{"id":38332,"date":"2022-11-05T22:42:59","date_gmt":"2022-11-05T14:42:59","guid":{"rendered":"https:\/\/swarma.org\/?p=38332"},"modified":"2022-11-05T22:42:59","modified_gmt":"2022-11-05T14:42:59","slug":"%e5%89%8d%e6%b2%bf%e8%bf%9b%e5%b1%95%ef%bc%9a%e7%b2%97%e7%b2%92%e5%8c%96%e6%a8%a1%e5%9e%8b%e5%af%b9%e6%a0%b8%e9%85%b8%e7%a9%ba%e9%97%b4%e7%bb%93%e6%9e%84%e7%9a%84%e4%bb%8e%e5%a4%b4%e9%a2%84%e6%b5%8b","status":"publish","type":"post","link":"https:\/\/swarma.org\/?p=38332","title":{"rendered":"\u524d\u6cbf\u8fdb\u5c55\uff1a\u7c97\u7c92\u5316\u6a21\u578b\u5bf9\u6838\u9178\u7a7a\u95f4\u7ed3\u6784\u7684\u4ece\u5934\u9884\u6d4b"},"content":{"rendered":"
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\u6838\u9178\uff08DNA\u548cRNA\uff09\u662f\u975e\u5e38\u91cd\u8981\u7684\u751f\u7269\u5927\u5206\u5b50\uff0c\u7814\u7a76\u5176\u7a7a\u95f4\u7ed3\u6784\u5bf9\u63ed\u793a\u5176\u529f\u80fd\u673a\u7406\u548c\u6307\u5bfc\u76f8\u5173\u751f\u7269\u533b\u5b66\u5e94\u7528\uff08\u5982\u836f\u7269\u8bbe\u8ba1\u3001DNA\u7eb3\u7c73\uff09\u81f3\u5173\u91cd\u8981\u3002\u7531\u4e8e\u901a\u8fc7\u5b9e\u9a8c\u65b9\u6cd5\uff08\u5982X-\u5c04\u7ebf\u884d\u5c04\u3001\u6838\u78c1\u5171\u632f\u3001\u51b7\u51bb\u7535\u955c\uff09\u6d4b\u5b9a\u6838\u9178\u7684\u7ed3\u6784\u5177\u6709\u4e00\u5b9a\u7684\u5c40\u9650\u6027\uff0c\u76ee\u524d\u5df2\u77e5\u7684\u6838\u9178\u7ed3\u6784\u6570\u91cf\u975e\u5e38\u6709\u9650\uff0c\u8fd9\u4e5f\u9650\u5236\u4e86\u8bf8\u5982AlphaFold2\u7684\u6df1\u5ea6\u5b66\u4e60\u9884\u6d4b\u65b9\u6cd5\u5728\u6838\u9178\u7ed3\u6784\u4e0a\u7684\u8fd0\u7528\u3002\u800c\u73b0\u6709\u7684\u6838\u9178\u7ed3\u6784\u9884\u6d4b\u65b9\u6cd5\u5f80\u5f80\u9700\u8981\u4f9d\u8d56\u6709\u9650\u7684\u6570\u636e\u5e93\u7ed3\u6784\u6216\u9884\u5148\u7ed9\u5b9a\u7684\u4e8c\u7ea7\u7ed3\u6784\uff0c\u4e5f\u5ffd\u7565\u4e86\u6838\u9178\u7ed3\u6784\u7684\u9ad8\u8d1f\u7535\u6027\u3002\u8fd1\u671f\uff0c\u53d1\u8868\u4e8ePLoS Computational Biology<\/em>\u4e0a\u7684\u4e00\u7bc7\u8bba\u6587\u63d0\u51fa\u4e86\u4e00\u4e2a\u7c97\u7c92\u5316\u6a21\u578b\uff0c\u901a\u8fc7\u8ba1\u5165\u9759\u7535\u53ca\u5e8f\u5217\u76f8\u5173\u7684\u78b1\u57fa\u5806\u79ef\u7b49\u76f8\u4e92\u4f5c\u7528\uff0c\u80fd\u591f\u4ec5\u57fa\u4e8e\u5e8f\u5217\u51c6\u786e\u9884\u6d4b\u5355\/\u53cc\u94feDNA\u5728\u79bb\u5b50\u6eb6\u6db2\u4e2d\u7684\u7a7a\u95f4\u7ed3\u6784\u3002\u6b64\u5916\uff0c\u8be5\u6a21\u578b\u8fd8\u80fd\u540c\u65f6\u5b9a\u91cf\u7ed9\u51fa\u7b80\u5355DNA\u7ed3\u6784\u7684\u70ed\u529b\u5b66\u7a33\u5b9a\u6027\u53ca\u5176\u4e2d\u7684\u79bb\u5b50\u6548\u5e94\u3002\u5c3d\u7ba1\u8be5\u6a21\u578b\u76ee\u524d\u5728\u5904\u7406\u590d\u6742DNA\u7ed3\u6784\u4e0a\u5b58\u5728\u56f0\u96be\uff0c\u4f46\u4ece\u5934\u9884\u6d4b\u7684\u63d0\u51fa\u80fd\u6709\u6548\u5f25\u8865\u73b0\u6709\u65b9\u6cd5\u7684\u4e0d\u8db3\u3002<\/span><\/strong><\/span><\/strong><\/strong><\/p>\n<\/section>\n

