A New Tool in Peptide Engineering: A Photoswitchable Stilbene‐type β‐Hairpin Mimetic

Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogenous peptides with new physicochemical and pharmacological properties. The development, synthesis, photochemical investigation, and conformational analysis of a stilbene‐type β‐hairpin mimetic capable of light‐triggered conformational changes have been achieved. In addition to standard spectroscopic techniques (nuclear Overhauser effects, amide temperature coefficients, circular dichroism spectroscopy), the applicability of self‐diffusion measurements (longitudinal eddy current delay pulsed‐field gradient spin echo (LED‐PGSE) NMR technique) in conformational studies of oligopeptides is demonstrated. The title compound shows photoisomerization of the stilbene chromophore, resulting in a change in solution conformation between an unfolded structure and a folded β‐hairpin.     

Mismatches Improve the Performance of Strand‐Displacement Nucleic Acid Circuits

Catalytic hairpin assembly (CHA) has previously proven useful as a transduction and amplification method for nucleic acid detection. However, the two hairpin substrates in a CHA circuit can potentially react non‐specifically even in the absence of a single‐stranded catalyst, and this non‐specific background degrades the signal‐to‐noise ratio. The introduction of mismatched base pairs that impede uncatalyzed strand exchange reactions led to a significant decrease of the background signal, while only partially damping the signal in the presence of a catalyst. Various types and lengths of mismatches were assayed by fluorimetry, and in many instances, our MismatCHA designs yielded 100‐fold increased signal‐to‐background ratios compared to a ratio of 4:1 with the perfectly matched substrates. These observations could be of general utility for the design of non‐enzymatic nucleic acid circuits.     

纳米金标记电化学检测DNA特异性结合蛋白

将单分子发夹寡核苷酸固相延伸形成双链寡核苷酸, 以纳米金颗粒标记NF-κB并银染放大, 采用阳极溶出电位法对NF-κB进行检测. 结果表明, 本法检测序列特异性蛋白质具有高度特异性、高灵敏度和快速等特点, 为转录因子调控机制、开放阅读框识别和功能基因检测等的研究提供了有利工具.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

Applications of synthetic oligoribonucleotide analogues in studies of RNA structure and function

The study of RNA structure and function has been considerably aided by the development of methods for the chemical synthesis of oligoribonucleotides into which have been incorporated modified nucleosides carrying site-specific alterations. Such modifications are designed to eliminate or alter individual functional groups in the RNA which potentially can take part in hydrogen-bonding or other non-covalent interactions. Comparison of the properties of the modified RNA with unmodified RNA models allows conclusions to be drawn concerning the importance or otherwise of specific functional groups within the RNA. The methods have been applied to studies of RNA structure, RNA catalysis, and interactions of RNA with proteins.     

Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination

Residual dipolar coupling (RDC) provides valuable information about the orientation of each internuclear vector in a macromolecule with respect to the static magnetic field. However, structure determination utilizing RDC still remains challenging without additional restraints such as NOE. In this context, a novel approach has been developed to efficiently extract structural information from RDC by successive application of singular value decomposition (SVD) method in the course of NMR structure determination. Force contribution from the alignment tensor is rigorously formulated in the context of SVD, and assessments have been made to verify its numerical accuracy. The efficacy of this approach is illustrated by showing that RDC restraints alone can restore a distorted beta-hairpin to native-like structure using the replica-exchange molecular dynamics simulations.     

银覆盖冠状硅柱阵列基底的制备、SERS特性分析及肿瘤标志物miRNA-106a的检测

以聚苯乙烯(PS)小球为模板,采用金属辅助刻蚀和湿法化学刻蚀技术,制备大面积冠状硅柱阵列,再原位生长银纳米粒子后得到银覆盖冠状硅柱阵列(Ag/Si CPA)基底。实验表明,制备的基底具有优良的表面增强拉曼散射(SERS)特性,电磁增强因子达到1.81×10~6。同时,将制备的罗丹明分子(R6G)标记的DNA发卡探针与基底链接,在与miRNA-106a互补杂交后进行SERS信号检测,获得相应的剂量-响应曲线。结果表明,基于(Ag/Si CPA)基底的SERS特性,开展miRNA-106a的检测,具有特异性好和灵敏度高的优势,检测范围为1 fmol·L~(-1)～100 pmol·L~(-1),检测极限为0.917 fmol·L~(-1)。此外,与实时荧光定量多聚核苷酸链式反应(RT-qPCR)方法相比,不仅检测结果一致,而且基于SERS光谱技术的检测方法具有更高的灵敏度。