Hexanucleotide template

An elegant example of thermodynamic templating has been reported by Lynn and co-workers [30]. The reversible reaction of amine 16 with aldehyde 17 to give hexanucleo-tide imine 19 is favored by a hexanucleotide template 18 (Scheme 1-5). The imine can then be reduced to the corresponding amine 20 to fix the new hexanucleotide and remove it from the thermodynamic cycle. The hexanucleotide template 18 has a catalytic role in this overall process because, amazingly, it binds 19 about 10 times more strongly than 20, so product inhibition is not a problem. (Systems of this type are described in detail in Chapter 5.)... 

This approach utilized a particular hexanucleotide CCGCGG-p as a template a 5 terminally protected trideoxynucleotide 3 -phosphate d(Me-CCG-p), indicated as A, and a complementary 3 -protected trideoxynucleotide d(CGG-p ), indicated as B,... 

Biotinylated dUTP can also be used to label DNA probes by a different method, namely random-primed labeling (4). The principle of this method is based on the reannealing of hexadeoxyribonucleotide primers, which have random specificity, to the denatured DNA strands. The DNA to be labeled has to be linearized and denatured before the strands are used as templates in the labeling reaction. The complementary strands are synthesized from the 3 OH termini of the reannealed hexanucleotides by the Klenow fragment of E. coli DNA polymerase I. The primers reanneal at random sites of the template strands, so that the synthesis of the complementary strands is primed at random sites. If one of the deoxyribonucleoside triphosphates present in the reaction mixture is labeled, the newly synthesized strands will become labeled by the incorporation of the labeled nucleotides. The end product of this reaction is a mixture of unlabeled (template) and labeled... 

Random hexanucleotides, which bind different complementary sites on the RNA template. 

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