The “Speed Limit” of DNA polymerase

During DNA replication, a double-stranded DNA molecule is split apart into two single strands. Each of these strands acts as a template; a complementary new strand is generated along with it. This process depends on DNA polymerase, a molecule that travels along each template strand and catalyzes the formation of the new strand. DNA polymerase adds bases that pair to the bases already present in the template strand, forming base pairs that are the “rungs” of the DNA molecule. The average distance between consecutive base pairs in a DNA strand is 3.4 Angstroms (1 Angstrom = ${10}^{-10}$‍ m). DNA polymerase can replicate a DNA strand even as it follows the twists and bends of the DNA strand.

Figure 1: DNA Polymerase Replicates Template Strand

The DNA polymerase molecule can form new base pairs quickly. However, quantifying its maximum replication rate is difficult, because individual polymerase molecules can accelerate, decelerate, pause, or fall off the template strand. Polymerase replication rates are often reported in bp / s, the number of base pairs generated per second.

One experiment determined the maximum replication rate of single DNA polymerase molecules by measuring the elasticity of single strands of DNA as they were being replicated. The total number of bases in the DNA molecule, Ntotal, was known. The elasticity of the molecule at each point in time was compared to the known elasticities of single-stranded and double-stranded DNA of the same length in order to infer the percentage of the DNA molecule that had been replicated, p(t). Finally, the number of base pairs replicated at any given time, N(t), was calculated using the following equation: N(t) = p(t) x Ntotal. Results of this analysis are shown below.

Figure 2: Activity of a Single DNA Polymerase Molecule