The Influence of Osmolytes on Nucleic Acid Helical Conformations

Abstract

In the cell, nearly 40% of the volume is occupied by macromolecular crowding agents and smaller osmolytes that accumulate in response to environmental stresses. The effects of these cosolutes were observed on the transition of helical conformation from B-DNA to Z-DNA. Distinct from the familiar, right-handed B-DNA, Z-DNA is a left-handed double helical structure with its phosphodiester backbone arranged in a pronounced zig-zag pattern. This pattern, unique to Z-DNA is formed from alternating purine-pyrimidine sequences in the DNA. Due to the correlation between Z-DNA formation potential and regions of active transcription, Z-DNA is believed to serve a vital role in the transcription process. Due to the distinctive characteristics of the two types of DNA, the changes in helical conformation may easily be examined using circular dichroism (CD). Spectral analyses revealed that osmolytes (PEG200) promoted the formation of Z-DNA as well as lessened the salt requirement for Z-form stabilization. These results suggest that the formation of Z-DNA is more energetically favorable as the nonpolar, hydrophobic surfaces of the Z-DNA are stabilized in water-poor conditions. The effects of these cosolutes were also observed on the helical conformation of DNA/RNA hybrid duplexes which play important roles in biological processes such as replication, transcription, reverse transcription, and mRNA degradation. Our analyses revealed that the helical conformation of the hybrid duplexes ranged from A-form like to B-form like, depending on the base composition of each strand. In the presence of macromolecular crowding agents, the conformations shifted to more A-form like while in the presence of osmolytes the conformations shifted to more B-form like. These results suggest that the accessibility of the helical grooves for a given hybrid sequence may be modulated by the cellular environment.