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Developmental Biology - DNA
DNA Does Not Like Water!
New research disproves the prevailing theory of how DNA's double helix holds together — finding it is held together by hydrophobic forces...
DNA is constructed of two strands made up of sugar molecules and phosphate groups, with hydrogen bonds between them. Until now, it was commonly thought those hydrogen bonds held the two strands together. But the natural resistance of DNA to water may be the reason for its structure.
The findings appear today in the journal PNAS.
Researchers from Chalmers University of Technology in Gothenburg, Sweden, show the secret to DNA's helical structure may be that the molecules have a hydrophobic - or water resistant - interior. Despite being in a watery cellular environment (hydrophilic means 'consisting mainly of water'), the interior of a DNA spiral is hydrophobic and resists interactions with water which could change hydrogen bonds and destabilize the intended outcome from that DNA molecule.
So, DNA molecules' nitrogen bases are hydrophobic, pushing away surrounding water. When hydrophobic units are in a hydrophilic environment, they pull together, to minimise exposure to water.
The role of the hydrogen bonds, which were previously seen as crucial to holding DNA helixes together, appear to be more about sorting the base pairs so that they link in a correct sequence.
The discovery is crucial for understanding DNA's relationship with its environment.
Explains Bobo Feng, a researcher on the study: "We believe that the cell keeps its DNA in a water solution most of the time, but as soon as a cell wants to do something like read, copy or repair its DNA - it chooses a hydrophobic environment."
Reproduction, for example, involves DNA base pairs dissolving away from one another to open up and recombine into two new molecules. Enzymes then copy both sides of the helix creating new DNA. When it comes to repairing DNA damage, damaged areas are subjected to catalytic proteins which induce a hydrophobic environment before damage is replaced. Catalytic proteins are central to all DNA repairs, meaning they could be key to fighting many serious illnesses.
Understanding these proteins could yield many new insights into how we might fight resistant bacteria and/or potentially attack cancers. Bacteria use a protein called RecA to repair their own DNA. Chalmer researchers believe their results could lead to potential methods for stopping RecA repair, thereby killing those bacteria.
In human cells, the protein Rad51 repairs DNA and fixes mutated DNA sequences, which otherwise could lead to cancer.
"To understand cancer, we need to understand how DNA repairs itself. To understand that, we first need to understand DNA," says Bobo Feng. "So far, we have not, because we believed that hydrogen bonds were what held DNA together. Now, we have shown that instead, hydrophobic forces lie behind it's structure. We have also shown that DNA behaves totally differently in a hydrophobic environment. This could help us to better understand DNA and how it repairs. Nobody had previously placed DNA in a hydrophobic environment like this and studied how it behaves. So, it's not surprising that nobody had discovered this until now."
The Chalmers University of Technology researchers are the first to study how DNA behaves in an environment more hydrophobic than normal.
Using a hydrophobic solution - polyethylene glycol - the researchers changed the DNA environment from naturally hydrophilic into a hydrophobic one. Their intention was to discover at what point DNA loses its structure when the environment is no longer hydrophilic. What they found was pushing the boundary between hydrophilic and hydrophobic, the characteristic spiral of the DNA molecule began to unravel.
Upon closer inspection, they saw base pairs split away from each other and holes form in the structure allowing water to leak into the interior of a DNA spiral. DNA wants to keep its interior dry in order to keep base pairs, and the proteins they create, stable. With added water, the molecules compressed and base pairs came together to squeeze out extra water. In a hydrophobic environment, water is missing and holes created may still keep some nitrogen bases intact.
Significance
The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power. We report that certain semihydrophobic agents depress the stacking energy (measurable in single-molecule experiments), leading to transiently occurring holes in the base-pair stack (monitorable via binding of threading intercalators). Similar structures observed in DNA complexes with RecA and Rad51, and previous observations of spontaneous strand exchange catalyzed in semihydrophobic model systems, make us propose that some hydrophobic protein residues may have roles in catalyzing homologous recombination. We speculate that hydrophobic catalysis is a general phenomenon in DNA enzymes.
Abstract
Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10-2 compared to 10-4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.
Authors
Bobo Feng, Robert P. Sosa, Anna K. F. Mårtensson, Kai Jiang, Alex Tong, Kevin D. Dorfman, Masayuki Takahashi, Per Lincoln, Carlos J. Bustamante, Fredrik Westerlund and Bengt Nordén.
Acknowledgments
This work was supported by Swedish Research Council Grant 2015-04020 (to B.N.); Swedish Research Council Grant 2015–5062 and Olle Engqvist Foundation Grant 2016/84 (to F.W.); NIH Grant R01-HG006851 (to K.D.D.); and NIH Grant R01GM032543 and US Department of Energy Office of Basic Energy Sciences Nanomachine Program Contract DE-AC02-05CH11231 (to C.J.B.). We thank Irfan Shaukat for early work (2010).
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Sep 23 2019 Fetal Timeline Maternal Timeline News
 Inside each cell, DNA produces proteins to keep each distinct species alive and well. However, the bonds holding the double helix together are most likely the result of hydrophobic forces - water resistance on the part of the stair step bonds and the catalytic protein creating a hydrophobic environment. CREDIT Illustration: Yen Strandqvist/Chalmers University of Technology.
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