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Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions<\/span><\/section>\n
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https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1010501<\/span><\/section>\n<\/section>\n<\/section>\n<\/blockquote>\n


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1. DNA\u7ed3\u6784\u8fd8\u9700\u8981\u9884\u6d4b\uff0c<\/span><\/strong><\/strong><\/p>\n

\u96be\u9053\u4e0d\u662f\u6807\u51c6\u53cc\u87ba\u65cb\u5417\uff1f<\/span><\/strong><\/strong><\/p>\n<\/section>\n

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DNA\u662f\u975e\u5e38\u91cd\u8981\u7684\u751f\u7269\u5927\u5206\u5b50\uff0c\u8d1f\u8d23\u9057\u4f20\u57fa\u56e0\u7684\u5b58\u50a8\u548c\u4f20\u9012\u3002\u7136\u800c\uff0c\u65e9\u57281953\u5e74J.D. Watson\u548cF.H. Crick\u5c31\u6307\u51fa\u4f4d\u4e8e\u67d3\u8272\u4f53\u4e0a\u7684DNA\u901a\u5e38\u5448\u73b0\u89c4\u5219\u7684\u53f3\u624b\u87ba\u65cb\u7ed3\u6784<\/span>\uff08\u5373B-\u578b\u7ed3\u6784\uff09<\/span>[1]\uff0c\u90a3\u4e48\uff0c\u5982\u6b64\u6807\u51c6\u7684\u7ed3\u6784\u4e3a\u4f55\u8fd8\u9700\u8981\u9884\u6d4b\u5462\uff1f\u8fd1\u671f\u7684\u4e00\u4e9b\u7814\u7a76\u53d1\u73b0\uff0c\u4eba\u7c7b\u57fa\u56e0\u7ec4\u4e2d\u7ea613%\u7684\u5e8f\u5217\u80fd\u6298\u53e0\u6210\u975e\u6807\u51c6<\/span>\uff08\u5373non-B\u578b\uff09<\/span>\u7684DNA\u7ed3\u6784<\/span>\uff08\u5982\u53d1\u5939\u3001\u5047\u7ed3\u3001\u4e09\u94fe\u4f53\u3001Z-DNA\u3001G-\u56db\u8054\u4f53\u3001i-motif\u7b49\uff09<\/span>\uff0c\u4ee5\u53c2\u4e0e\u91cd\u8981\u7684\u7ec6\u80de\u8fc7\u7a0b<\/span>\uff08\u5982\u8c03\u63a7\u57fa\u56e0\u8868\u8fbe\u3001\u534f\u52a9\u7aef\u7c92\u4fdd\u62a4\u3001\u4fc3\u8fdb\u7a81\u53d8\u3001\u8c03\u63a7\u67d3\u8272\u8d28\u7684\u8868\u89c2\u9057\u4f20\u3001\u627f\u62c5\u86cb\u767d\u7ed3\u5408\u7684\u9776\u70b9\u7b49\uff09<\/span>\uff0c\u5e76\u4e0e\u591a\u79cd\u4eba\u7c7b\u75be\u75c5\u6709\u5173 [2-4]\uff1b\u89c1\u56fe1\u3002\u4f8b\u5982\uff0cG-\u56db\u8054\u4f53\u7ed3\u6784\u7684\u5f62\u6210\u53ef\u4ee5\u8c03\u8282\u764c\u75c7\u76f8\u5173\u57fa\u56e0\u7684\u8868\u8fbe\uff0c\u4ece\u800c\u62df\u5236c-myc\u542f\u52a8\u5b50\u57df\u7684\u8f6c\u5f55\u7075\u6d3b\u6027\uff0cDNA\u4e09\u94fe\u4f53\u7ed3\u6784\u53ef\u4ee5\u7528\u4e8e\u963b\u65ad\u5404\u79cd\u81f4\u75c5\u57fa\u56e0\u7684\u8f6c\u5f55[4]\u3002<\/span><\/section>\n

