Nucleotide modification, localization

The chemical modification of nucleic acids at specific sites within individual nucleotides or within oligonucleotides allows various labels to be incorporated into DNA or RNA probes. This labeling process can produce conjugates having sensitive detection properties for the localization or quantification of oligo binding to a complementary strand using hybridization assays. 

Figure 28-10 Sequence of an E. coli tyrosine tRNA precursor drawn in a hypothetical secondary structure. Nucleotides found modified in the mature tRNA are indicated with their modifications (S4, 4-thiouridine Gm, 2 -0-methylgua-nosine 1°, N6-isopentenyladenosine jt, pseudouridine T, ribothymidine see also Fig. 5-33).241 A partial sequence of the tRNA gene past the CCA end is also shown. Note the region of local 2-fold rotational symmetry (indicated by the bars and the dot). The anticodon 3 -CUA (shaded) of this suppressor tRNA pairs with termination codon 5 -UAG.

Comparison of the psbA sequence of wild-type and AzV The analysis of the psbA gene sequence showed two nucleotide changes in AzV with respect to the wild type. These changes result in a modification of Phe 211 to Ser and of Ala 251 to Val in the AzV Dj protein (Fig. 2). Both modifications are localized in the Qg pocket. 

Finkel T, Der CJ, Cooper GM (1984) Activation olras genes in human tumors does not affect localization, modification, or nucleotide binding properties of p21. Cell 37 151-158... 

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. 

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