Using a simple sphere-tip compression system,the local radial mechanical properties of DNA are systematically studied by changing the tip size.When the tip size decreases,the radial compression elastic properties unde...Using a simple sphere-tip compression system,the local radial mechanical properties of DNA are systematically studied by changing the tip size.When the tip size decreases,the radial compression elastic properties under external loads become sensitive to the tip size and the local DNA conformation.A sudden force break appears in the compression-force curve when the tip size is less than or equal to 12 nm in diameter.The analysis of the hydrogen bonds and the base stacking interaction shows that a local unwinding process occurs.During the compression process,firstly the hydrogen bonds between complement base pairs are broken.With the compression accumulating,the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation.This local unwinding behavior deduced by external loads is helpful to understand the biological process and is important to DNA-based nanomechanical devices.展开更多
Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction.The conformations from different stretching methods give us a further understanding o...Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction.The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA.We study the conformational variations of a 22-mer DNA caused by stretching both 3'-and 5'-termini by molecular dynamics simulations.It requires 250kJ/mol to stretch the DNA molecule by 3'5'-termini for 3.5 run and the force plateau is at 123.8 pN.The stretching 3'5'-termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair,the double helix untwists from 34°to 20°and the successive base pairs rolls to the side of the DNA major groove.The distances between successive base pairs increases from 3.2.(A)to 5.6(A).展开更多
基金Supported by the National Natural Science Foundation of China under Grant Nos 11305237 and 11174310China Post-doctoral Science Foundation Project under Grant No 2012M511159Shanghai Supercomputer Center,and Supercomputing Center of Chinese Academy of Sciences.
文摘Using a simple sphere-tip compression system,the local radial mechanical properties of DNA are systematically studied by changing the tip size.When the tip size decreases,the radial compression elastic properties under external loads become sensitive to the tip size and the local DNA conformation.A sudden force break appears in the compression-force curve when the tip size is less than or equal to 12 nm in diameter.The analysis of the hydrogen bonds and the base stacking interaction shows that a local unwinding process occurs.During the compression process,firstly the hydrogen bonds between complement base pairs are broken.With the compression accumulating,the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation.This local unwinding behavior deduced by external loads is helpful to understand the biological process and is important to DNA-based nanomechanical devices.
基金Supported by the National Natural Science Foundation of China under Grant No 10825520the Shanghai Supercomputer Center of China.
文摘Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction.The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA.We study the conformational variations of a 22-mer DNA caused by stretching both 3'-and 5'-termini by molecular dynamics simulations.It requires 250kJ/mol to stretch the DNA molecule by 3'5'-termini for 3.5 run and the force plateau is at 123.8 pN.The stretching 3'5'-termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair,the double helix untwists from 34°to 20°and the successive base pairs rolls to the side of the DNA major groove.The distances between successive base pairs increases from 3.2.(A)to 5.6(A).
