Triple-Resonance Experiments for Correlation of H5 and Exchangeable Pyrimidine Base Hydrogens in C,N-Labeled RNA

Triple-resonance two-dimensional H5(C5C4N)H experiments are described that provide through-bond H5 to imino/amino connectivities in uridines and cytidines in ¹³C, ¹⁵N-labeled RNAs. The experiments employ selective INEPT steps for transferring magnetization from the H5 hydrogens through the intervening C5, C4, and N3/N4 nuclei to the imino/amino hydrogens. The improved sensitivity of these experiments for assignments in a large 43-nucleotide RNA is demonstrated.     

Construction and Characterization of Lentiviral shRNA Expression Vector Targeting Rat CD40 Gene in Dendritic Cells

To construct a lentiviral shRNA vector targeting rat CD40 gene and detect its effectiveness of gene silencing in dendritic cells(DCs), specific siRNA targets with short hairpin frame were designed and synthesized according to the mRNA sequence of rat CD40 gene. DNA oligo was cloned into lentiviral expression vector, and then PCR and sequencing analyses were conducted to verify the constructs. The verified plasmids were transfected into 293T cells that over-express recombinant CD40 in order to select the mos...     

RNA碱基的太赫兹光谱和拉曼光谱特征研究

应用傅里叶红外光谱仪和激光拉曼光谱仪测试了RNA碱基在太赫兹波段(1～10 THz)的红外和拉曼光谱,同时结合Guassian09软件和周期性边界条件下基于能量的分块方法(PBC—GEBF),分析了RNA碱基晶体的红外和拉曼光谱特征,得到了所有特征峰位置及其对应的振动模式,且计算光谱与测试光谱一致吻合,表明碱基粉末样品为无定形晶体结构。通过对红外光谱的分析可知,在太赫兹波段,腺嘌呤和鸟嘌呤都有6个红外活性振动模式,胞嘧啶和尿嘧啶分别为6个和3个红外活性振动模式,与实验结果相比,除了鸟嘌呤6.35 THz处的弱吸收峰没能重现,4.83和5.39 THz处的吸收峰简并;胞嘧啶4.3和4.79 THz处吸收峰简并;尿嘧啶3.32和3.82 THz处的吸收峰简并外,其他吸收峰的位置和强度均被准确地模拟重现。通过对拉曼光谱的分析可知,理论和实验光谱基本一致,除了尿嘧啶3.52和4.48 THz处特征峰简并;鸟嘌呤7.26和8.03 THz,3.57,4.02,4.49,4.89和5.98 THz处特征峰简并外,其他特征峰的位置和强度均被准确的模拟重现。通过对特征峰的分析和辨认,可知在1～10 THz,RNA碱基的振动模式均来源于晶格内分子的集体振动,分子间的氢键和弱相互作用力对振动模式的贡献很大,进一步分析可知,在1～5.5 THz,其振动模式来自所有原子参与的集体振动,在5.5～10 THz,振动模式来自于部分原子参与的集体振动。此项研究对揭示RNA碱基在构成生物大分子结构、生物大分子鉴定以及太赫兹波段光谱的形成机制等方面,具有重要的理论和实际参考价值。     

Flexibility of nucleic acids: From DNA to RNA

The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid flexibility, extensive studies have been performed using various experimental methods and theoretical models. In this review, we will introduce the progress that has been made in understanding the flexibility of nucleic acids including DNAs and RNAs,and will emphasize the experimental findings and the effects of salt, temperature, and sequence. Finally, we will discuss the major unanswered questions in understanding the flexibility of nucleic acids.     

基于链置换循环无标记检测端粒酶RNA的荧光法

以氧化石墨烯(GO)作为DNA载体和荧光猝灭剂, SYBR Green Ⅰ(SGⅠ)为荧光信号探针, 发夹核酸探针为分子识别探针, 基于目标物启动的发夹核酸探针链置换循环反应, 建立了一种利用荧光共振能量转移和链置换循环放大技术检测端粒酶RNA(hTR)的荧光新方法. 发夹核酸探针hpDNA1和hpDNA2吸附在GO表面, 嵌插在发夹DNA探针茎部的SGⅠ的荧光信号被GO猝灭. 当人工合成的目标物(T1)存在时, T1与hpDNA1杂交打开hpDNA1的茎-环结构而引发hpDNA2与T1之间的链置换循环反应, 由此累积产生大量的hpDNA1/hpDNA2杂交双链. 刚性的双链DNA脱离GO表面, 导致所嵌插的SGⅠ产生较强的荧光信号. 基于荧光信号的变化, 可定量检测0.2~50 nmol/L的T1, 检出限为90 pmol/L. 该方法为端粒酶RNA检测提供了一种高灵敏、 高特异性且无需标记的荧光新途径.     

Computational Analysis Reveals Monomethylated Triazolopyrimidine as a Novel Inhibitor of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp)

The human population is still facing appalling conditions due to several outbreaks of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus. The absence of specific drugs, appropriate vaccines for mutants, and knowledge of potential therapeutic agents makes this situation more difficult. Several 1, 2, 4-triazolo [1, 5-a] pyrimidine (TP)-derivative compounds were comprehensively studied for antiviral activities against RNA polymerase of HIV, HCV, and influenza viruses, and showed immense pharmacological interest. Therefore, TP-derivative compounds can be repurposed against the RNA-dependent RNA polymerase (RdRp) protein of SARS-CoV-2. In this study, a meta-analysis was performed to ensure the genomic variability and stability of the SARS-CoV-2 RdRp protein. The molecular docking of natural and synthetic TP compounds to RdRp and molecular dynamic (MD) simulations were performed to analyse the dynamic behaviour of TP compounds at the active site of the RdRp protein. TP compounds were also docked against other non-structural proteins (NSP1, NSP2, NSP3, NSP5, NSP8, NSP13, and NSP15) of SARS-CoV-2. Furthermore, the inhibition potential of TP compounds was compared with Remdesivir and Favipiravir drugs as a positive control. Additionally, TP compounds were analysed for inhibitory activity against SARS-CoV RdRp protein. This study demonstrates that TP analogues (monomethylated triazolopyrimidine and essramycin) represent potential lead molecules for designing an effective inhibitor to control viral replication. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-CoV-2.     

RNA中腺嘌呤编辑分析方法研究进展

RNA腺嘌呤编辑(Ade-to-Ino)是RNA上最丰富的转录后修饰之一.腺苷到肌苷的转变通过作用于RNA上的腺苷脱氨酶(ADARs)催化腺苷C6位上的氨基水解脱氨产生.RNA腺嘌呤编辑参与调控基因表达和蛋白功能.研究发现异常的RNA腺嘌呤编辑与多种人类疾病相关.深入研究RNA腺嘌呤编辑的生理功能需要高灵敏检测、准确定...     

信号核酸识体用于药物托普霉素的高灵敏度检测

提出了一种利用RNA核酸识体和光开关化合物[Ru(phen)2dppz\]2+ (RU)高灵敏检测药物分子的荧光分析新方法. 以托普霉素(TOB)为靶分子, 检测限可达到10 nmol/L, 同时该方法有较好的选择性, 能在溶液中实现无需分离的实时检测. 这种无标记检测方法有利于不稳定RNA核酸识体在分析检测中的应用, 简化实验操作, 为其它药物分子的检测提供了新思路.