Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA.
Philos Trans R Soc Lond B Biol Sci. 2023 Feb 27;378(1871):20220028. doi: 10.1098/rstb.2022.0028. Epub 2023 Jan 11.
The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA should also be able to adopt B-form. Using a host-guest system in which Moloney murine leukemia virus reverse transcriptase serves as the host and DNA as the guests, we determined high-resolution crystal structures of three complexes including 5'-CTTAAG, 5'-CTTAAG and 5'-CTTAAG with 10 consecutive unnatural nucleobase pairs in B-form within self-complementary 16 bp duplex oligonucleotides. We refer to this ALternative Isoinformational ENgineered (ALIEN) genetic system containing two nucleobase pairs (, pairing 2-amino-imidazo-[1,2-]-1,3,5-triazin-(8)-4-one with 6-amino-5-nitro-(1)-pyridin-2-one, and , 6-amino-4-hydroxy-5-(1)-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one) as ALIEN DNA. We characterized both position- and sequence-specific helical, nucleobase pair and dinucleotide step parameters of and pairs in the context of B-form DNA. We conclude that ALIEN DNA exhibits structural features that vary with sequence. Further, can participate in alternative stacking modes within a similar sequence context as captured in two different structures. This finding suggests that ALIEN DNA may have a larger repertoire of B-form structures than natural DNA. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
1953 年，沃森（Watson）和克里克（Crick）首次提出了双链 DNA 的结构模型，该模型呈现出 B 型结构，基因组 DNA 在大部分时间都以这种形式存在。因此，试图模拟天然 DNA 特性的人工 DNA 也应该能够采用 B 型结构。我们使用一个主体-客体系统，其中莫洛尼鼠白血病病毒逆转录酶（Moloney murine leukemia virus reverse transcriptase）作为主体，DNA 作为客体，确定了三种复合物的高分辨率晶体结构，包括 5'-CTTAAG、5'-CTTAAG 和 5'-CTTAAG，它们在自我互补的 16 个碱基对双链寡核苷酸中以 B 型形成了 10 个连续的非天然核碱基对。我们将这个包含两个核碱基对（ ，嘌呤-2-酮与 6-氨基-5-硝基-1-吡啶-2-酮配对，以及 ，6-氨基-4-羟基-5-嘌呤-2-酮与 3-甲基-6-氨基嘧啶-2-酮配对）的替代同型异构工程（ALIEN）遗传系统称为 ALIEN DNA。我们描述了在 B 型 DNA 中 和 碱基对的位置和序列特异性螺旋、核碱基对和二核苷酸步参数。我们得出结论，ALIEN DNA 表现出随序列变化的结构特征。此外， 可以在类似的序列背景下参与替代堆积模式，这在两个不同的结构中得到了捕捉。这一发现表明，ALIEN DNA 可能具有比天然 DNA 更多的 B 型结构。本文是主题为“化学和合成生物学中的反应性和机制”的特刊的一部分。
