Synthesis and Characterization of Artificial Ribonucleases

Abstract

RNA cleaving molecules were synthesized by conjugating components of ribonucleases A and T1 catalytic centers (imidazole, aliphatic amino and/or carboxy residues) to intercalating and cationic structures. The artificial ribonucleases were shown cleave RNA at Py-Pu sites in single-stranded regions.     

Stability and Transformations of bis-PNA/DNA Triplex Structural Isomers

Abstract

Structurally isomeric complexes formed between homopyrimidine bis-PNAs (T₂JT₂JT₄-linker-T₄CT₂CT₂) and single- and double-stranded DNA targets were investigated. These complexes are triplexes designated S1, S2 and S3 in order of increased mobility by polyacrylamide gel electrophoresis. It is shown that the S3 isomer is formed only on double-stranded DNA and possesses highest stability. Isomers S2 and S1 are formed upon binding of bis-PNA to double-stranded as well as to single-stranded DNA. It was found that the stability of the isomer S1 increases dramatically in the presence of excess single-stranded oligonucleotide complementary to the bis-PNA. The structure of the stabilized S1 isomer is proposed to consist of two bis-PNA/DNA triplexes. The relationship between the yield of the isomer S1 formed on single-stranded DNA and the bis-PNA concentration was investigated and a kinetic model of the formation of S1 is presented.     

Synthesis and Activity of Modified Cytidine 5′-Monophosphate Probes for T4 RNA Ligase 1

We describe the synthesis of a series of unique base modified ligation probes such as p(5′)C-4-ethylenediamino 3, p(5′)C-4-biotin 4, and pre-adenylated form A(5′)pp(5′)C-4-biotin 6 and tested their biological activity with T4 RNA ligase 1 using a standard pCp probe 1 as a control. The intermolecular ligation assay was developed using a 5′-FAM labeled 24 mer single-stranded (ss) RNA and the average ligation efficiencies for pCp 1, p(5′)C-4-ethylenediamino 3, p(5′)C-4-biotin 4, and pre-adenylated form A(5′)pp(5′)C-4-biotin 6 were found to be 44%, 81%, 39% and 16% respectively, as determined using a denaturing gel analysis. Furthermore, confirmation of the ligation activity of the biotinylated probes to the RNA substrate was confirmed by streptavidin conjugation and analysis by nondenaturing gel electrophoresis. These results strongly suggest that the new probes are valid substrates for T4 RNA ligase 1 and therefore could be useful for developing a miRNA detection system that includes rapid isolation, efficient labeling and detection of miRNAs on sensitivity-enhanced microarrays.     

A Model for the Complex Between the Helix Destabilizing Protein GP32 of Bacteriophage T4 and Single-Stranded DNA

Abstract

A model for the structure of the complex between the helix-destabilizing protein of bacteriophage T4, GP32, and single-stranded DNA is proposed. In this model the bases are arranged in a helix, that is characterized by a relatively large distance between successive bases, a substantial base tilt, in combination with a small rotation per base. This helix is further organized into a tertiary structure, possibly a superhelix, of which the corresponding protein shell corresponds to the relatively rigid and rod-like structure that is observed in hydrodynamic experiments. It is proposed that similar structural features apply to other single-stranded DNA binding proteins in complex with polynucleotides.     

Affinity and Conformation of the Estrogen Receptor When Bound to Single-Stranded vs. Double-Stranded Nonspecific DNA

Abstract

The affinity of the hormone-bound estrogen receptor for single-stranded and double-stranded DNA was compared using isocratic elution chromatography. The receptor bound single-stranded DNA with a two-fold higher affinity than double-stranded DNA (17.9 × 10⁴ M^?1 vs. 9.1 × 10⁴ M^?1) at 0.2 M KCl. The same number of ions were released when the receptor bound either single-stranded or double-stranded DNA (11.8 vs. 10.6, respectively). These results indicate the hormone-bound estrogen receptor has no strong preference for single-stranded vs. double-stranded nonspecific DNA, and has a similar conformation when bound to either form of DNA at physiological salt concentrations.     

