Nucleic acid abbreviated structures

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

Figure 3.21 Abbreviated surface chemistry structures PLL, epoxysilane, APS, and DAB. (From Taylor, S. et al.. Nucleic Acid Res., 31(16), 1-19, 2003. With permission.)...

The structure of nucleic acids depends on the sequence of individual nucleotides. The actual base sequences for many nucleic acids from various species are available to date. Instead of writing the full name of each nucleotide, abbreviations are used, e.g. A for adenine, T for thymidine, G for guanosine and C for cytidine. Thus, a typical DNA sequence might be presented as TAGGCT. 

Nucleic acid structures are abbreviated in several ways. For example, the sugar rings may be portrayed by vertical lines. The abbreviations A, C, U, T, and G for the individual bases or Pu (purine) and Py (pyrimidine) are placed at the upper ends of the lines, and slanted lines with P in the centers represent the 3 -5 phosphodiester linkages in a polynucleotide. 

Table 4.4 Summary of the main extrinsic fluorophores that may be combined with proteins or nucleic acids. Main absorption and fluorescence characteristics are given. See Fig. 4.15 and Table 4.1 for structure abbreviations and other abbreviations used in the table.

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... 

Under such circumstances, it makes little sense to ask which specific positive ions are attributed to DNA as its own counterions — protons H+ or some of the present positive metal ions. This may lead to the question whether DNA and RNA deserve the character A in their abbreviated names, which stands for acid , or, maybe, it is more productive to think of DNA as a salt of the corresponding acid This question seems purely terminological to a physicist, but a chemist may have a different opinion. On this topic we can only cite the very first sentence from the famous very first paper by J. Watson and F. Crick, where they announce their discovery of the double helix We wish to suggest a structure for the salt of deoxyribose nucleic acid (DNA) . 

The identification of DNA as a primary target for metal-based drugs, especially cisplatin, has focused attention on the interactions of metal complexes with nucleic acid constituents, which include the simple purine and pyrimidine bases and their nucleoside and nucleotide derivatives. The structures, with abbreviations, are represented in Appendix 1. Simple complexes can represent models for cross links in DNA, which can be studied in more detail with small polynucleotides, from the simpler dinucleotides to oligonucleotides and this topic is covered in Section 4.4. There has been extensive use of substituted purines and pyrimidines as models for the DNA bases and in the examination of steric and electronic effects. The structures of many of these analogues are also collected in Appendix 1. 

The coenzyme isolated from yeast - has been assigned the structure of a glucose-l-phosphate molecule attached to uridine-5 -phosphate through a pyrophosphate link (Fig. 7). It has been abbreviated as UDPG. The discovery of a uridine-5 -phosphate in this compound preceded the recent demonstration of such a moiety in ribose nucleic acid. 

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