Mono- and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes
Mono- and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes
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DOI：
10.1073/pnas.2019996118
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发表时间：
2021-03
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通讯作者：
Prabesh Gyawali;R. Saha;Gregory P Smith;M. Salamończyk;Prakash Kharel;S. Basu;Ruipeng Li;M. Fukuto;J. Gleeson;N. Clark;A. Jákli;H. Balci;S. Sprunt
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作者：
Prabesh Gyawali;R. Saha;Gregory P Smith;M. Salamończyk;Prakash Kharel;S. Basu;Ruipeng Li;M. Fukuto;J. Gleeson;N. Clark;A. Jákli;H. Balci;S. Sprunt
DNA的液晶行为已经被研究了几十年，但直到最近才在这个系统中证明了最基本的液晶相之一-近晶相，其中棒状物体组装成流体层的堆叠。在这里，我们描述了不同的双层和单层近晶相的解决方案中的“缺口”DNA（GDNA），由两个DNA双链连接的单链。近晶有序是向异性的（对温度以及浓度敏感），并且层结构对于GDNA构建体的显著扰动是稳定的（例如，“缺口”长度变化和双链体长度的不对称性）。温度敏感性可以提供一种方法来比较在生物相关浓度下DNA双链体之间的端对端相互作用强度。虽然它的介晶性质已经研究了很多年，但直到最近才开始揭示其丰富的液晶行为的真实范围。端到端之间的相互作用集中，超短DNA链驱动的自组装聚集体，组织成液晶相，并纳入灵活的单链“间隙”，否则完全配对的链，生产明确的证据，基本层状（smectic-A）相在DNA解决方案是两个令人兴奋的发展，开辟了发现的途径。在这里，我们报告了一个更广泛的调查近晶有序的性质和温度依赖性的各种“缺口”DNA（GDNA）结构的浓缩溶液。我们研究了对称的GDNA结构组成的两个48个碱基对的双链体片段桥接的单链序列的2至20个胸腺嘧啶碱基。当DNA浓度在230 ~ 280 mg/mL范围内时，观察到两种不同的近晶层结构。一种表现出与双链体长度相当的层间周期性（“双层”结构），另一种具有与单链体长度类似的周期性（“单层”结构）。观察到间隙长度为10个碱基的双层结构，并且在30 °C和35 °C之间的温度下熔化成双相。单层结构占主导地位的间隙长度为10个碱基，并持续到>40 °C。我们讨论了两层结构的模型和它们的稳定性机制。我们还报告了不对称的缺口结构和末端突出的结构，这进一步支持模型层结构的结果。
Significance Liquid crystalline behavior of DNA has been studied for decades, yet only recently has one of the most fundamental liquid crystal phases—the smectic phase in which rod-like objects assemble into stacks of fluid layers—been demonstrated in this system. Here, we describe distinct bilayer and monolayer smectic phases in solutions of “gapped” DNA (GDNA), consisting of two DNA duplexes connected by a single strand. The smectic order is amphotropic (sensitive to temperature as well as concentration), and the layer structure is stable against significant perturbations of the GDNA construct (e.g., “gap” length variation and asymmetry in duplex lengths). The temperature sensitivity may provide a means to compare end-to-end interaction strengths between DNA duplexes at biologically relevant concentrations. Although its mesomorphic properties have been studied for many years, only recently has the molecule of life begun to reveal the true range of its rich liquid crystalline behavior. End-to-end interactions between concentrated, ultrashort DNA duplexes—driving the self-assembly of aggregates that organize into liquid crystal phases—and the incorporation of flexible single-stranded “gaps” in otherwise fully paired duplexes—producing clear evidence of an elementary lamellar (smectic-A) phase in DNA solutions—are two exciting developments that have opened avenues for discovery. Here, we report on a wider investigation of the nature and temperature dependence of smectic ordering in concentrated solutions of various “gapped” DNA (GDNA) constructs. We examine symmetric GDNA constructs consisting of two 48-base pair duplex segments bridged by a single-stranded sequence of 2 to 20 thymine bases. Two distinct smectic layer structures are observed for DNA concentration in the range ∼230to∼280 mg/mL. One exhibits an interlayer periodicity comparable with two-duplex lengths (“bilayer” structure), and the other has a period similar to a single-duplex length (“monolayer” structure). The bilayer structure is observed for gap length ≳10 bases and melts into the cholesteric phase at a temperature between 30 °C and 35 °C. The monolayer structure predominates for gap length ≲10 bases and persists to >40 °C. We discuss models for the two layer structures and mechanisms for their stability. We also report results for asymmetric gapped constructs and for constructs with terminal overhangs, which further support the model layer structures.