C-termini are essential and distinct for nucleic acid binding of human NABP1 and NABP2

BackgroundHuman Nucleic Acid Binding Protein 1 and 2 (hNABP1 and 2; also known as hSSB2 and 1, respectively) are two newly identified single-stranded (ss) DNA binding proteins (SSB). Both NABP1 and NABP2 have a conserved oligonucleotide/oligosaccharide-binding (OB)-fold domain and a divergent carboxy-terminal domain, the functional importance of which is unknown.MethodsRecombinant hNABP1/2 proteins were purified using affinity and size exclusion chromatography and their identities confirmed by mass spectrometry. Oligomerization state was checked by sucrose gradient centrifugation. Secondary structure was determined by circular dichroism spectroscopy. Nucleic acid binding ability was examined by EMSA and ITC.ResultsBoth hNABP1 and hNABP2 exist as monomers in solution; however, hNABP2 exhibits anomalous behavior. CD spectroscopy revealed that the C-terminus of hNABP2 is highly disordered. Deletion of the C-terminal tail diminishes the DNA binding ability and protein stability of hNABP2. Although both hNABP1 and hNABP2 prefer to bind ssDNA than double-stranded (ds) DNA, hNABP1 has a higher affinity for ssDNA than hNABP2. Unlike hNABP2, hNABP1 protein binds and multimerizes on ssDNA with the C-terminal tail responsible for its multimerization. Both hNABP1 and hNABP2 are able to bind single-stranded RNA, with hNABP2 having a higher affinity than hNABP1.ConclusionsBiochemical evidence suggests that the C-terminal region of NABP1 and NABP2 is essential for their functionality and may lead to different roles in DNA and RNA metabolism.General significanceThis is the first report demonstrating the regulation and functional properties of the C-terminal domain of hNABP1/2, which might be a general characteristic of OB-fold proteins.     

Secondary structure of mouse and rabbit α- and β-globin mRNAs: Differential accessibility of α and β initiator AUG codons towards nucleases

The nucleotide sequence from the 5′ terminus inward of one third of mouse α- and β^maj-globin messenger RNAs has been established. In addition, using 5′ ³²P end-labeled mRNAs as substrates and S1 and T1 nucleases as probes for single-stranded regions, the secondary structures of mouse and rabbit α- and β-globin mRNAs have been analyzed. Our results indicate that the AUG initiator codon in both mouse and rabbit β-globin mRNA is quite susceptible to cleavage with S1 and T1 nucleases, suggesting that it resides in a single-stranded exposed region. In contrast, the initiator AUG in the α-globin mRNA of both species is inaccessible to cleavage, indicating that it is either buried by tertiary structure or is base-paired. Since the rate of initiation of protein synthesis with β-globin mRNA in rabbit reticulocyte is 30–40% faster than for α-globin mRNA, these results imply a possible correlation between the differential rates of initiation with these two mRNAs and the accessibility of the respective AUG initiator codons.     

Competitive Binding Between Unmodified and Etheno DNA Provides Information About Structure and Stoichiometry of RECA-DNA Complexes

Abstract

RecA is found to form three different complexes with single-stranded DNA with stoichiometries of 3, 6, and  9 nucleotides per RecA monomer. In the first two complexes the DNA bases are oriented preferentially perpendicular to the fiber axis of the complex. The second complex is shown to involve two different DNA strands.     

