Replication fidelity Watson-Crick base pairs

The virtuosity of the DNA polymerase first isolated from E. coli still amazes me. Holding one or two turns of one chain of DNA helix as template, it assembles a complementary chain thousands of nucleotides long. It does so by Watson-Crick base pairing with an accuracy which exceeds chemical predictions. The enzyme achieves this fidelity of replication by a proof-reading exonuclease in its active center. This 3 5 exonuclease... 

This scheme (Fig. 2.5) thus shows how oligonucleotides can direct the synthesis of polypeptides in the absence of protein or ribosomal machinery and, as such, is an appealing bioorganic model for the origin of prebiotic protein synthesis (see Section 3.7.2.1). Indeed, it seems most probable that primitive biosystems used a similar concept to carry out primitive protein synthesis where Watson-Crick base pairing provided the intrinsic mechanism for achieving fidelity of replication and direction of protein synthesis. In time, the carrier oligonucleotides could have evolved into more efficient species such as the present-day tRNA molecules. 

Strand (57). Other problems such as the formation of G-quadruplexes by G-rich template strands, and non-Watson-Crick base pairings (e.g., G-U wobble pairing) further inhibit high-fidelity sequence transfer in template-directed synthesis. These problems would greatly restrict the sequence space for evolving ribozymes and proto-ribozymes as newly mutated sequences that possess new catalytic properties may not be replicable (i.e., heritable). 

DNA must be replicated with high fidelity. Each base added to the growing chain should with high probability be the Watson-Crick complement of the base in the corresponding position in the template strand. The binding of the NTP containing the proper base is favored by the formation of a base pair, which is stabilized by specific hydrogen bonds. 

Reversible bond formation is utilized by living organisms during the first step of replication as a primary means of proofreading via the thermodynamic selection of the lowest energy base pair (i.e., correct Watson-Crick complement) (Scheme 1). The reversible condensation of the nucleoside triphosphate is followed by hydrolysis of the pyrophosphate product to kinetically trap the newly formed phosphodiester bond (Scheme 1). In emulating this two-step process, we maintain that both the initial step that exploits the stability of template association, and the subsequent reaction that traps the thermodynamically-favored product are necessary for high-fidelity repUcation. 

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