Present in the cells of all living organisms, DNA is composed of two intertwined strands and contains the genetic “blueprint” through which all living organisms develop and function. Individual strands consist of nucleotides, which include a base, a sugar and a phosphate moiety.
Understanding hybridization, the process through which single DNA strands combine to form a double helix is fundamental to biology and central to technologies such as DNA microchips or DNA-based nanoscale assembly. The research by the Wisconsin group begins to unravel how DNA strands come together and bind to each other, says Juan J. de Pablo, UW-Madison Howard Curler Distinguished Professor of Chemical and Biological Engineering.
The team published its findings today (Oct. 5), in the Proceedings of the National Academy of Sciences. In addition to senior author de Pablo, the group included David C. Schwartz, a UW-Madison professor of chemistry and genetics, and former postdoctoral research fellow Edward J. Sambriski, now an assistant professor of chemistry at Delaware Valley College in Pennsylvania.
The three drew on detailed molecular DNA models developed by de Pablo’s research group to study the reaction pathways through which double-stranded DNA undergo denaturation, where the molecule uncoils and separates into single strands, and hybridization, through which complementary DNA strands bind, or “hybridize.” In Watson-Crick base pairing, A (adenine) pairs with T (thymine), while G (guanine) pairs with C (cytosine). Reaction pathways are the trajectories single DNA strands follow to find each other and connect via such complementary pairs.
The researchers studied both random and repetitive base sequences. Random sequences of the four bases — A, T, G and C — contained little or no regular repetition. To the researchers’ surprise, a couple of bases located toward the center of the strand associate early in the hybridization process. The moment they find each other, they bind and the entire molecule hybridizes rapidly and in a highly organized manner.
Conversely, in repetitive sequences, the bases alternated regularly, and the group found that these sequences bind through a so-called diffusive process. “The two strands of DNA somehow find each other, they connect to each other in no particular order, and then they slide past each other for a long time until the exact complements find one another in the right order, and then they hybridize,” says de Pablo.
Results of the team’s study show that DNA hybridization is very sensitive to DNA composition, or sequence. “Contrary to what was thought previously, we found that the actual process by which complementary DNA strands hybridize is very sensitive to the sequence of the molecules,” he says.
Knowledge of how the process occurs could enable researchers to more strategically design technologies such as gene chips. For example, says de Pablo, if a researcher wanted to design sequences that bind very rapidly or with high efficiency, he or she could place certain bases in specific locations, so that the hybridization reaction could occur faster or more reliably.
Ultimately, the research could help biologists understand why some hybridization reactions are faster or more robust than others. “One of the really exciting things about this work is that the hybridization reaction between two strands of DNA is really fundamental to life itself,” says de Pablo. “It is the basis for much of biology. And it is amazing to me that, until now, we knew little of how this reaction actually proceeds.”
The National Science Foundation-funded Nanoscale Science and Engineering Center on Templated Synthesis and Assembly at the Nanoscale at UW-Madison sponsored the research.
Renee Meiller | Newswise Science News
Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory
How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.
Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.
The results will be published on March 22 in the journal „Astronomy & Astrophysics“.
Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...
Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.
Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...
In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...
20.03.2017 | Event News
14.03.2017 | Event News
07.03.2017 | Event News
24.03.2017 | Materials Sciences
24.03.2017 | Physics and Astronomy
24.03.2017 | Physics and Astronomy