DNA replication is an enzymatic process that is key for sustaining all life forms on Earth. In a recent Journal of Physics: Condensed Matter paper, Yong-Shun Song et al. of the Chinese Academy of Sciences provided the first quantitative understanding of this process using nearest neighbor interactions. Read on to find out more form the authors themselves:
Template-directed DNA replication is the most important reaction in cells, and high replication fidelity is crucial to maintain the genetic stability of cells. The replication process is catalyzed by DNA polymerase (DNAP) which has two domains. One is a polymerase (P site) which can add correct units (nucleotides forming Waston-Crick base pair with the template) to the reactive end of the growing DNA chain with a much higher efficiency than incorrect ones. The other domain is an exonuclease (E site) which can excise the ending unit of the growing chain once it’s peeled off the template and transferred from P to E. It is believed that both domains contribute to the overall fidelity of the copolymerization process significantly. But how they cooperate is not yet quantitatively understood.
In our recent work we propose a comprehensive kinetic model and obtain analytical solutions of the corresponding kinetic equations to address the above issue systematically. The basic assumption is that there can be nearest or even higher-order neighbor interactions in the copolymerization process. Our analytical calculations, by using the method proposed in our previous paper, definitively show that the neighbor effects (reflected in the kinetic rate parameters) are the key factor of the overall fidelity. Considering the nearest neighbor effect for instance, if the P site can add a correct unit to the correct terminus with a much faster rate than adding an incorrect one, the ratio of these two rates can be very large, meaning that the P site contributes significantly to the overall fidelity. When an incorrect unit is incorporated, the E site may discard it if the unstable terminus is transferred from P to E quickly enough before the incorrect unit is buried by the next incorporation of correct unit. In this way, the E site can also make a significant contribution to fidelity. With similar logic, we analytically proved that even the buried incorrect units can be efficiently proofread by the E site if higher-order neighbor effects exist, and the E site is in perfect kinetic coordination with the P site. These analytical results were further demonstrated by two real DNAPs whose fidelity is well described by the 1st-order and 2nd-order neighbor effect respectively.
About the Authors
Yong-Shun Song is a PhD candidate in School of Physical Sciences of University of Chinese Academy of Sciences (UCAS). Now he focuses on theoretical and simulation studies of biomolecules.
Yao-Gen Shu receives his PhD from Xiamen University in 2004. He is now an associate professor in Institute of Theoretical Physics of Chinese Academy of Sciences (ITP, CAS). His research interests include theoretical modeling of biomolecular motors and designing motor-based nano-devices.
Xin Zhou received his PhD from ITP, CAS in 2001. From 2001 to 2003 he worked as JSPS fellow in Tokyo Institute of Technology. From 2003 to 2005 he worked as Humboldt Fellow in Max-Planck Institute for Polymer in Mainz, Germany. From 2008 to 2011, he was adjunct professor in Pohang University of Science and Technology, Korea and also a group leader in Asia Pacific Center for Theoretical Physics, Pohang, Korea. He is now a professor in UCAS funded by the 100 Talents Program of CAS. His research focuses on computational and theoretical biophysics, statistical physics and soft condense matter physics.
Zhong-Can Ou-Yang received his PhD from Tsinghua University in 1984. From 1985 to 1986 he was a postdoc in ITP, CAS and then worked in Freie University Berlin as a Humboldt fellow in 1986. After that He came back to ITP and became a professor since 1992. He was elected as Academician of Chinese Academy of Sciences in 1997 and Fellow of Third World Academy of Sciences (TWAS) in 2003. From 1998 to 2007, he was the director of ITP. Now his research focuses on liquid crystal, biological membrane, and other soft matter systems.
Ming Li received his PhD from ITP, CAS in 2006. Since 2006, he worked in School of Physical Sciences, UCAS, and became an associate professor in 2010. His research field is theoretical biophysics and related statistical physics, with a particular focus on the physics of biomolecular motors.
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