连续股神经阻滞与静脉自控镇痛对全膝关节置换术后患者凝血功能的影响

目的:比较连续股神经阻滞(CFNB)与静脉自控镇痛(PCIA)在全膝关节置换术中的应用效果及对患者凝血功能的影响。方法:选取2014年1月至2015年12月间我院行单侧全膝关节置换术的患者80例,按照随机数字表法分为CFNB组和PCIA组,每组各40例,两组患者分别接受CFNB和PCIA治疗。观察两组患者术后6 h、12 h、24 h、48 h视觉模拟疼痛评分(VAS),两组患者分别于麻醉前(T1)、术毕(T2)、术后1 d(T3)、术后2 d(T4)进行血栓弹力图检查,观察两组凝血功能变化。并于术后随访1年,比较两组患者膝关节功能。结果:术后6 h、12 h、24 h、48 h CFNB组患者VAS评分显著低于PCIA组患者(P0.05)。T2、T3、T4时点CFNB组患者凝血反应时间(R)、血凝块形成时间(K)较T1升高,血凝块聚合形成速率(α角)、血凝块最大振幅(MA)较T1降低,PCIA组患者R、K较T1降低,α角、MA较T1升高,T2、T3、T4时点CFNB组患者R、K高于PCIA组患者,α角、MA低于PCIA组患者,差异均有统计学意义(P0.05)。两组患者术后均完成1年的随访,两组患者KSS评分、膝关节最大屈曲度、膝关节最大伸直度比较无统计学差异(P0.05)。结论:CFNB对于全膝关节置换术术后患者镇痛效果优于PCIA,有利于改善患者凝血功能,不影响术后患者膝关节功能的恢复。     

Combinatorial antigen targeting strategies for acute leukemia: application in myeloid malignancy

Background aimsEfforts to safely and effectively treat acute myeloid leukemia (AML) by targeting a single leukemia-associated antigen with chimeric antigen receptor (CAR) T cells have met with limited success, due in part to heterogeneous expression of myeloid antigens. The authors hypothesized that T cells expressing CARs directed toward two different AML-associated antigens would eradicate tumors and prevent relapse.MethodsFor co-transduction with the authors’ previously optimized CLL-1 CAR currently in clinical study (NCT04219163), the authors generated two CARs targeting either CD123 or CD33. The authors then tested the anti-tumor activity of T cells expressing each of the three CARs either alone or after co-transduction. The authors analyzed CAR T-cell phenotype, expansion and transduction efficacy and assessed function by in vitro and in vivo activity against AML cell lines expressing high (MOLM-13: CD123 high, CD33 high, CLL-1 intermediate), intermediate (HL-60: CD123 low, CD33 intermediate, CLL-1 intermediate/high) or low (KG-1a: CD123 low, CD33 low, CLL-1 low) levels of the target antigens.ResultsThe in vitro benefit of dual expression was most evident when the target cell line expressed low antigen levels (KG-1a). Mechanistically, dual expression was associated with higher pCD3z levels in T cells compared with single CAR T cells on exposure to KG-1a (P < 0.0001). In vivo, combinatorial targeting with CD123 or CD33 and CLL-1 CAR T cells improved tumor control and animal survival for all lines (KG-1a, MOLM-13 and HL-60); no antigen escape was detected in residual tumors.ConclusionsOverall, these findings demonstrate that combinatorial targeting of CD33 or CD123 and CLL-1 with CAR T cells can control growth of heterogeneous AML tumors.     

The effect of Pot1 binding on the repair of thymine analogs in a telomeric DNA sequence

Telomeric DNA can form duplex regions or single-stranded loops that bind multiple proteins, preventing it from being processed as a DNA repair intermediate. The bases within these regions are susceptible to damage; however, mechanisms for the repair of telomere damage are as yet poorly understood. We have examined the effect of three thymine (T) analogs including uracil (U), 5-fluorouracil (5FU) and 5-hydroxymethyluracil (5hmU) on DNA–protein interactions and DNA repair within the GGTTAC telomeric sequence. The replacement of T with U or 5FU interferes with Pot1 (Pot1pN protein of Schizosaccharomyces pombe) binding. Surprisingly, 5hmU substitution only modestly diminishes Pot1 binding suggesting that hydrophobicity of the T-methyl group likely plays a minor role in protein binding. In the GGTTAC sequence, all three analogs can be cleaved by DNA glycosylases; however, glycosylase activity is blocked if Pot1 binds. An abasic site at the G or T positions is cleaved by the endonuclease APE1 when in a duplex but not when single-stranded. Abasic site formation thermally destabilizes the duplex that could push a damaged DNA segment into a single-stranded loop. The inability to enzymatically cleave abasic sites in single-stranded telomere regions would block completion of the base excision repair cycle potentially causing telomere attrition.     

