Nucleic acid abbreviations

Residue name - one of the standard amino acids (lliree-letler abbreviations are used), nucleic acids (one- or two-lctter abbreviations), or the non-standard group designation as dc ncd in lire HHT dictionary 23-26 Residue sequence nuniber,... 

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. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

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 bases that occur in nucleic acids are aromatic heterocyclic compounds derived from either pyrimidine or purine. Five of these bases are the main components of nucleic acids in all living creatures. The purine bases adenine (abbreviation Ade, not A ) and guanine (Gua) and the pyrimidine base cytosine (Cyt) are present in both RNA and DNA. In contrast, uracil (Ura) is only found in RNA. In DNA, uracil is replaced by thymine (Thy), the 5-methyl derivative of uracil. 5-methylcyto-sine also occurs in small amounts in the DNA of the higher animals. A large number of other modified bases occur in tRNA (see p. 82) and in other types of RNA. 

When a nucleic acid base is N-glycosidically linked to ribose or 2-deoxyribose (see p.38), it yields a nucleoside. The nucleoside adenosine (abbreviation A) is formed in this way from adenine and ribose, for example. The corresponding derivatives of the other bases are called guanosine (G), uridine (U), thymidine (T) and cytidine (C). When the sugar component is 2-deoxyribose, the product is a deoxyribonucleoside—e. g., 2 -deoxyadeno-... 

NUCLEOTIDES AND NUCLEIC ACIDS Abbreviations and symbols for nucleic acids, polynucleotides and their constituents /. Biol. Chem. (1970) 245, 5171-5176 Corrections, J. Biol Chem. (1971) 246, 4894 Abbreviations and symbols for the description of conformations of polynucleotide chains Eur. J. Biochem. (1983) 131, 9-15 Nomenclature for incompletely specified bases in nucleic acid sequences... 

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. 

FIGURE 8-4 Deoxyribonucleotides and ribonucleotides of nucleic acids All nucleotides are shown in their free form at pH 7.0. The nucleotide units of DNA (a) are usually symbolized as A, G, T, and C, sometimes as dA, dG, dT, and dC those of RNA (b) as A, G, U, and C. In their free form the deoxyribonucleotides are commonly abbreviated dAMR dGMR dTMR and dCMP the ribonucleotides, AMR... 

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. 

DNA Abbreviation for deoxyribonucleic acid. It belongs to a group of biopolymers called the nucleic acids. It is involved in the polymerisation of amino acids in a specific order to form the particular protein required by a cell. 

Abbreviations DNA, deoxyribose nucleic acid ECD, electrochemical detection LIF, laser induced fluorescence LOD, limit of detection PDMS, poly(dimethylsiloxane) PSA, prostate specific antigen TOF-MS, time-of-flight mass spectrometer TNT, 2,4,6-trinitrotoluene. 

Additional nucleic acids as their triphosphates may add to the 3 end of the existing oligonucleotide. This entire process is catalyzed and controlled by DNA polymerases, a family of enzymes that can replicate and repair DNA. The synthesis of DNA is always performed in the 5 to 3 direction.2 Furthermore, oligonucleotide strands are written with the letters of the nucleic acid monomers, starting from the 5 end. Oligonucleotide abbreviations should be read with an open mind because the literature contains many slightly different notation styles. 

Based on Fraenkel-Conrat (1974), ss and ds refer to whether the nucleic acid is single stranded or double-stranded. +env. indicates whether or not the virus is enveloped. The abbreviations for the viruses can be found in Appendix 6. 

Table 12-4 presents the standard abbreviations for nucleic acids. 

Because nucleic acids contain a large number of nucleotides, biochemists have devised an abbreviation system to indicate the nucleotide sequence of nucleic acids (see Fig. V-2). This system assumes the 3, 5 -phosphodiester linkages and lists, in a 5 to 3 order, the nucleotide sequence of the nucleic acid with p (phosphate) between each nucleotide. Using this latter system, the RNA nucleotide sequence shown in Figure V-2 is. .. ApGpCpUp. You may also encounter an even simpler abbreviation system where the phosphate (p) between each nucleotide is omitted (e.g.,. . . AGCU. . . ). 

FIGURE B.l Abbreviations for double-stranded nucleic acids. 

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