Nucleotides abbreviations, Table

Table 8.1 The genetic code as a three-letter code, with the normal abbreviations for the 20 pro-teinogenic amino acids. The first base corresponds to the 5 end, the third to the 3 end of the nucleotide chain... 

In nature, eight common nucleotides exist, four found in DNA and four in RNA. In the standard abbreviations for DNA nucleotides, a lowercase d specifies the presence of deoxyribose. RNA nucleotides lack this designation. Nucleosides have names of one word (e.g., deoxyadenosine, cytidine, and uridine). The ending monophosphate completes the nucleotide names. Table 16.1 lists correct names for all common nucleotides and nucleosides, and Figure 16.9 shows linkages and structures for all eight nucleotides. 

Figure 26-7 Genetic map of cloning plasmids pBR322 and pUC18. Abbreviations ori, origin of replication Amp1, ampicillin resistance gene Tet1, tetracycline resistance gene. Other abbreviations are for sites cleaved by specific restriction endonucleases, a few of which are defined in Table 26-2. The nucleotide sequence numbers and directions of transcription are also indicated. Reproduced by permission of Amersham Pharmacia Biotech Inc.

The symbol X in the Table means that an activated form of the monosaccharide is not known a dash shows that the monosaccharide has not been identified as a component of bacterial polysaccharides. For references, see the text. 6 See Ref. 101 for abbreviations. c Primary glycosyl nucleotide. 4 See comments in the text. 

DNA sequences corresponding to the transcript are aligned on the basis of the TTTA /tA motif which is underlined and centred 25-27 nucleotides upstream from the putative transcriptional start sites. Putative transcriptional start sites are preceded by a space. The first nucleotide of mature 5S rRNAs or tRNAs is denoted by a single lower-case letter. Putative start codons are indicated by three lower-case letters. Accession Numbers to sequence databases, and literature references, are listed in Table 2. Names of organisms are abbreviated as in Table 1. 

The method colmnn denotes procedures or processes used in the synthesis of the nucleotides. The Roman munerals refer to the phos-phorylating agent or system described in Table I. The other abbreviations denote the following AN = by way of anhydronucleotide intermediate(s) D = deamination Enz = enzymic hydrolysis pE] = hydrogenation HA = halogenation Hy = hydrolysis NA = W-alkylation NOx = iV-oxidation Ph = phosphorolysis of the activated nucleoside by the phosphate anion (seep. 369) R = by rearrangement RO = by ring-... 

Because the full names of the nucleotides are so cumbersome, a simple abbreviation is generally used. These abbreviations are summarized in Table 24.2. 

Abbreviations CCK, cholecystokinin RNase. ribonuclease G-protein, guanine nucleotide binding protein GPCR, G-protein-coupled receptor. SDS sodium dodecylsulfate, CTAH. hexadecyltrimethyl ammonium hydroxide DMPC. di-myristoylphosphatidylcholine DPPC, di-palmitoylphosphatldylcholine CMC, critical micellar concentration SUV, small unilamellar vesicles CD, circular dichroism NMR, nuclear magnetic resonance hs-DC, high sensitivity differential scanning calorimetry IR-ATR, infrared attenuated total reflection spectroscopy NOE, nuclear Overhauser effect MD, molecular dynamics DMSO, dimethylsulfoxide TFE, trifluoroethanol for abbreviations of peptides see tables land 2, and fig. 11. 

Table 1. Purine and pyrimidine bases, the nucleosides, nucleotides, and corresponding abbreviations.

Nucelotides are the repeating building blocks of nucleic adds (which are polynucleotides or polymers of nucleotides). A nucleotide is made up of a het-erocycHc base (a purine or pyrimidine), a cychc sugar unit (ribose or deoxyri-bose), and a phosphate group. A nucleotide is either a ribonucleotide, the repeating unit in ribonucleic acid (RNA), or a deoxyribonudeotide, the repeating unit in deoxyribonucleic acid (DNA). Table 1 below fists the names of purine and pyrimidine bases, the nucleosides (base + ribose), the corresponding 5 -nucleotides (base + ribose + phosphate), and the abbreviations. 

Listed below are miscellaneous examples used in this work and found elsewhere. See also Table 1.3 for P-containing compounds, Table 10.7 for amino acids, Table 10.15 for bases, nucleosides and nucleotides and Table 14.4 for symbols in use for analytical techniques. Symbols in commercial use for branded products are mostly excluded from all these tables. Symbols for the elements are also excluded. While some symbols and abbreviations appear to be here to stay, it should be remembered that the use of some of them can be very subject to fashion or personal choice. 

Nucleotides are named as the 3 - or 5 -monophosphate esters of a nucleoside, as shown above. These names are frequently abbreviated as in Table 18.1. In these abbreviations, letter d stands for 2-deoxy-D-ribose, the next letter refers to the heterocyclic base, and MP stands for monophosphate. (Later we will see that some nucleotides are diphosphates, abbreviated DP, or triphosphates, TP.) Unless otherwise stated, the abbreviations usually refer to the 5 -phosphates. 

Uracil differs from thymine only in lacking the C-5 methyl group. Like thymine, it forms nucleotides at N-1, and their names are similar to those in Table 18.1. In the abbreviations of these names, letter d (which stands for deoxyribose) is omitted because the sugar is ribose. 

These three compounds have abbreviations that are commonly used 126 is abbreviated AMP, 129 is ADP, and 130 is ATP. These abbreviations stem from a one-letter code for each heterocycle used to form the nucleotide—in this case, A for adenine. These codes are shown in Table 28.2, but they are trivial the code simply takes the first letter from each heterocycle. 

Table la - c. List of constituents of nucleotides abbreviations and chemical structure (a) Phosphate groups, (b) sugar residues, and (c) polymerized nucleosides. 

Table 5 Representation of various nucleosides, nucleotides of DNA and abbreviations used to designate these are shown in this table...

The name of a nucleoside that contains a purine ends with osine, whereas a nucleoside that contains a pyrimidine ends with idine. The names of the nucleosides of DNA add deoxy to the beginning of their names. The corresponding nucleotides in RNA and DNA are named by adding -5 -monophosphate. Although the letters A, G, C, U, and T represent the bases, they are often used in the abbreviations of the respective nucleosides and nucleotides. The names and abbreviations of the bases, nucleosides, and nucleotides in DNA and RNA are listed in Table 17.2. 

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