Topologically Modified Biopolymers: Properties of Synthetic Circular DNAs and RNAs

Abstract

Circular nucleic acid molecules can have chemical and biological properties very different from those of the corresponding linear nucleic acid polymers. Described here are methods used recently for construction of such circular molecules, and some of the properties that can arise from making this topological change. Among the unusual properties found for circular nucleic acids are: strong resistance to degradation in biological media; high affinity of binding to other nucleic acids; high sequence selectivity in nucleic acid binding; topological linkage to biomolecules; and the ability to template the synthesis of specific repeating nucleic acid and protein polymers. These properties may be useful in biochemical, medical diagnostic and therapeutic applications.

Fig. 1

(a) The structures of the two classical Watson–Crick base pairs in DNA. G and Care guanine and cytosine; A and T are adenine and thymine. (b) Illustration of how circles are formed from linear DNA/RNA strands using a Watson–Crick complementary ‘template’ or ‘splint’ (a short oligonucleotide) to bring the ends together.

Fig. 2

Illustration of how circular oligonucleotides {DNA or RNA) can form double helical or Triple helical complexes with a single target strand of DNA or RNA.

Fig. 3

Data for the susceptibility to degradation (monitored by gel electrophoresis) of linear and circular DNAs in undiluted human serum at 37°C. The ‘5′ p’ symbol indicates a phosphate group at the 5′ end of the linear strand.

Fig. 4

Illustrations of rolling circle reactions for synthesis of repairing polymers, (a) Synthesis of DNA, using a DNA circle, a DNA polymerase and dNTP (deoxynucleoside triphosphate) monomers. The end where active synthesis occurs is marked ‘3′’. (b) Synthesis of RNA using a DNA circle, an RNA polymerase and rNTP (ribonucleoside triphosphate) monomers, (c) Synthesis of protein using an RNA circle, ribosomes. tRNAs and amino acid monomers. The ‘notch’ on the circle in each case indicates the initiation site; the (+) and (−) signs are shown to indicate that a copied strand is not identical, but is complementary to the circle in the Watson–Crick sense.