Nucleic acid structures representation

Reasonable representation of nucleic acid structure Simulations of DNA and RNA. 

Polymers are found in nature and may also be produced by laboratory synthesis. Important examples of naturally occurring macromolecules, or biopolymers, are proteins, polysaccharides, terpenes, and nucleic acids. General representations of these substances are provided by structures 3-6, respectively, in which the monomeric subunits of an a-amino acid, 3, a pyranose, 4, an isoprene, 5, and a ribonucleotide phosphate, 6, are seen. Synthetic, or man-made, polymers are represented by the myriad plastics, elastomers, and fibers that are commonplace in contemporary society. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

By convention, the structure of a single strand of nucleic acid is always written with the 5 end at the left and the 3 end at the right—that is, in the 5 — 3 direction. Some simpler representations of this pentade-oxyribonucleotide are pA-C-G-T-AoH, pApCpGpTpA, and pACGTA... 

Figure 8.1 The two sugars, five nitrogenous bases, and phosphate that occur in nucleic acids. Each fundamental unit of nucleic acid is a nucleotide, an example of which is shown. The single letter beside the structural formula of each of the nitrogenous bases is used to denote the base in shorthand representations of the nucleic acid chains.

Figure 1.28 (a) The general structure of a nucleotide, (b) A schematic representation of a section of a nucleic acid chain, (c) The bases commonly found in DNA and RNA. These bases are indicated by the appropriate letter in the structures of Nucleic acids. Thymine is not found in RNA it is replaced by uracil, which is similar in shape and structure, (d) Examples of nucleosides found in DNA and RNA... 

Each representation of a protein or nucleic acid conveys to the viewer different aspects of its structure line drawings give the bones, space-filling models the flesh, and schematic diagrams the gestalt of the design. No single representation of a protein or nucleic acid is adequate for all purposes, but the combination of several is more powerful than the total of all taken independently. 

Figure 1.5 Diagrammatic representation of (a) a nucleic acid and (b) double helix structure of DNA. Illustrations, Irving Geiss. Rights owned by Howard Hughes Medical Institute. Reproduction by permission only.

Jeffrey H.J. (1990) Chaos game representation of gene structure. Nucleic Acids Res., 18, 2163-2170. 

The most important naturally occuring diazines are the pyrimidine bases uracil, thymine and cytosine, which are constituents of the nucleic acids (see 32.4). The nucleic acid pyrimidines are often drawn horizontally transposed from the representations used in this chapter, i.e. with N-3 to the north-west , mainly to draw attention to their structural similarity to the pyrimidine ring of the nucleic acid purines, which are traditionally drawn with the pyrimidine ring on the left. There are relatively few naturally occurring pyr-azines or pyridazines. 

Discovery of the structure of DNA in 1953 and subsequent elucidation of how DNA directs synthesis of RNA, which then directs assembly of proteins—the so-called central dogma—were monumental achievements marking the early days of molecular biology. However, the simplified representation of the central dogma as DNA—>RNA— protein does not reflect the role of proteins in the synthesis of nucleic acids. Moreover, as discussed in later chapters, proteins are largely responsible for regulating gene expression, the entire process whereby the information encoded in DNA is decoded into the proteins that characterize various cell types. 

Drawing structures of nucleic acids becomes very difficult when more than a few nucleotide residues are involved. Various abbreviated schematic representations are used. Figure 21-3 shows some of these representations for the nucleotide sequence AMP-CMP-UMP-GMP-CMP. Note that many structural details are understood when such drawings are used. One knows whether the nucleic acid sequence is that for an RNA or DNA by other information that is supplied. By... 

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