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A-DNA 双链的外消旋晶体结构。

Racemic crystal structures of A-DNA duplexes.

机构信息

Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), 33600 Pessac, France.

Université de Bordeaux, CNRS, INSERM, Institut Européen de Chimie et Biologie (UAR3033 and US001), 33600 Pessac, France.

出版信息

Acta Crystallogr D Struct Biol. 2022 Jun 1;78(Pt 6):709-715. doi: 10.1107/S2059798322003928. Epub 2022 May 9.

DOI:10.1107/S2059798322003928
PMID:35647918
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9159285/
Abstract

The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A-form DNA. This form differs from the Z-form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo-helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self-assembled nanomaterials and nanostructures.

摘要

与等效的手性体系相比,外消旋混合物结晶的容易程度通常被利用来生产小分子晶体。然而,生物大分子如 DNA 和蛋白质是天然手性的,因此可用的手性空间群的有限范围阻碍了此类分子的结晶。过去 15 年的鼓舞人心的工作表明,通过蛋白质化学合成的令人印象深刻的进展,可以实现蛋白质的外消旋混合物,这确实可以提高蛋白质结晶实验的成功率。最近,外消旋结晶方法已扩展到包括核酸,作为确定对映纯 DNA 晶体结构的一种可能辅助手段。在这里,报告的研究结果表明,其益处可能不止于此。描述了两个 DNA 序列 d(CCCGGG)的外消旋晶体结构,发现它们折叠成 A 型 DNA。这种形式与固态中手性等同物采用的 Z 型 DNA 构象不同,表明使用外消旋混合物也可能有利于新构象的出现。重要的是,外消旋混合物在固态中形成的相互作用与手性等同物不同(包括形成外消旋假螺旋),这表明使用外消旋 DNA 混合物可以为精确自组装纳米材料和纳米结构的设计提供新的可能性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/839a787d497d/d-78-00709-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/5a414e3871ce/d-78-00709-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/390b4d07ce3c/d-78-00709-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/e7940c2bda48/d-78-00709-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/839a787d497d/d-78-00709-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/5a414e3871ce/d-78-00709-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/390b4d07ce3c/d-78-00709-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/e7940c2bda48/d-78-00709-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa4a/9159285/839a787d497d/d-78-00709-fig4.jpg

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本文引用的文献

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The crystal structure of a natural DNA polymerase complexed with mirror DNA.天然 DNA 聚合酶与镜像 DNA 复合物的晶体结构。
Chem Commun (Camb). 2020 Feb 18;56(14):2186-2189. doi: 10.1039/c9cc09351f. Epub 2020 Jan 23.
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Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.调节自组装三维 DNA 晶体的腔室大小和手性。
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Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes.基因编码的 DNA-蛋白质杂合纳米形状的自组装。
Science. 2017 Mar 24;355(6331). doi: 10.1126/science.aam5488.
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Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.Z-DNA 的超高分辨率中心对称晶体结构揭示了大量的交替构象。
Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1203-1211. doi: 10.1107/S205979831601679X. Epub 2016 Oct 28.
6
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