Template directed polymerization

Khan A, Haddleton DM, Hannon MJ, Kukulj D, Marsh A. Hydrogen bond template-directed polymerization of protected 5 -acryloylnucleosides. Macromolecules 1999 32 6560-6564. 

Recent work from Christoff Biebricher s group showed that a very efficient template-directed polymerization of adeifine - with a degree of polymerization of up to 400 - could be achieved based on a poly(U) template (Trinks et al., 2003). 

Assuming the existence of an RNA template, the polymerization of activated ribonucleotides into polymers containing 3, 5 -phosphodiester linkages proceeds readily. Using RNA homopolymers as templates, products of up to 50 bases in length have been observed,30 and when RNA heteropolymers are used as templates the reaction is faithful.31 These reactions can be catalyzed by a variety of metal ions,32 33 and seem to occur most easily with ribose-linked nucleotides.34 Short oligonucleotides can also serve as substrates for template-directed polymerization,35 36 and they... 

So far, we have constructed an unsatisfying picture of the earliest days of an RNA world although some prebiotic mechanisms may exist for the untemplated formation of oligonucleotides, these molecules would have been short, would have contained a variety of monomers besides ribotides, and could not have been faithfully copied by the template-directed polymerization of monomers. Given this model, it is difficult to imagine the accumulation of RNA sequences necessary for the Darwinian selection of a multitude of active ribozymes. Nevertheless, these precursors may have been adequate for the first critical step in the formation of life the formation of an RNA replicase. 

I acknowledge Jennifer Doudna, Michael Famulok, and Jack Szostak for helpful discussions during the preparation of the manuscript, and David Bartel for insights into the importance of fidelity in template-directed polymerizations. 

A major goal of directed evolution of DNA polymerases has been to elucidate the structural elements that confer high fidelity during DNA replication. If DNA polymerases were to rely solely on the stability of nucleotides that aligned with template for discrimination of correct template-directed polymerization, the error frequency would be in the order of one mispaired nucleotide per 100 incorporated [23], The measured error rate for incorporation and extension of a mismatched nucleotide attributable to DNA polymerases lacking an error correcting exonucleolytic activity range... 

An oligonucleotide that base-pairs with a template polynucleotide strand and is extended tlarough template-directed polymerization is a/an... 

Gao SH, Wang W, Wang BH (2001) Building fluorescent sensors for carbohydrates using template-directed polymerizations. Bioorg Chem 29(5) 308-320... 

Since it has not been possible to cover all the valuable contributions that have been made in these fields of study, we have instead organized the discussion around a minimal scheme for template directed ligation. This minimal scheme will be compared with the autonomous natural genomes that self-replicate via template directed polymerization reactions. The advantages and limitations of each step in the minimal scheme are discussed with respect to the structural diversity in the template that will make it possible to extend these reactions to new materials and new polymerization strategies. 

DNA and RNA polymerases catalyze the template-directed polymerization of deoxyribonucleoside or ribonucleoside triphosphates. DNA polymerase allows one to copy any DNA molecule starting from the 5 end. RNA polymerase makes possible the preparation of any RNA molecule complementary to any DNA molecule ( transcription ). The DNA segment to be transcribed must follow a segment of DNA ( promoter ) that serves as a recognition site for the RNA polymerase. The following sequence is obeyed ... 

Fig. 9.5 Spontaneous template-directed polymerization. 5 -phosphorimidazolide activated nucleotide forms a new bond with the terminal 3 nucleophile of the primer (here an amino group for rapid reaction). Rj = H for DNA, OH for RNA R2 = CH3 for DNA, H for RNA (Reproduced with permission from [27])...

How do the resulting 0 values compare to experimental error ratios O for non-enzymatic template-directed polymerization Using chemically activated nucleotides, ref. [27] reported the measured errors incurred during non-enzymatic template-directed polymerization for all combinations of DNA and RNA templates and primers. The resulting mis-incorporation probabilities are plotted in Fig. 9.11... 

Kanaya, E. and Yanagawa, H. (1986) Template-directed polymerization of oligoadenylates using cyanogen bromide. Biochemistry 25,7423-7430. 

That said, metabolic interconversion of the amine backbone linkage of the ANPs would require oxidation, and thus would be a redox process rather than condensation/hydrolysis. Water remains a necessity for life and certainly life on Earth exploits condensation in the linkages of the nucleic acid monomers (phosphoester bonds), the amides of polypeptides, and the acetals of polysaccharides, and utilizes the reverse reaction of hydrolysis for metaboUsm. Therefore we have sought to extend the principles learned with the amine backbones to possible backbone chemistries that allow equilibrium control of template-directed polymerization through condensation and hydrolysis reactions. 

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