刘悦-凝聚态-墙报-精品文档资料整理.ppt

DNA is a key molecule in life activities and has been studied for decades, experimentally and theoretically. The high-resolution X-ray imaging technology and other imaging methods have revealed that DNA is a long double-helix molecule and there are different forms of DNA including A, B, Z and others. And some nano-scale experiments using optical and magnetic tweezers have shown us some of the DNAs behaviour in stretching. And there are researches of DNA using theoretical methods, too. Classical force field methods are widely used to study long DNA oligonucleotides, while quantum methods, because of the high cost of the calculation, are employed in small systems such as several base pairs of DNA, though they are theoretically more accurate. Fig. 1 Side view of 12 base pair A-form DNA However, thanks to the rapid development of computational resources and methods in the last few decades, it has become realisable to run a series of simulations on geometry and properties of more than a few base pairs, but a full circle of a section of DNA oligonucleotides using DFT method. This enables us to study a complete unit of a DNA double-helix on a quantum level, providing a more accurate picture of DNAs behaviour under certain conditions, which may be difficult for experiments, and help us get a better understanding of DNA and its interaction with other biomolecules. To accomplish this, we did a series of geometrical optimization of a full circle of a section of A-form DNA oligonucleotides and calculated its static properties and geometrical changes in stretching, including its flexibility, diameter, the length of the minor groove, the length of the major groove and the length of the hydrogen bonds in the DNA base pairs. 2.MethodA DFT study of the static geometrical properties and the changes in stretching of a full circle of A-form DNAYue Liu1,2, Xinguo Ren1,2, Lixin He1,2 ( 1. Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui, 2300262.Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, Anhui, 230026Email: )Bibliography All of the optimised DNA structures were obtained by the ABACUS (Atomic-orbital Based Ab-initio Computation at USTC) package 1 . By using a basis set of linear combination of atomic orbitals (LCAO), which is far more efficient in calculations of large-scale systems than the plane-wave (PW) basis set for taking the advantage of real-space locality, ABACUS is designed to carry out large-scale density functional theory simulations. The generalised gradient approximation was used. The energy cutoff was set to be 50 Ry and the radius cutoffs of numerical atomic orbitals were set to be 8.0 bohr. The atomic orbitals basis set of C, N, O, P included two s, two p and one polarised (d) orbitals, while the atomic orbitals basis set of H included two s and one polarised (p) orbitals. Periodic boundary conditions were used in all calculations. Fig.3 The length of different kinds of hydrogen bonds in pure 5-A or pure 5-C (without hybrid) and hybrid 5-AC (with hybrid) sequences of DNA. ONum stands for the ordinal number of each base pair of the DNA sequence. HBL stands for hydrogen bond length. We generated initial geometries 1, 2, and 3 by an online tool using conformational parameters taken from experimental fibre-diffraction studies 2 . Initial geometry 1, 2, and 3 were corresponding to pure 5-A, pure 5-C and hybrid 5-AC DNA sequences. The long axis of DNA was located on the Z axis. One hydrogen atom was added near to each phosphate group to simulate the natural ion environment and cancel the unpaired electrons to make the calculation converge. The geometry of the initial geometry 1 was optimised to 0.02eV / angstrom to obtain the rough geometry the stretch rate of which is 0 percent.Four carbon atoms at both ends of the rough geometry of which the stretch rate is 0 percent were fixed, then the DNA oligonucleotides were stretched uniformly along the long axis by one percent of the original length (Z-axis coordinate multiplied by 1.01). The resulting geometry was optimised to 0.05eV / angstrom to obtain the rough geometry of which the stretch rate is 1 percent. The rough geometry of which the stretch rate is 1 percent was optimised to 0.02eV/angstrom to obtain the fine geometry of which the stretch rate is 1 percent. Similarly, We obtained the rough and fine geometries stretched by 2, 5, 10 and 15 percent.1.M. Chen, G.-C. Guo, and L. He, J. Phys.: Condens. Matter 22, 445501 (2010).2.S. Arnott, P.J. Campbell-Smith & R. Chandrasekaran. In Handbook of Biochemistry and Molecular Biology, 3rd ed. Nucleic Acids-Volume II, G.P. Fasman, Ed. Cleveland: CRC Press, (1976). pp. 411-422.3.J. Xu , L. Zhao , Y. Xu , W. Zhao , P. Sung & H.-W. Wang. Nature Structural & Molecular Biology, (2017) 24, 4046. We carried out a series of geometrical optimisations of a full circle of three kinds of A-form DNA oligonucleotides by the ABACUS to observe the parameters of unstretched A-form DNA, and to observe the changes of DNAs geometrical parameters in stretching. As Fig.3 shows, compared with those in the pure 5-A and the pure 5-C sequences, the length of the hydrogen bond of N(A)-H(T)-N(T) and O(G)-H(C)-N(C) has become larger in the hybrid 5-AC sequence, while the length of the hydrogen bond of N(A)-H(A)-O(T) and N(G)-H(G)-O(C) has become smaller, and the length of the hydrogen bond of N(G)-H(G)-N(C) remains almost the same (or has become very slightly larger). As Fig.4 shows, only very little energy (less than 0.9eV for 12 DNA base pairs) is needed to stretch a section of A-form DNA oligonucleotides to up to 115% of its original length. This impressive flexibility make sure the biochemical reactions with stretching of DNA are easy to happen. Recent studies show that some proteins like RAD51 can stretch DNA to 150% of its original length 3 . If the energy needed for DNA in stretching is much greater, which means DNA is much harder to stretch, it would then be much more difficult for RAD51 to interact with DNA. Another interesting thing in stretching of A-form DNA is that its major and minor groove will not become larger synchronously. As Fig.6 and Fig.7 show, it is only the minor groove that will be stretched, while the length of the major groove actually becomes smaller in stretching, which is counter-intuitive. As we know that some molecules interact with DNA by its major groove, some by its minor groove and some others by both of its major groove and minor groove, their interaction with DNA will be affected differently in stretching. In summary, we have used DFT method to do a comprehensive and detailed study of the static geometrical properties of a full circle of an A-form DNA oligonucleotide and its geometrical changes in stretching, which leads to a more accurate picture of DNAs behavior in stretching.1.Introduction3. Results and Conclusions Fig. 2 The hydrogen bonds between AT and CG DNA base pairs. From top to bottom the hydrogen bonds are, in order, N(A)-H(A)-O(T),N(A)-H(T)-N(T), O(G)-H(C)-N(C), N(G)-H(G)-N(C), N(G)-H(G)-O(C)Fig.4 The total energy of (from top to bottom) pure 5-A, pure 5-C, andhybrid 5-AC sequences of DNA.Fig.5 The diameter of (from top to bottom) pure 5-A, pure 5-C, andhybrid 5-AC sequences of DNA.Fig.6 The length of the major groove of (from top to bottom) pure 5-A, pure 5-C, andhybrid 5-AC sequences of DNA.Fig.7 The length of the minor groove of (from top to bottom) pure 5-A, pure 5-C, andhybrid 5-AC sequences of DNA.