Structural basis for a six nucleotide genetic alphabet.
Structural basis for a six nucleotide genetic alphabet.
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DOI：
10.1021/jacs.5b03482
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发表时间：
2015-06-03
影响因子：
15
通讯作者：
Richards NG
中科院分区：
文献类型：
--
作者：
Georgiadis MM;Singh I;Kellett WF;Hoshika S;Benner SA;Richards NG
合成生物学在多大程度上可以用来扩展与天然酶和细胞兼容的遗传信息系统，这将取决于多个和连续的非自然碱基对在多大程度上符合DNA的标准双螺旋构象。为了实现这一目标，设计了两个非标准碱基(Z，6-氨基-5-硝基-2(1H)-吡啶酮和P，2-amino-imidazo[1，2-a]-1，3，5-triazin-4(8H)one))来形成Z：P对，具有标准的Watson-Crick几何构型，但具有重排的氢键给体和受体基团。在这里，我们介绍了两个含有Z：P对的自互补16聚体寡核苷酸的晶体结构。第一个含有两个连续的Z：P碱基对，并被发现以B形式在主客体复合体中结晶。第二个含有六个连续的Z：P对；它被发现结晶为A型DNA双链，但从圆二色谱推测它在溶液中可以采取B型。虽然Z：P对具有一些类似于G：C对的结构性质，但独特的特征包括Z上的硝基与A-DNA中相邻的杂环核苷酸碱环堆积。在B-DNA和A-DNA中，由于Z中硝基的存在，与Z：P对相关的主要沟槽宽度大约比可比的G：C对的宽度宽。因此，我们的结构研究表明，多个和连续的Z：P对很容易被天然聚合酶识别的DNA双链结构所容纳，因此GACTZP合成遗传系统具有扩大序列空间的必要性质。
The extent to which synthetic biology can be used to expand genetic information systems compatible with natural enzymes and cells will depend on the extent to which multiple and contiguous non-natural nucleobase pairs fit within the standard double helical conformations of DNA. Toward this goal, two non-standard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) were designed to form a Z:P pair with a standard “edge on” Watson-Crick geometry, but with rearranged hydrogen bond donor and acceptor groups. Here, we present the crystal structures of two self-complementary 16-mer oligonucleotides containing Z:P pairs. The first contained two consecutive Z:P nucleobase pairs and was found to crystallize within a host-guest complex in B-form. The second contained six consecutive Z:P pairs; it was found to crystallize as an A-form DNA duplex, although it can adopt B-form in solution as inferred from circular dichroism spectra. Although Z:P pairs have some structural properties that are similar to those of G:C pairs, unique features include stacking of the nitro group on Z with the adjacent heterocyclic nucleobase ring in A-DNA. In both B-and A-DNA, major groove widths associated with the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs potentially due to the presence of the nitro group in Z. Thus, our structural studies suggest that multiple and consecutive Z:P pairs are readily accommodated in DNA duplex structures recognized by natural polymerases, and therefore the GACTZP synthetic genetic system has the requisite properties to expand sequence space.