Neutrons take a deep dive into water networks surrounding DNA


Vanderbilt University researchers used neutrons at ORNL to disclose the hydrogen bonding patterns between water molecules (proven in blue) and DNA. The findings may assist present insights into how water influences DNA operate. Credit: ORNL/Jill Hemman

Water performs a number of necessary roles throughout the human physique, even affecting the DNA in our cells. The complete floor of a DNA double helix is coated in layers of water molecules. This sheath of water attaches to the genetic materials by means of hydrogen bonds, made by sharing hydrogen atoms between molecules. Through hydrogen bonds, water can affect how DNA takes form and interacts with different molecules. In some circumstances, water will help proteins acknowledge DNA sequences.

Scientists can estimate the place hydrogen bonds happen and the way hydrogen atoms are shared, however it’s troublesome to assemble experimental proof. A analysis crew led by Vanderbilt University has used a technique that efficiently captured probably the most detailed view thus far of water’s hydrogen bonding patterns round DNA, opening new potentialities for finding out how water impacts DNA operate. Details on the methodology and the outcomes, produced partly by means of neutron scattering on the Department of Energy’s (DOE’s) Oak Ridge National Laboratory (ORNL), are revealed within the journal Nucleic Acids Research.

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“Water serves as a mediator between DNA and other molecules, even for very specific interactions. Before any molecule can bind to a segment of DNA, it must first go through this water shell,” stated Martin Egli, a biochemistry professor at Vanderbilt University and corresponding writer of the research. “To advance our understanding of DNA processes, it’s important to know exactly what the surrounding water does and how it arranges itself around molecules.”

X-ray diffraction experiments have make clear the place water molecules are positioned round DNA, however the hydrogen bonding patterns between these molecules have remained hidden. Neutrons, then again, are extra delicate to gentle components, just like the hydrogen atoms in water, which allow researchers to find out the place hydrogen bonds happen and from which molecules they originate.

“With X-rays, the typical electron density you get for a water molecule is a sphere, like a soccer ball. You cannot see hydrogen atoms, so the molecule has no directionality to it,” stated Leighton Coates, an ORNL scientist concerned on this research. “Whereas, with neutrons, water molecules look more like boomerangs. You can see how the hydrogens are oriented and determine hydrogen bonding patterns.”

To conduct this analysis, the crew used a crystalized pattern of a well-studied DNA fragment with six base pairs, alternating between cytosine and guanine. Known as d(CGCGCG), this fragment was the primary DNA sequence to have its crystal construction decided in 1979. Using a deuterium oxide answer, the scientists changed most of the hydrogen atoms within the fragment with deuterium atoms. Deuterium, an isotope of hydrogen, is “seen” in another way by neutrons in contrast with hydrogen, permitting the researchers to make use of deuterium to selectively gather info on the DNA and water buildings.

The analysis crew collected neutron diffraction knowledge on this fragment utilizing the macromolecular neutron diffractometer (MaNDi) at ORNL’s Spallation Neutron Source (SNS). To cut back water motion, the crew cooled the pattern to 100 Okay (practically –280°F) utilizing chilly nitrogen fuel.

“By lowering water mobility in our sample, we can keep the water molecules in a lattice-like arrangement, allowing us to lock down where they are and how they are positioned,” stated Egli. “If we collected this data at room temperature, the positions of many water molecules would essentially be smeared, distributed over various locations in space.”

“With neutrons, we could also differentiate water molecules by the number of hydrogen bonds, such as whether they are involved in multiple bonds or just one,” added Joel Harp, a analysis assistant professor of biochemistry at Vanderbilt University and research co-author.

X-ray diffraction experiments had been carried out on the same crystal on the Biomolecular Crystallography Facility on the Vanderbilt University Center for Structural Biology to find out the place the oxygen atoms of water molecules are located across the DNA fragment.

By combining these complementary methods, the researchers achieved probably the most detailed evaluation but of water molecule orientations round a DNA double helix. They captured the orientations of 64 water molecules both in direct contact with the DNA fragment or close by. The research revealed how hydrogen bonds are donated or accepted by water molecules inside distinguished components of the DNA construction, together with inside its grooves and round its sugar-phosphate spine. Some of the hydrogen bonds had been sudden, going towards earlier assumptions, demonstrating that this technique may assist confirm molecular dynamics fashions for DNA water networks.

The analysis crew is now utilizing this technique to check how water behaves round different macromolecules, reminiscent of RNA.

“Now, I believe it’s time to apply what we have learned in more challenging projects,” stated Egli. “Water is such a basic entity of life, and there are still many things to be discovered.”

Water surface molecules lose energy through rotation of free OH group

More info:
Joel M Harp et al, Water construction round a left-handed Z-DNA fragment analyzed by cryo neutron crystallography, Nucleic Acids Research (2021). DOI: 10.1093/nar/gkab264

Neutrons take a deep dive into water networks surrounding DNA (2021, November 4)
retrieved 4 November 2021

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