Ribose nucleotide sequences

Deoxyribonucleic acid A nucleic acid containing a deoxygenated ribose sugar, having a double helical structure, and carrying genetic code in the nucleotide sequence. 

The bases are in syn or anti orientation. The orientation of the base relative to the sugar moiety is defined by torsion angle x which is constrained by steric interactions, and by the anomeric effect. The main conformations are referred to as syn and anti (see Fig. 17.5). In syn, j X is close to 0° (sp for torsion angle definition, see Box 13.3 Fig. 13.12), and the base is I oriented "above the ribose ring causing steric interactions which in the anti conformation with x close to 180° (ap) are avoided. The anti conformation is therefore preferred and is the j only form observed in double-helical DNA and RNA. An exception is the left-handed Z-DNA with alternating purine/pyrimidine nucleotide sequence where the purines are in the syn conformation. 

RNA Ribonucleic acid. A macromolecule made of nucleotide sequences similar to DNA, but with uracil instead of thymine as a base and ribose as the backbone sugar instead of deoxyribose. RNA plays a major role in transcription and translation of the genetic code. There are several classes of RNA including mRNA, tRNA and rRNA. 

RNA is chemically very similar to DNA but differs in important ways. The sugar miit is ribose with an added hydroxyl group at the 2 position, and the methylated pyrim-idine uracil (U) replaces thymine. RNA exists in various functional forms but typically as a single-stranded polymer that is much shorter than DNA and that has an irregular three-dimensional structure. Research from recent years has revealed that RNA conformations are not random structures and the folding mechanism of RNA molecules is complex. The secondary structure adopted by an RNA molecule is to a large extent related to its nucleotide sequence. The secondary structure for particular RNA sequences can be as regular as the secondary structure of a protein. It is now known that RNA molecules can further interact to form complex tertiary structures, which are intimately related to novel functions of RNA, such as the catalytic activity of ribozymes, ... 

The essential elements of Table 2.1 meet these demands. In all cases they are components of the metabolic system in cell or of important final products for example, cellulose for the upright standing of the plant. The function as constituents of such compounds is clear for C, H, and O. These three elements are together components of nearly all organic compounds in the plant [only hydrocarbons (e.g., carotins) are free of O], and therefore they build up the planfs shape. A similarly clear situation holds true for N and P, both of which are constituents of the information carriers DNA and RNA. N is a component of their purine and pyrimidine bases, while phosphoric acid esters of D-ribose or 2-deoxy-D-ribose form the backbone of their nucleotide sequences. Moreover, P plays a very important role in energy metabolism, the key compounds being nucleotide phosphates (e.g., adenosine triphosphate, ATP) (see Scheme 2.1) and the homologous molecules... 

The prefixes d and r, which represent deoxyribose of DNA and ribose of RNA respectively, are omitted where an implication of the type of polynucleotides is obvious from the context of nucleotides involved (i.e. T for DNA, while U for RNA). In the linear code representation, the nucleotide sequence is written from the left for the 5 -end to the right for the 3 -end (e.g. coding nucleotide sequence for human lysozyme (Pasta format))... 

Fig. 2. Nucleotide sequence of the Okayayma-Berg pcD>poly(ADPR)p cDNA insert and the deduced amino acid sequence of the 113, 135-kDa protein. The protein contains sequences coding for three poly(ADP-ribose) polymerase peptides (underlined and sequentially numbered), in the 3 untranslated region a putative mRNA processing signd (AATAAA) is underlined. In the 5 region two nucleotides that correspond to the Kozak criteria for initiation are underlined. (Taken from Ref. 3).

Fig. 1. Nucleotide sequence of cloned cDNA encoding human poly(ADP-ribose) synthetase. Nucleotide residues are numbered in the 5 to 3 direction, beginning with the first residue of the ATG triplet encocHng the initiative methionine and the nucleotides on the 5 side of residue 1 are indicated by negative numbers the number of the nucleotide residue at the right end of each line is given. The deduced amino acid sequence of poly(ADP>ribose) synthetase is shown above the nucleotide sequence and the amino acid residues are numbered beginning with the initiative methionine. Open triangles denote the sites cleaved by papain, and closed triangles indicate the sites cleaved by a-chymotrypsin.

Note After submission of this manuscript we and other investigators published the nucleotide sequence of full-length cDNAs for human fibroblast and placental poly(ADP-ribose) polymerases (Biochem Biophys Res Commun 148 617-622, 1987 J Biol Chem 262 15990-15997, 1987 Proc Natl Acad Sci USA 84 8370-8374,1987). 

As it was shown also by the data reported above, tRNA methyl-transferases exibit a very complex kind of specificity toward the tRNA substrate. In fact, three requirements must be fulfilled in order to achieve the enzymatic attachment of a methyl group to tRNA. Each enzyme must recognize (i) the proper moiety along the polynucleotide chain (either the specific base of the ribose) (ii) the position of the modification at the purine, pyrimidine or furanosic rings (Hi) the localized nucleotide sequence and the spatial locus of the three-dimensional configuration in which the methyl-atable nucleoside is positioned. These three requirements allow us to define three different types of specificity for tRNA methyltrans-ferase, namely moiety specificity, ring-atom specificity and site specificity, respectively. 

---