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.     

Oscillatory and anti-oscillatory motifs in genetic regulatory networks

Recently,self-sustained oscillatory genetic regulatory networks(GRNs) have attracted significant attention in the biological field.Given a GRN,it is important to anticipate whether the network could generate oscillation with proper parameters,and what the key ingredients for the oscillation are.In this paper the ranges of some function-related parameters which are favorable to sustained oscillations are considered.In particular,some oscillatory motifs appearing with high-frequency in most of the oscillatory GRNs are observed.Moreover,there are some anti-oscillatory motifs which have a strong oscillation repressing effect.Some conclusions analyzing these motif effects and constructing oscillatory GRNs are provided.     

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...     

不同结构的DNA激活序列对Cas12a反式切割活性的影响

CRISPR－Cas12a系统的反式切割活性在其识别特定的DNA激活序列后被激活,这不仅能实现特定DNA靶标的直接定量分析,同时也为构建针对多种生物标志物的体外传感体系带来了新的思路。然而,已有文献中所采用的双链DNA（dsDNA）和单链DNA（ssDNA）激活序列结构多种多样,缺乏全面、系统的设计指导原则。针对该问题,该文系统研究了不同结构的DNA激活序列对LbaCas12a反式切割活性的影响。通过对比研究,得出以下结论：（1）前间区序列邻近基序（PAM）位点有助于LbaCas12a更高效地靶向结合dsDNA激活序列和ssDNA激活序列;（2）PAM近端区域缺少序列片段会降低Cas12a-crRNA定位激活序列的效率;（3）删除PAM远端序列片段有利于增强LbaCas12a的反式切割活性;（4）由于省略了dsDNA解链过程,ssDNA激活序列在激活LbaCas12a的反式切割活性方面普遍比dsDNA激活序列产生的效果更好。根据这些发现,该文提出了一种LbaCas12a所青睐的高效激活序列结构,其激活的LbaCas2a反式酶切活性较采用含PAM位点的标准dsDNA激活序列高出3.7倍。研究结果为构建基于CRISPR-Cas12a的高效体外生物传感系统提供了重要支撑。     

钼酸根阴离子在增强聚苯胺包覆的镍钴层状氢氧化物的电容和析氧行为中的关键作用

理论容量大且过电位低的层状氢氧化物(LDHs)是极有前景的超级电容电池和析氧反应的电极材料;然而,体相LDHs的低电导率和活性位点不足增加了电极的内阻,降低了电极容量和产氧效率.本文采用两步法制备了聚苯胺包覆的MoO42?插层的镍钴层状双金属氢氧化物复合电极(M-LDH@PANI).随着LDH中MoO42?含量的增加,针状的LDH微球逐渐演化为具有较高比表面积的片状M-LDH微球,这为整个电极提供了更多的电化学位点.此外,非晶态的聚苯胺包覆提高了复合电极的电导率.在引入适量MoO42?插层离子时,M-LDH@PANI表现出显著强化的储能和催化性能.所获得的M-LDH@PANI-0.5在析氧反应中表现出优越的电催化活性(10 mA cm?2时的过电位为266 mV),作为超级电容电池电极则具有864.8 C g?1的高容量.采用M-LDH@PANI-0.5作为正极及以活性炭作为负极组装的超级电容电池在功率密度为8,300.0 W kg?1时能量密度为44.6 Wh kg?1,且具有优异的循环稳定性(10000次循环后保留83.9％的初始容量).本文为LDH基材料的阴离子插层改性增强材料性能的机理提供了一个非传统的解释.在上述研究基础上,采用射线衍射(XRD)、X射线光电子能谱(XPS)、扫描电子显微镜(SEM)、高分辨透射电镜(HRTEM)和比表面积测试(BET)等手段对样品进行了深入表征.XRD结果表明,MoO42?插层的LDH材料的层间晶面(003)的峰随着MoO42?含量的增加而逐渐消失,这是由于晶面间距越大越容易受到晶粒细化的影响,间距大的晶格更容易受到破坏,导致晶格的展宽和弱化,从而间接证明MoO42?的成功插层.SEM、HRTEM和BET测试结果表明,MoO42?的含量对材料的形貌和比表面积具有重大影响.利用XPS对样品的价态进行了研究,发现随着MoO42?含量的增加,Co和Ni的价态没有明显变化.电化学测试结果表明,电极的储能和催化性能随MoO42?含量的增加而先增加后减小.利用理论计算分析了MoO42?在LDH中的插层行为,发现少量的MoO42?有利于扩大LDH的层间间距,而过量的MoO42?则会与LDH的H原子结合,从而与电解液中的OH?竞争,导致复合电极的电化学性能下降.此外,MoO42?插层的片状微球能有效调节材料的去质子化能,大大加速电极表面的氧化还原反应.因此,MoO42?插层能够显著强化LDH基材料的超级电容电池电极和OER催化剂电化学性能.     

Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

Discrete and symmetric three-dimensional(3D)DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization(e.g.dye molecules,proteins,inorganic nanoparticles,etc.)to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA point-star motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron(E-TET),rhombic dodecahedron(R-DOD),and rhombic triacontahedron(R-TRI)are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis(PAGE),atomic force microscope(AFM)imaging,and cryogenic transmission electron microscope imaging(cryo-TEM)associated with single particle reconstruction.     

A concise enantioselective synthesis of l-(−)-733,061 and (2S,3S)-methyl 3-aminopiperidine-2-carboxylate using catalytic enantioselective aza-Henry reaction as key step

An efficient enantioselective synthesis of l-(−)-733,061 and (2S,3S)-methyl 3-aminopiperidine-2-carboxylate is accomplished by means of catalytic enantioselective aza-Henry reaction. A key feature of this protocol is organocatalysis as genesis of chirality to ensure high degree of distereo- and enantiocontrol.     

A biomimetic approach to the synthesis of a mycolic acid motif

A new method for the stereoselective synthesis of the (R,R)-β-hydroxy-α-alkyl fatty acid fragment of mycolic acids, via an asymmetric anti-aldol reaction is reported. The ‘mycolic acid motif’ fragment was prepared in three steps and >98% ee.     

Systematic investigation of sequence and structural motifs that recognize ATP

Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP–protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP.