Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication

Abstract

The frequency of errors during genome replication limits the amount of functionally important information that can be passed on from generation to generation. During the origin of life, mutation rates are thought to have been quite high, raising a classic chicken-and-egg paradox: could nonenzymatic replication propagate sequences accurately enough to allow for the emergence of heritable function? Here we show that the theoretical limit on genomic information content may increase substantially as a consequence of dramatically slowed polymerization after mismatches. As a result of postmismatch stalling, accurate copies of a template tend to be completed more rapidly than mutant copies and the accurate copies can therefore begin a second round of replication more quickly. To quantify this effect, we characterized an experimental model of nonenzymatic, template-directed nucleic acid polymerization. We found that most mismatches decrease the rate of primer extension by more than 2 orders of magnitude relative to a matched (Watson-Crick) control. A chemical replication system with this property would be able to propagate sequences long enough to have function. Our study suggests that the emergence of functional sequences during the origin of life would be possible even in the face of the high intrinsic error rates of chemical replication.

Figure 1

Examples of nonenzymatic primer extension over time. (Insets) Denaturing polyacrylamide gel at reaction time points. Exponential curve fits are drawn to guide the eye. (A) Correct incorporation of ImpdT across A. (B) Incorrect incorporation of ImpdG across A. (C) Extension of matched primer terminus (blue). (D) Extension of mismatched primer terminus (blue/red).

Figure 2

Misincorporation frequencies and stalling factors in nonenzymatic polymerization. (A) Incorporation frequencies of each nucleotide across each base. (B) Stalling factors associated with mismatched termini. Error bars show standard deviations calculated from duplicate sets of reactions. Primer N refers to the primer containing base N at the 3′ terminus.

Figure 3

Modified error threshold. (A) Ratio of the maximum genome information including the effect of stalling and strand separation relative to the classical maximum. (B) Maximum genome information for different values of r using experimentally determined values for μ_ave and S_ave during nonenzymatic polymerization. Curves were calculated for the classical model (black) or with the modified model (red).