Z-DNA: vacuum ultraviolet circular dichroism.

Abstract

In concentrated salt or ethanolic solutions, the self-complementary copolymer poly(dG-dC)-poly(dG-dC) forms a left-handed double-helical structure that has been termed "Z-DNA." The first evidence for this structure came from changes observed in the circular dichroism (CD) spectrum between 230 and 300 nm for low-and high-salt solutions (Pohl, F. M. & Jovin, T. M. (1972)J. MoL BioL 67,. In 3 M NaCl, the CD spectrum is approximately inverted compared to the B-form spectrum observed in low-salt solution. We measured the vacuum ultraviolet CD spectrum of poly(dG-dC)poly(dG-dC) down to 180 nm under conditions in which the 230-to 300-nm spectrum is inverted. Below 200 nm, where the B form exhibits the large positive peak at 187 nm that is characteristic ofright-handed double-helical DNAs, the Z form exhibits a large negative peak at 194 nm and a positive band below 186 nm. Therefore, the Z-form vacuum ultraviolet CD spectrum resembles an inverted and red-shifted B-form spectrum. The magnitudes ofthe differences observed between the B and Z forms in the CD spectrum below 200 nm are about 10 times greater than those observed between 230 and 300 nm. The vacuum ultraviolet CD spectrum of poly(dG-dC)-poly(dG-dC) in 3 M Cs2SO4 also is inverted compared to the B-form spectrum; however, between 230 and 300 nm, it is nonconservative with a negative maximum at 290 nm and a weak positive CD signal above 300 nm, presumably reflecting differential light scattering and indicating the existence of molecular aggregates. Our results suggest that the vacuum ultraviolet CD spectrum is sensitive to the handedness of doublehelical DNA structures. The CD spectrum in this region should complement other spectroscopic methods in relating the structures of poly(dG-dC)poly(dG-dC) existing in solution to those determined in the solid state by x-ray crystallography.The first indications of the existence of the Z form of DNA were the dramatic changes in the 230-to 300-nm circular dichroism (CD) spectrum ofthe copolymer poly(dG-dC)-poly(dG-dC) produced by increasing salt concentrations (1). In low concentrations ofNaCl, the 230-to 300-nm CD spectrum is approximately conservative, with a positive peak near 275 nm and a negative peak near 253 nm, resembling the spectrum of B-form DNA. As the concentration of NaCl is increased, a cooperative transition with a midpoint at about 2.5 M NaCl leads to an inverted CD spectrum with a negative maximum near 292 nm and a positive maximum near 265 nm.The dramatic spectral changes caused by high salt (1-5) prompted several x-ray diffraction investigations (6-8) of the three-dimensional structure ofcrvstals ofshort, defined lengths of dG-dC oligomers and led to the discovery of what is now called Z-DNA, a zig-zag, left-handed helix in which the guanine residues adopt a syn conformation relative to the glycosidic bond. Fiber diffraction patterns of much longer chains of poly(dG-dC)'poly(dG-dC) have been interpreted as having a similar conformation (9). Crystallographic studies show that more than one fo...

Synchrotron radiation circular dichroism of various G‐quadruplex structures

“…30 There have been past attempts to associate VUV CD bands with a specific property of DNA. 7,31 It has been postulated that the CD signal is indicative of the handedness of the helical structure of DNA, and that a strong negative band at $190 nm is related to the left-handedness of Z-DNA. 7 The inversion of the $190-nm peak upon addition of salt was observed later in a complex containing only G syn Á G syn and A anti Á A anti base pairs, suggesting that it is not the handedness but the syn configuration at the guanine that is responsible for this negative band.…”

“…7,31 It has been postulated that the CD signal is indicative of the handedness of the helical structure of DNA, and that a strong negative band at $190 nm is related to the left-handedness of Z-DNA. 7 The inversion of the $190-nm peak upon addition of salt was observed later in a complex containing only G syn Á G syn and A anti Á A anti base pairs, suggesting that it is not the handedness but the syn configuration at the guanine that is responsible for this negative band. 31 However, our measurements show that this cannot be the case either because all Gs in the d(G n ) quadruplex have anti conformation, yet the VUV CD band has a negative sign.…”

“…8 To obtain additional spectral information, the wavelength region has been extended down into the vacuum ultraviolet (VUV), pioneered by Johnson and Sutherland and their coworkers. 2,[5][6][7] Such experiments are nontrivial due to strong absorption by air and water, but they are greatly aided by the high VUV flux provided by synchrotron radiation (SR).…”

“…importance of G-quads, 1 there is great interest in structural diagnostics. Although UV circular dichroism (CD) has been used for many years to characterize nucleic acid structures, [2][3][4][5][6][7] it has proven difficult to definitively associate particular CD spectral features with specific G-quadruplex topologies. 8 To obtain additional spectral information, the wavelength region has been extended down into the vacuum ultraviolet (VUV), pioneered by Johnson and Sutherland and their coworkers.…”

Comparison of base inclinations for left‐handed DNA and RNA

“…All the Ztype polymers shown in the figure have an intense band in the far UV region at about 195-196 nm, which is a hallmark for all the left-handed helices. 34 The LD and A spectra for the 2-form were ana- , guanine bands ( ---) , and cytosine bands…”