The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

Takeshi Fujimoto,Naoki Sugimoto,Shu-Ichi Nakano,Daisuke Miyoshi

doi:10.4061/2011/857149

Abstract

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions.

Highlights

Biomolecules have evolved to function within living cells, which contain a variety of macromolecules including nucleic acids, proteins, polysaccharides, and metabolites
These results demonstrated that the effect of molecular crowding on the thermodynamics of G-quadruplexes is determined by the enthalpy change during formation, which depends on the position of the abasic site
We examined the effects of molecular crowding on the structure and stability of G-quadruplexes with abasic sites at different positions

Summary

Introduction

Biomolecules have evolved to function within living cells, which contain a variety of macromolecules including nucleic acids, proteins, polysaccharides, and metabolites. It has been reported that molecular crowding is a critical factor determining the structure, stability and function of proteins and nucleic acids [6,7,8,9,10,11,12,13,14,15,16,17,18] Because of this importance, molecular crowding effects on the structure and stability of DNA duplexes, triplexes, Gquadruplexes, and other structures have been studied [9,10,11,12,13,14,15,16,17,18]. A recent study has shown that the RNA cleavage activity of a ribozyme composed of noncanonical base-pairs and tertiary interactions was enhanced by molecular crowding [18] These results indicate that noncanonical structures of nucleic acids can be stabilized by molecular crowding, leading to a polymorphic nature of function and structure in living cells. It is generally accepted that noncanonical structures of nucleic acids, especially G-quadruplexes, play important roles in various biological systems [19,20,21]

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