Replication, Transcription and Nuclease Digestion of the Unusual X-DNA Double Helix of Poly(amino²dA-dT)

Abstract

The alternating copolymer poly(amino2dA-dT) isomerizes into the unusual X-DNA double helix at low-salt aqueous conditions (Vorlicková et al., J. Biomolec. Struct. Dyn. 6, 503-510 (1988)). This observation allowed us to start studies on how the X-DNA is recognized, copied and hydrolyzed by various enzymes. In the present paper X-DNA replication, transcription and digestion by various polymerases and nucleases, respectively, are examined and compared to appropriate controls. It is found that X-DNA is a poor primer-template for DNA synthesis by the E. coli Klenow DNA polymerase (12% of the activity observed with B-DNA), the Micrococcus luteus DNA polymerase I (25%) and the AMV reverse transcriptase (51%). In contrast, X-DNA is a better template by 74% than B-DNA for calf thymus DNA polymerase alpha. For transcription by E. coli RNA polymerase enzyme poly(amino2dA-dT) did not serve as a template at all in either B or X conformation. Poly(amino2dA-dT) in its B form proved to be much more stable than poly(dA-dT) against hydrolysis by pancreatic DNase and snake venom phosphodiesterase. Formation of the X conformation in poly(amino2dA-dT) decreased this large difference in nuclease stability.