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Science

DNA In an Aqueous Solution

From: General Han Solo​​​​

Here’s a 2013 study that was done in literally visualizing DNA in an aqueous solution because the aqueous solution helped the visualization. Here’s the abstract:

The DNA double helix was first elucidated by J.D. Watson and F.H.C. Crick over a half century ago. However, no one could actually “see” the well-known structure ever. Among all real-space observation methods, only atomic force microscopy (AFM) enables us to visualize the biologically active structure of natural DNA in water. However, conventional AFM measurements often caused the structural deformation of DNA because of the strong interaction forces acting on DNA. Moreover, large contact area between the AFM probe and DNA hindered us from imaging sub-molecular-scale features smaller than helical periodicity of DNA. Here, we show the direct observation of native plasmid DNA in water using an ultra-low-noise AFM with the highly sensitive force detection method (frequency modulation AFM: FM-AFM). Our micrographs of DNA vividly exhibited not only overall structure of the B-form double helix in water but also local structures which deviate from the crystallographic structures of DNA without any damage. Moreover, the interaction force area in the FM-AFM was small enough to clearly discern individual functional groups within DNA. The technique was also applied to explore the synthesized DNA nanostructures toward the current nanobiotechnology. This work will be essential for considering the structure–function relationship of biomolecular systems in vivo and for in situ analysis of DNA-based nanodevices.

And here’s the conclusion of this excellent study:

We used FM-AFM to directly visualize the double helix structure of plasmid DNA in an aqueous solution. The major and minor grooves between the sugar phosphate backbones of B-DNA were differentiated, and periodic corrugations corresponding to individual phosphate groups in the DNA backbones were resolved. We determined the AFM tip radius as 1.0 nm by comparing the simulated AFM images assuming various tip radii with the FM-AFM image, and the interpretation of the experimental results was validated by the precise comparison of the cross-sectional profiles on the DNA backbones. In addition, we used FM-AFM to perform high-resolution imaging of DNA tiles in an aqueous solution, which showed the righthandedness of B-DNA in the tile and the two different connecting configurations. The results demonstrate the applicability of AFM to sub-molecular-scale investigations of correlations between the structures and functions of DNA under physiological conditions. For example, the approach may allow determination of the structures of various proteinnucleic acid complexes or reveal the mechanisms of sequence recognition by DNA-binding proteins. Finally, it should be noted that the technique presented here is one of the most promising analytical tools for investigating the structures of self-assembled DNA nanostructures, such as DNA tiles and DNA origami, which are being developed for applications in DNA computing and other DNA-based nanoscale devices that use the structures and functions of DNA in solution.

Here’s the link: https://drive.google.com/open?id=0B1gMXJ3-ViIgQk80WW5zNzNiZ3c

And to top it off, here’s an entire PhD dissertation titled, “On the Structure of DNA in an Aqueous Solution” that was published in 1980!

The abstract is as follows:

This thesis deals with the structure of DNA under a variety of conditions of concentration, ionic strength, and association with proteins. I have investigated the behavior of rod-like DNA under conditions of high DNA concentration and low counterion concentration. I have found that the DNA forms specific aggregates, each consisting of seven monomers. Electric dichroism revealed that the conformation of the DNA changes upon formation of these aggregates, with the base tilt angle changing from 17(DEGREES) to 0(DEGREES). I have prepared restriction fragments of DNA and, by combining translational and rotational hydrodynamic data, I have deduced that the diameter of DNA in solution is 24 (+OR-) 2 (ANGSTROM), and the helical rise per residue is 3.15 (+OR-) 0.15 (ANGSTROM). To facilitate analysis of hydrodynamic data, I have developed a technique to measure rotational frictional coefficients of macroscopic objects. I have confirmed the standard equations for cylinders of axial ratio greater than ten, and have developed a relation which is accurate for cylinders of axial ratio down to one. I have developed new equations for the rotation of discs, and I have shown that large perturbations in the draining properties of the object have only a small effect on the frictional coefficient. I have used hydrodynamic measurements to deduce size parameters for the chromatin thick fiber. I have concluded that, in high salt conditions, the thick fiber is 340 (+OR-) 20 (ANGSTROM) thick, with 7-8 nucleosomes per turn. Finally, I have studied the effect of histone H1 on the structure of the nucleosome. I have found that H1 causes some compaction, without much altering the path of the DNA. H1 has an effect on the low salt transition to an unfolded form, but it does not eliminate the transition.

Here’s the link: https://drive.google.com/open?id=0B1gMXJ3-ViIgTkxhUmVUTTBqNFU

-General Han Solo

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