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\u6b64\u5916\uff0c\u7531\u4e8eDNA\u7ed3\u6784\u7684\u591a\u6837\u6027\uff0c\u81ea\u7ec4\u88c5DNA\u7ed3\u6784\u5df2\u88ab\u8bc1\u660e\u662f\u8bbe\u8ba1\u4e0e\u5b9e\u73b0\u7eb3\u7c73\u7ed3\u6784\u53ca\u8bbe\u5907\u7684\u4f18\u79c0\u6750\u6599\u3002\u76ee\u524d\u5df2\u7ecf\u5b9e\u73b0\u7684\u529f\u80fdDNA\u7eb3\u7c73\u7ed3\u6784\u5305\u62ec\u954a\u5b50\u3001\u9a6c\u8fbe\u3001\u7a7f\u68ad\u5668\u3001\u6298\u7eb8\u3001\u903b\u8f91\u7535\u8def\u3001\u7eb3\u7c73\u5bb9\u5668\u7b49\uff0c\u5b83\u4eec\u5728\u5149\u5b50\u5668\u4ef6\u3001\u836f\u7269\u8f93\u9001\u3001\u7ec4\u7ec7\u518d\u751f\u53ca\u751f\u7269\u6210\u50cf\u7b49\u9886\u57df\u6709\u7740\u5e7f\u9614\u7684\u5e94\u7528\u524d\u666f<\/span>\uff08\u56fe1\uff09<\/span>[5,6]\u3002\u65e0\u8bbanon-B DNA\u7684\u6298\u53e0\uff0c\u8fd8\u662fDNA\u7eb3\u7c73\u7684\u7ec4\u88c5\uff0c\u90fd\u57fa\u4e8e\u7b80\u5355\u7684DNA\u6a21\u4f53\u7ed3\u6784<\/span>\uff08\u5982\u5355\u94feDNA\u53d1\u5939\/\u5047\u7ed3\u53ca\u77ed\u94feDNA\u87ba\u65cb\uff09<\/span>\u3002\u56e0\u6b64\uff0c\u57fa\u4e8e\u5e8f\u5217\u83b7\u53d6\u5355\/\u53ccDNA\u7684\u7a7a\u95f4\u7ed3\u6784\u5bf9\u7406\u89e3\u5176\u65b0\u5947\u7684\u751f\u7269\u529f\u80fd\u53ca\u6307\u5bfcDNA\u65b0\u578b\u7eb3\u7c73\u7ed3\u6784\u7684\u8bbe\u8ba1\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/span><\/section>\n

