Water molecules characterize the structure of DNA genetic material

 

Water molecules surround the genetic material DNA in a very specific way. German scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) have discovered that, on the one hand, the texture of this hydration shell depends on the water content and, on the other hand, actually influences the structure of the genetic substance itself. These findings are not only important in understanding the biological function of DNA; they could also be used for the construction of new DNA-based materials.

The DNA's double helix never occurs in isolation; instead, its entire surface is always covered by water molecules which attach themselves with the help of hydrogen bonds. But the DNA does not bind all molecules the same way. "We've been able to verify that some of the water is bound stronger whereas other molecules are less so," notes Dr. Karim Fahmy, Head of the Biophysics Division at the Institute of Radiochemistry. This is, however, only true if the water content is low. When the water sheath swells, these differences are adjusted and all hydrogen bonds become equally strong. This, in turn, changes the geometry of the DNA strand: The backbone of the double helix, which consists of sugar and phosphate groups, bends slightly. "The precise DNA structure depends on the specific amount of water surrounding the molecule," summarizes Dr. Fahmy.

Analyses of the genetic material were conducted at the HZDR by the doctoral candidate Hassan Khesbak. The DNA, which came from salmon testes, was initially prepared in thin films and then wetted with ultrafine doses of water within a few seconds. With the help of infrared spectroscopy, Hassan Khesbak was able to verify that the strength of hydrogen bonds varies and that water molecules exhibit different rest periods in such configurations. Oscillations of the water bonds in the hydration shell of the double helix can be excited by infrared light. The higher the frequency of the oscillation, the looser the hydrogen bond. It became apparent that the sugar components and the base pairs create particularly strong bonds with the water sheath while the bonds between the water and the phosphate groups are weaker. The results were published just recently in the professional magazine Journal of the American Chemical Society.

"DNA is, thus, a responsive material," explains Karim Fahmy. "By this, we refer to materials which react dynamically to varying conditions. The double helix structure, the strength of the hydrogen bonds, and even the DNA volume tend to change with higher water contents." Already today, genetic material is an extraordinarily versatile and interesting molecule for so-called DNA nanotechnology. Because with DNA it is possible to realize highly ordered structures with new optical, electronic, and mechanical properties at tiny dimensions which are also of interest for the HZDR. The bound water sheath is not just an integral part of such structures. It can also assume a precise switching function because the results indicate that increasing the hydration shell by only two water molecules per phosphate group may cause the DNA structure to "fold" instantly. Such water dependent switching processes might be able to control, for example, the release of active agents from DNA-based materials.

It does not come as a complete surprise that the water sheath of the genetic material is also of great relevance to the natural biological function of DNA. Because every biomolecule which is bound to the DNA has to first displace the water sheath. The Dresden scientists have analyzed this process for the peptide indolicidin. This antimicrobial protein is less structured and very flexible. That it still "identifies" the double helix so precisely is due to the fact that highly structured water molecules are released when it coalesces with the genetic material. The water sheath's restructuring, which is actually an energetic advantage, increases the binding of the active agent. Such details are really important for the development of DNA-binding drugs, for example, in cancer therapy because they can be ascertained with the method developed at the HZDR.

More information: doi: 10.1021/ja108863v

Provided by Helmholtz Association of German Research Centres (news : web)

Chemists fabricate 'impossible' material

When atoms combine to form compounds, they must follow certain bonding and valence rules. For this reason, many compounds simply cannot exist. But there are some compounds that, although they follow the bonding and valence rules, still are thought to not exist because they have unstable structures. Scientists call these compounds "impossible compounds." Nevertheless, some of these impossible compounds have actually been fabricated (for example, single sheets of graphene were once considered impossible compounds). In a new study, scientists have synthesized another one of these impossible compounds -- periodic mesoporous hydridosilica -- which can transform into a photoluminescent material at high temperatures.

The researchers, led by Professor Geoffrey Ozin of the Chemistry Department at the University of Toronto, along with coauthors from institutions in Canada, China, Turkey, and Germany, have published their study in a recent issue of the Journal of the American Chemical Society.

Like graphene, periodic mesoporous hydridosilica (meso-HSiO1.5) consists of a honeycomb-like lattice structure. Theoretically, the structure should be so thermodynamically unstable that the mesopores (the holes in the honeycomb) should immediately collapse into a denser form, HSiO1.5, upon the removal of the template on which the material was synthesized.

In their study, the researchers synthesized the mesoporous material on an aqueous acid-catalyzed template. When they removed the template, they discovered that the impossible material remains stable up to 300 °C. The researchers attribute the stability to hydrogen bonding effects and steric effects, the latter of which are related to the distance between atoms. Together, these effects contribute to the material’s mechanical stability by making the mesopores resistant to collapse upon removal of the template.

“The prevailing view for more than 50 years in the massive field of micro-, meso-, or macroporous materials is that a four-coordinate, three-connected open framework material (called disrupted frameworks) should be thermodynamically unstable with respect to collapse of the porosity and therefore should not exist,” Ozin told PhysOrg.com. “The discovery that this class of material can indeed exist with impressive stability is not a special effect related to the choice of the template, but rather that intrinsic hydrogen bonding between the silicon hydride O3SiH units and silanol O3SiOH that pervade the pore walls is strong enough to provide the meso-HSiO1.5 open-framework material with sufficient mechanical strength for it to be able to sustain the porosity intact in the as-synthesized template-containing and template-free material. This discovery is the big scientific surprise – so never say never when it comes to chemical synthesis.”

When raising the temperature above 300 °C, the researchers discovered that the mesoporous material undergoes a “metamorphic” transformation. This transformation eventually yields a silicon-silica nanocomposite material embedded with brightly photoluminescent silicon nanocrystals. Because the novel nanocomposite material retains its periodic mesoporous structure, the nanocrystals are evenly distributed throughout the structure. According to the researchers, the origin of the photoluminescence likely arises from quantum confinement effects inside the silicon nanocrystals.

In addition, the researchers found that they could control the photoluminescent properties of the nanocrystals by changing the thermal treatment. They predict that this ability could allow the bright nanocrystals to be used in the development of light-emitting devices, solar energy devices, and biological sensors.

“Now we have a periodic mesoporous hydridosilica in which we can exploit the chemistry of the silicon-hydride bonds that permeate the entire void space of the material,” Ozin said. “Every silicon in the structure has a Si-H bond to play creative synthetic games. This is a big deal in terms of it serving as a novel solid-state reactive host material within which one can perform novel chemistry limited only by one’s imagination, and a myriad new materials will emerge with a cornucopia of opportunities for creative discovery and invention.”

More information: Zhuoying Xie, et al. “Periodic Mesoporous Hydridosilica – Synthesis of an ‘Impossible’ Material and Its Thermal Transformation into Brightly Photoluminescent Periodic Mesoporous Nanocrystal Silicon-Silica Composite.” Journal of the American Chemical Society. DOI:10.1021/ja111495x

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