The construction of a processive catalyst; a DNA-polymerase mimic

Nature has developed very efficient processive catalysts that can convert polymeric substrates like DNA and RNA. By pre-organizing substrate and catalyst, very high turnover numbers and selectivities can be achieved. One example is DNA-polymerase (Figure 1A) that consists of two main parts: A circular sliding clamp (purple) and the catalytic center (blue) that polymerizes base pairs, using the ss-DNA as a template to create ds-DNA.

Figure 1. A: DNA-Polymerase, B: Porphyrin-containing macrocycle

 

In order to mimic such systems we intend to use a ruthenium-porphyrin-containing macrocycle (Figure 1B) that is able to form a double bond, when coupling two diazo esters.

Figure 2.Schematic representation of the polymerase mimic

 

When a di-diazo-ester (Figure 2) is used, a polymer should be formed, thereby mimicking a polymerase. We intend to follow this process by Atomic Force Microscopy (AFM) and confocal fluorescence microscopy by first immobilizing a diazo-endfunctionalized monomer on a surface and, secondly, by allowing the functionalized surface to react with the catalyst. Upon the addition of di-diazo-esters a polymer should grow from the inside of the macrocyclic catalyst.