Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.     

Construction of Organelle-Like Architecture by Dynamic DNA Assembly in Living Cells

The design of controllable dynamic systems is vital for the construction of organelle-like architectures in living cells, but has proven difficult due to the lack of control over defined topological transformation of self-assembled structures. Herein, we report a DNA based dynamic assembly system that achieves lysosomal acidic microenvironment specifically inducing topological transformation from nanoparticles to organelle-like hydrogel architecture in living cells. Designer DNA nanoparticles are constructed from double-stranded DNA with cytosine-rich stick ends (C-monomer) and are internalized into cells through lysosomal pathway. The lysosomal acidic microenvironment can activate the assembly of DNA monomers, inducing transformation from nanoparticles to micro-sized organelle-like hydrogel which could further escape into cytoplasm. We show how the hydrogel regulates cellular behaviors: cytoskeleton is deformed, cell tentacles are significantly shortened, and cell migration is promoted.     

d(C4)相关序列形成四分子i-Motif结构的电喷雾质谱研究

设计了与富含胞嘧啶(C)的DNA序列d(C4)相关的DNA序列d(C4), d(TC4), d(AC4), d(T2C4), d(A2C4), d(C4T), d(C4A)和d(TC4T); 采用电喷雾质谱测定发现这些序列形成四分子非共价复合物离子, 根据离子的相对丰度可确定形成四链i-motif结构的数量和可能性; 同时考察了腺嘌呤(A)和胸腺嘧啶(T)在d(C4)序列的5'和3'端对其形成四分子i-motif结构的影响. 结果表明, 在d(C4)的5'端增加A碱基或T碱基更易形成四分子复合物; 5'端含T碱基比含A碱基更利于形成四分子复合物; 而在d(C4)序列中增加2个A碱基或T碱基比增加相应的单个碱基形成了更高丰度的四分子离子峰.     

基于i-motif的生物医学应用纳米系统:pH成像、药物控释和肿瘤诊疗

I-motif作为一种新型pH敏感元件,因其在不同pH条件下可以进行快速的构象转变,以及具有自动化合成、优异的生物相容性和灵活的功能化整合等优点,在生物医学领域引起了广泛的关注和研究热潮.该文介绍了i-motif的基本性能,综述了基于i-motif的纳米系统在细胞pH成像、pH控制的药物释放和pH响应型肿瘤诊疗一体化等...     

基于小分子的核酸结构探针最新研究进展

本文主要综述了基于小分子的核酸结构探针的最新研究进展.所探索的核酸结构主要有四链核酸（包括G-四链体以及i-motif）结构、三链核酸结构、左手螺旋DNA结构以及不规则核酸结构（包括突起结构以及环状结构）等;所探索的小分子包括过渡金属配合物、大环共轭化合物、环肽以及寡糖抗生素等.     

Orthogonal Dual‐Triggered Shape‐Memory DNA‐Based Hydrogels

DNA‐based shape‐memory hydrogels revealing switchable shape recovery in the presence of two orthogonal triggers are described. In one system, a shaped DNA/acrylamide hydrogel is stabilized by duplex nucleic acids and pH‐responsive cytosine‐rich, i‐motif, bridges. Separation of the i‐motif bridges at pH 7.4 transforms the hydrogel into a quasi‐liquid, shapeless state, that includes the duplex bridges as permanent shape‐memory elements. Subjecting the quasi‐liquid state to pH 5.0 or Ag⁺ ions recovers the hydrogel shape, due to the stabilization of the hydrogel by i‐motif or C‐Ag⁺‐C bridged i‐motif. The cysteamine‐induced transformation of the duplex/C‐Ag⁺‐C bridged i‐motif hydrogel into a quasi‐liquid shapeless state results in the recovery of the shaped hydrogel in the presence of H⁺ or Ag⁺ ions as triggers. In a second system, a shaped DNA/acrylamide hydrogel is generated by DNA duplexes and bridging Pb²⁺ or Sr²⁺ ions‐stabilized G‐quadruplex subunits. Subjecting the shaped hydrogel to the DOTA or KP ligands eliminates the Pb²⁺ or Sr²⁺ ions from the respective hydrogels, leading to shapeless, memory‐containing, quasi‐liquid states that restore the original shapes with Pb²⁺ or Sr²⁺ ions.     

A regenerated electrochemical biosensor for label-free detection of glucose and urea based on conformational switch of i-motif oligonucleotide probe

Improving the reproducibility of electrochemical signal remains a great challenge over the past decades. In this work, i-motif oligonucleotide probe-based electrochemical DNA (E-DNA) sensor is introduced for the first time as a regenerated sensing platform, which enhances the reproducibility of electrochemical signal, for label-free detection of glucose and urea. The addition of glucose or urea is able to activate glucose oxidase-catalyzed or urease-catalyzed reaction, inducing or destroying the formation of i-motif oligonucleotide probe. The conformational switch of oligonucleotide probe can be recorded by electrochemical impedance spectroscopy. Thus, the difference of electron transfer resistance is utilized for the quantitative determination of glucose and urea. We further demonstrate that the E-DNA sensor exhibits high selectivity, excellent stability, and remarkable regenerated ability. The human serum analysis indicates that this simple and regenerated strategy holds promising potential in future biosensing applications.     

Identifying i-motif formation using capillary electrophoresis

Over the past few years, intercalated motifs (i-motifs) have attracted attention due to the direct visualization of their existence in the nuclei of human cells. Traditionally, i-motifs have been studied using expensive and complicated NMR, and/or relatively inexpensive but less common circular dichroism spectrometry. The aim of this study was to investigate the feasibility of using less expensive, less complicated, and more widely available CE as an alternative for i-motif related research. The mobilities of two DNA and RNA i-motifs in CE were determined under different pH conditions. Our results demonstrate that CE is able to identify and differentiate mostly folded, partially folded, and mostly unfolded DNA and RNA i-motifs through changes in peak shape and migration time, thus providing a new method to study both i-motif conformation and the interactions between i-motifs and their ligands.