Abstract

The DNA in the left-handed conformation (Z-conformation) was first discovered by A. Rich, who revealed the crystalline structure of a DNA oligomer d(GC)3 by X-ray diffraction method. Later it was also found that DNA molecules change their conformations from typical right-handed form (B-DNA) to the left-handed form (Z-DNA) under specific conditions (B–Z transition). Furthermore, the detailed structures of the interface between B- and Z-DNAs, B-Z junction, was also determined with an atomic resolution. Recently it was found that some proteins have the Z-DNA binding domains, but the biological functions of Z-DNA are not well understood yet. Therefore the investigation of Z-DNA under physiological conditions is highly essential. In this study, we demonstrated the high-resolution real-space imaging of DNA molecules having the Z- and B-form conformations by frequency-modulation atomic force microscopy (FM-AFM), that has made a great progress in recent years, in an aqueous solution. The major and minor grooves of both DNA conformations were clearly visualized. Furthermore, the surface charge density was measured by three-dimensional (3D) force mapping method. We found that Z-form region was less negatively charged than the B-form region.

Highlights

  • DNA molecules contain four bases; i.e., adenine (A), thymine (T), guanine (G) and cytosine (C)

  • Z-form DNA (Z-DNA) molecules consisting of d(GC)[36] and dA32 in 50 mM NiCl2

  • The B- and Z-DNAs were adsorbed onto a substrate at the same time to compare the structure of the Z-DNA to that of the B-DNA

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Summary

Introduction

DNA molecules contain four bases; i.e., adenine (A), thymine (T), guanine (G) and cytosine (C). The complementary DNA molecules form a double-stranded (ds) structure as proposed by Watson and Crick in 19531. Since the transition of the B-form into the Z-form (B–Z transition) and the stability of the Z-form conformation under high ionic concentration conditions are related to the difference in the surface charge density of B-form and Z-form dsDNAs8,15,16, the surface charge measurement of the B- and Z-form DNAs in physiological solutions is highly demanded. B-DNA molecules and other non-B-form DNA molecules have been visualized by AFM in liquids[23,25], there have been only a few reports. We visualized the double-stranded structure of Z-form DNA in isolated Z-DNA and DNA having the B–Z junction (B–Z–B DNA), and measured the surface charge density of the B–Z–B DNA in an aqueous solution by FM-AFM

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