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前沿进展:粗粒化模型对核酸空间结构的从头预测

2022年11月06日 09:10 时亚洲 点击:[]

转载:时亚洲等 | 前沿进展:粗粒化模型对核酸空间结构的从头预测


   


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  1. Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953, 171:737-8.
  2. Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet. 2022,13:959258.
  3. Crespi M, Ariel F. Non-B DNA structures emerging from plant genomes. Trends Plant Sci. 2022, 27:624-626.
  4. Guiblet WM, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Res. 2021, 49:1497-1516.
  5. Ma W, Zhan Y, Zhang Y, Mao C, Xie X, Lin Y. The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther. 2021, 6:351.
  6. Sharma A, Vaghasiya K, Verma RK, Yadav AB. DNA nanostructures: chemistry, self-assembly, and applications. Curr Prospects Future Trends Micro Nano Tech. 2018, 71-78.
  7. Marko JF, Siggia ED. Fluctuations and supercoiling of DNA. Science. 1994, 265:506-8.
  8. Zhang Y, Xiong Y, Xiao Y. 3dDNA: A computational method of building DNA 3D structures. Molecules. 2022, 27: 5936.
  9. Ouldridge TE, Louis AA, Doye JP. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys. 2011, 134: 085101.
  10. Chakraborty D, Hori N, Thirumalai D. Sequence-dependent three interaction site model for single- and double-stranded DNA. J Chem Theory Comput. 2018, 14: 3763–3779.
  11. Knotts TAt, Rathore N, Schwartz DC, de Pablo JJ. A coarse grain model for DNA. J Chem Phys. 2007, 126: 084901.
  12. He Y, Maciejczyk M, Oldziej S, Scheraga HA, Liwo A. Mean-field interactions between nucleic-acid base dipoles can drive the formation of a double helix. Phys Rev Lett. 2013, 110: 098101.
  13. Cragnolini T, Derreumaux P, Pasquali S. Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B. 2015, 117:8047–8060.
  14. Shi YZ, Wang FH, Wu YY, Tan ZJ. A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect. J Chem Phys. 2014, 141:105102.
  15. Shi YZ, Jin L, Feng CJ, Tan YL, Tan ZJ. Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions. PLoS Comput Biol. 2018, 14:e1006222.
  16. Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA. 2019, 25:1532–1548.


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