Spectroscopic Visualization of Right- and Left-Handed Helical Alignments of DNA in Chiral Vortex Flows

Abstract

In a vortex generated by mechanical rotary stirring in an optical cell, DNA molecules in pure water temporarily align helically to the spiral flow, and dynamically display strong induced circular dichroism (CD) and linear dichroism (LD) responses. Although a sample solution without stirring provided the characteristic CD spectral pattern of DNA, an entirely different macroscopic CD spectral pattern with a much larger intensity and LD spectrum appeared upon mechanical rotary stirring of the sample solution. Clockwise (CW) and counterclockwise (CCW) stirring resulted in mirror-image CD spectral profiles and virtually the same LD profiles with different intensities. The CW stirring of the sample solution in LD spectroscopy always resulted in larger spectral intensities than CCW stirring, but the differences became negligible upon addition of NaCl or ethidium bromide. The observed CD and LD responses of the stirred sample solution decreased simultaneously as the double-stranded structure denatures with increasing temperatures. The results obtained in this study indicate that DNA, when it forms a double-stranded structure, can effectively align in the vortex flows, and show hydrodynamic preference to a right-handed vortex than to a left-handed vortex.Chiral hydrodynamic interactions between DNA and macroscopic torsional fluids attract considerable interest because of the involvement of microscopic and macroscopic chirality in biomolecular systems. DNA can hydrodynamically align and stretch in certain linear fluid flows, 15 where a worm-like chain model can reasonably account for the elastic behaviors and hydrodynamic interactions of DNA. 6 Here, as an innovative subject related to those studies, we noticed for the torsional flow dynamics of DNA, having a right-handed helical doublestranded structure, in chiral fluids such as a vortex that is recognized as one possible origin of chiral symmetry breaking in nature.710 Strick et al. reported the first single-molecule measurements of DNA topology using magnetic tweezers; they measured the extension and force of individual -phage DNA molecules and found that positively supercoiled DNA was more difficult to stretch than negatively supercoiled DNA. 11Other studies have also demonstrated experimentally the intrinsic chiral twist elasticity of DNA.1215 These studies raise an important question: What happens to DNA in a chiral macroscopic vortex generated by clockwise (CW) or counterclockwise (CCW) stirring? The present study reports a successful spectroscopic visualization of macroscopic helical alignments of DNA in a vortex. DNA, when it forms a doublestranded structure, can effectively align in the vortex flows, and it shows hydrodynamic preference to a right-handed vortex than to a left-handed vortex.It is known that certain achiral molecules form optically active assemblies in torsional fluids generated upon rotary stirring.9,10 Kaizu and co-workers 10a and Ribó and co-workers 10b10d have reported pioneering examples in which electrostatic J-aggregates of (4-sulfophenyl)p...

Surface chirality induced by rotational electrodeposition in magnetic fields

“…These differences in activity depending on the chirality of biomolecules are related to the origin of life on Earth and are one of the most attractive mysteries in the life sciences. A number of reports have proposed1 mechanisms of homochirality, such as those for circularly polarised light23, magneto-chiral fields4, vortex and stirring conditions56789, and nonlinear autocatalysis101112. However, a final conclusion regarding a universal homochirality mechanism has not yet been reached.…”

“…demonstrated the chiral sign induction in the aggregation of achiral porphyrins in aqueous solutions through vortices. Tsujimoto et al 9. reported that DNA molecules could align helically in a vortex generated by mechanical stirring.…”

Hydrodynamic Helical Orientations of Nanofibers in a Vortex

“…In this review article, I have summarized and extended our findings presented in references [13,19,20]. Small molecules do not orient in response to macroscopic fluid flows of solvent molecules, because Brownian motions are dominant over hydrodynamic interactions at the molecular level.…”

“…Next, a one-handedly twisted supramolecular nanofiber was found to show unequal LD responses in right-and left-handed vortex flows, owing to unequal helical alignment of the nanofiber [19]. Such phenomena were observed not only in the artificial helical supramolecular nanofibers but also in biological nanofibers such as double-stranded DNA [20].…”

“…These studies raise an important question: what happens to DNA in a chiral macroscopic vortex generated by clockwise (CW) or counterclockwise (CCW) stirring? We revealed that DNA molecules in pure water align helically with the spiral flow generated by mechanical rotary stirring in an optical cell, and display strong induced circular dichroism (CD) and linear dichroism (LD) responses [20].…”