Differential inhibitory activities and stabilisation of DNA aptamers against the SARS coronavirus helicase

Chembiochem. 2008 Dec 15;9(18):3037-45. doi: 10.1002/cbic.200800491.

Abstract

The helicase from severe acute respiratory syndrome coronavirus (SARS-CoV) possesses NTPase, duplex RNA/DNA-unwinding and RNA-capping activities that are essential for viral replication and proliferation. Here, we have isolated DNA aptamers against the SARS-CoV helicase from a combinatorial DNA library. These aptamers show two distinct classes of secondary structure, G-quadruplex and non-G-quadruplex, as shown by circular dichroism and gel electrophoresis. All of the aptamers that were selected stimulated ATPase activity of the SARS-CoV helicase with low-nanomolar apparent K(m) values. Intriguingly, only the non-G-quadruplex aptamers showed specific inhibition of helicase activities, whereas the G-quadruplex aptamers did not inhibit helicase activities. The non-G-quadruplex aptamer with the strongest inhibitory potency was modified at the 3'-end with biotin or inverted thymidine, and the modification increased its stability in serum, particularly for the inverted thymidine modification. Structural diversity in selection coupled to post-selection stabilisation has provided new insights into the aptamers that were selected for a helicase target. These aptamers are being further developed to inhibit SARS-CoV replication.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / chemistry
  • Aptamers, Nucleotide / pharmacology*
  • Base Sequence
  • DNA Helicases / antagonists & inhibitors
  • DNA Helicases / metabolism*
  • G-Quadruplexes
  • Inhibitory Concentration 50
  • Kinetics
  • Severe acute respiratory syndrome-related coronavirus / enzymology*
  • Viral Proteins / antagonists & inhibitors
  • Viral Proteins / metabolism*

Substances

  • Aptamers, Nucleotide
  • Viral Proteins
  • DNA Helicases