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\u56fe1. Non-B \u578b\u7ed3\u6784\u793a\u4f8b\u53ca\u5178\u578bDNA\u7eb3\u7c73\u7ed3\u6784\u5c55\u793a[3-6]\u3002<\/span><\/section>\n

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\u5c3d\u7ba1\u73b0\u6709\u7684\u4e00\u4e9b\u5b9e\u9a8c\u624b\u6bb5<\/span>\uff08\u5982\u51b7\u51bb\u7535\u955c\u3001X\u5c04\u7ebf\u884d\u5c04\u3001NMR\u3001\u5149\u954a\/\u78c1\u954a\u7b49\uff09<\/span>\u80fd\u591f\u7528\u6765\u6d4b\u5b9aDNA\u7684\u7a7a\u95f4\u7ed3\u6784\u6216\u529b\u5b66\u6027\u80fd\uff0c\u4f46\u662f\u7531\u4e8e\u5176\u8017\u65f6\u8017\u529b\uff0c\u5728\u7814\u7a76DNA\u6298\u53e0\u65b9\u9762\u5b58\u5728\u5c40\u9650\u6027\u3002\u56e0\u6b64\uff0c\u4eba\u4eec\u5f00\u53d1\u4e86\u4e00\u4e9b\u57fa\u4e8e\u8ba1\u7b97\u673a\u7684\u6a21\u578b\u6216\u65b9\u6cd5\u4ee5\u9884\u6d4bDNA\u7684\u7ed3\u6784\u6216\u63a2\u7d22DNA\u7684\u7ed3\u6784\u6298\u53e0\u548c\u70ed\u529b\u5b66\u6027\u8d28\uff0c\u5982WLC\u6a21\u578b[7]\u30013dRNA\/DNA[8]\u3001oxDNA[9]\u3001TIS[10]\u30013SPN[11]\u3001NARES-2P[12]\u3001HiRE-RNA[13]\u7b49\uff0c\u4f46\u8fd9\u4e9b\u65b9\u6cd5\u5f80\u5f80\u4f9d\u8d56DNA\u4e8c\u7ea7\u7ed3\u6784\u4fe1\u606f\u6216\u9884\u8bbe\u7684\u7ea6\u675f\u6761\u4ef6\u6216\u6709\u9650\u7684\u6570\u636e\u5e93\u7ed3\u6784\u3002\u6b64\u5916\uff0c\u7531\u4e8eDNA\u7684\u805a\u7535\u6027\u8d28\uff0c\u6eb6\u6db2\u4e2d\u7684\u91d1\u5c5e\u79bb\u5b50<\/span>\uff08\u5982Na+<\/sup>\u548cMg2+<\/sup>\uff09<\/span>\u5728DNA\u7684\u6298\u53e0\u8fc7\u7a0b\u4e2d\u53d1\u6325\u7740\u975e\u5e38\u91cd\u8981\u4f5c\u7528\uff0c\u7136\u800c\u73b0\u6709\u8fd9\u4e9b\u6a21\u578b\u5927\u90fd\u5ffd\u7565\u4e86\u79bb\u5b50\u5bf9DNA\u6298\u53e0\u7684\u5f71\u54cd\u3002\u56e0\u6b64\uff0c\u5728\u8be5\u8bba\u6587\u4e2d\uff0c\u4f5c\u8005\u63d0\u51fa\u4e86\u4e00\u4e2a\u65b0\u7684DNA\u7c97\u7c92\u5316\u6a21\u578b\uff0c\u4ee5\u4ec5\u57fa\u4e8e\u5e8f\u5217\u9884\u6d4b\u7b80\u5355DNA\u5206\u5b50\u5728\u79bb\u5b50\u6eb6\u6db2\u4e2d\u7684\u7a7a\u95f4\u7ed3\u6784\u53ca\u5176\u70ed\u529b\u5b66\u7a33\u5b9a\u6027\u3002<\/span><\/section>\n

