another property of pyrimidines and purines is their strong absorbance of ultraviolet (UV) light, which is also a consequence of the aromaticity of their heterocyclic ring structures. Figure 11.8 shows characteristic absorption spectra of several of the common bases of nucleic acids—adenine, uracil, cytosine, and guanine—in their nucleotide forms AMP, UMP, CMP, and GMP (see Section 11.4). This property is particularly useful in quantitative and qualitative analysis of nucleotides and nucleic acids. 

The possibility of interfering with the structure or formation of nucleic acids with the aid of such antimetabolites obviously has great practical significance. An interference with growth of neoplastic tissue and influence on the genetic properties of an organism should be mentioned in the first place. 

Modern concepts have been extended to the chemistry of heterocyclic compounds more slowly than to the chemistry of aromatic and aliphatic systems, but efforts are now being made to classify and explain the properties and reactions of heterocyclic compounds in terms of these newer ideas (cf. reference 11). However, many of the most important heterocyclic compounds are potentially tautomeric, and elucidation of their tautomeric composition must precede a logical treatment of their properties. Further, many natural products such as the nucleic acids and alkaloids contain potentially tautomeric groups and information of this type is needed for a detailed explanation of th reactions which they undergo,... 

Dialdehyde-containing nucleic acids and their components, synthesis, properties, and affine modification of proteins 99UK267. 

Synthesis and properties of analogs of nucleic acids 95MI10. 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

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