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。     

Distance-Dependent Electron Transfer Kinetics in Axially Connected Silicon Phthalocyanine-Fullerene Conjugates

The effect of donor-acceptor distance in controlling the rate of electron transfer in axially linked silicon phthalocyanine-C₆₀ dyads has been investigated. For this, two C₆₀-SiPc-C₆₀ dyads, 1 and 2 , varying in their donor-acceptor distance, have been newly synthesized and characterized. In the case of C₆₀-SiPc-C₆₀ 1 where the SiPc and C₆₀ are separated by a phenyl spacer, faster electron transfer was observed with k_cs equal to 2.7×10⁹ s⁻¹ in benzonitrile. However, in the case of C₆₀-SiPc-C₆₀ 2 , where SiPc and C₆₀ are separated by a biphenyl spacer, a slower electron transfer rate constant, k_cs=9.1×10⁸ s⁻¹, was recorded. The addition of an extra phenyl spacer in 2 increased the donor-acceptor distance by ∼4.3 Å, and consequently, slowed down the electron transfer rate constant by a factor of ∼3.7. The charge separated state lasted over 3 ns, monitoring time window of our femtosecond transient spectrometer. Complimentary nanosecond transient absorption studies revealed formation of ³SiPc* as the end product and suggested the final lifetime of the charge separated state to be in the 3–20 ns range. Energy level diagrams established to comprehend these mechanistic details indicated that the comparatively high-energy SiPc^.+-C₆₀^.− charge separated states (1.57 eV) populated the low-lying ³SiPc* (1.26 eV) prior returning to the ground state.     

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.     

少节点基因调控网络的控制

近年来,自组织振荡网络受到越来越多科学家的关注,对生物体的生长、发育起调控作用的基因调控网络即是其中的一种.本文研究了少节点基因调控网络的控制问题.运用多相位超前驱动方法对该种网络进行调控,可以有效地提高对网络的控制效率.通过数值模拟,发现对于少节点基因调控网络,当系统参数确定时,网络的有效控制率可以达到95％以上(10节点网络);当系统参数不确定时,控制的效率也非常高.     

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.     

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.     

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.     

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.