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\u672c\u6587\u63d0\u51fa\u7684DNA\u7c97\u7c92\u5316\u6a21\u578b\u662f\u57fa\u4e8e\u4f5c\u8005\u56e2\u961f\u4e4b\u524d\u4e0e\u6b66\u6c49\u5927\u5b66\u8c2d\u5fd7\u6770\u6559\u6388\u5408\u4f5c\u5f00\u53d1\u7684RNA\u6a21\u578b\u7684\u8fdb\u4e00\u6b65\u63a8\u5e7f[14-16]\u3002\u8be5\u6a21\u578b\u5c06DNA\u6216RNA\u4e2d\u7684\u4e00\u4e2a\u6838\u82f7\u9178\u7b80\u5316\u4e3a\u4e09\u4e2a\u7c97\u7c92\u5316\u7684\u7403\u539f\u5b50\uff0c\u5206\u522b\u4ee3\u8868\u5176\u4e2d\u4e09\u4e2a\u91cd\u8981\u7684\u529f\u80fd\u57fa\u56e2\uff1a\u78f7\u9178\u57fa\u56e2<\/span>\uff08P\uff09<\/span>\u3001\u7cd6\u73af<\/span>\uff08C4\u2019\uff09<\/span>\u548c\u78b1\u57fa<\/span>\uff08N1\u6216N9\uff09<\/span>\uff0c\u5e76\u8ba1\u5165\u4e00\u4e2a\u5355\u4f4d\u7684\u8d1f\u7535\u8377\uff0c\u653e\u7f6e\u5728P\u7684\u4e2d\u5fc3<\/span>\uff08\u56fe2\uff09<\/span>\u3002\u4e3a\u4e86\u6709\u6548\u63cf\u8ff0DNA\u7684\u6298\u53e0\uff0c\u9488\u5bf9\u7c97\u7c92\u5316\u6a21\u578b\uff0c\u63d0\u51fa\u4e86\u5982\u4e0b\u80fd\u91cf\u51fd\u6570\uff1a<\/span><\/section>\n

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U=Ub<\/sub>+U<\/span>a<\/sub>+U<\/span>d<\/sub>+U<\/span>exc<\/sub>+U<\/span>bp<\/sub>+U<\/span>bs<\/sub>+U<\/span>cs<\/sub>+U<\/span>el<\/sub>
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\u56fe2. DNA\u6a21\u578b\u7b80\u5316\u53ca\u78b1\u57fa\u914d\u5bf9\u548c\u78b1\u57fa\u5806\u79ef\u4f5c\u7528\u793a\u610f\u56fe\u3002<\/span><\/section>\n

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    Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953, 171:737-8.<\/section>\n<\/li>\n
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    Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet. 2022,13:959258.<\/section>\n<\/li>\n
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    Crespi M, Ariel F. Non-B DNA structures emerging from plant genomes. Trends Plant Sci. 2022, 27:624-626.<\/section>\n<\/li>\n
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    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.<\/section>\n<\/li>\n
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    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.<\/section>\n<\/li>\n
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    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.<\/section>\n<\/li>\n
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    Marko JF, Siggia ED. Fluctuations and supercoiling of DNA. Science. 1994, 265:506-8.<\/section>\n<\/li>\n
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    Zhang Y, Xiong Y, Xiao Y. 3dDNA: A computational method of building DNA 3D structures. Molecules. 2022, 27: 5936.<\/section>\n<\/li>\n
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    Ouldridge TE, Louis AA, Doye JP. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys. 2011, 134: 085101.<\/section>\n<\/li>\n
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    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\u20133779.<\/section>\n<\/li>\n
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    Knotts TAt, Rathore N, Schwartz DC, de Pablo JJ. A coarse grain model for DNA. J Chem Phys. 2007, 126: 084901.<\/section>\n<\/li>\n
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    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.<\/section>\n<\/li>\n
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    Cragnolini T, Derreumaux P, Pasquali S. Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B. 2015, 117:8047\u20138060.<\/section>\n<\/li>\n
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    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.<\/section>\n<\/li>\n
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    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.<\/section>\n<\/li>\n
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    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\u20131548.<\/section>\n<\/li>\n<\/ol>\n

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