Interruptions in Single Strands of the DNA in Slime Mold and Other Organisms

The molecular weight of single-stranded DNA from the slime mold Physarum polycephalum has been determined by alkaline gradient centrifugation. The average molecular weight during DNA synthesis (~1.5 × 10⁷ D) is less than that observed in nonsynthetic periods (~4 × 10⁷ D). On the basis of a chromosome number of 50 per nucleus and a DNA content of 1 μμg per nucleus, we are led to conclude that at pH 12 each chromosome dissociates into 300 (single-stranded) pieces of DNA. We have also compared the sedimentation profiles of single-stranded DNA from Escherichia coli, PPLO, and T2 bacteriophage. These data support the conjecture that each bacterial chromosome can be dissociated into 10 or 12 single-stranded pieces of DNA. Dissociation of DNA into multiple pieces under our experimental conditions is best interpreted in terms of interruptions in the continuity of the DNA either by naturally occurring gaps or at alkali-labile bonds.     

七氟醚联合骶管阻滞麻醉对小儿疝气手术的麻醉效果分析

目的:观察七氟醚联合骶管阻滞麻醉对小儿疝气手术的麻醉效果。方法:选取80例行腹股沟疝气手术患儿,按随机数字表法分为两组,对照组(39例)静脉注射氯胺酮,观察组(41例)先吸入8%七氟醚,然后进行骶管阻滞麻醉,通过观察并记录两组患儿生命体征、麻醉诱导时间、苏醒时间、手术麻醉时间、苏醒期躁动评分(Pediatric anesthesia emergence delirium,PAED)和麻醉诱导期合作量表(Induction Compliance Checklist,ICC)及麻醉期间不良反应情况,评价七氟醚联合骶管阻滞麻醉对小儿疝气手术的麻醉效果。结果:两组切皮后T1、T2时心率(HR)、平均动脉压(MAP)水平均高于T0时的值(P0.05),两组切皮后T1、T2时组间HR、MAP水平相比,无统计学差异(P0.05)。两组切皮后T3时HR、MAP水平基本恢复到T0时的水平。两组切皮前后4个时间点的血氧饱和度(Sp O2)相比,无统计学差异(P0.05)。观察组患儿麻醉诱导时间,苏醒时间均明显短于对照组患儿(P0.05),两组术中麻醉持续时间相比,无统计学差异(P0.05),均能达到期望麻醉时间,观察组患儿PAED评分和ICC评分均低于对照组患儿(P0.05),不良反应组间比较无统计学差异(P0.05)。结论:七氟醚联合骶管阻滞麻醉对小儿疝气手术具有良好的麻醉效果,麻醉诱导快,苏醒快,小儿配合度高,术后躁动少,值得临床推广使用。     

Antiviral activity of green tea and black tea polyphenols in prophylaxis and treatment of COVID-19: A review

BackgroundThe rapid spread of novel coronavirus called SARS-CoV-2 or nCoV has caused countries all over the world to impose lockdowns and undertake stringent preventive measures. This new positive-sense single-stranded RNA strain of coronavirus spreads through droplets of saliva and nasal discharge.PurposeUS FDA has authorized the emergency use of Remdesivir looking at the increasing number of cases of COVID-19, however there is still no drug approved to treat COVID-19. An alternative way of treatment could be the use of naturally derived molecules with known antiviral properties.MethodWe reviewed the antiviral activities of two polyphenols derived from tea, epigallocatechin-3-gallate (EGCG) from green tea and theaflavins from black tea. Both green tea and black tea polyphenols have been reported to exhibit antiviral activities against various viruses, especially positive-sense single-stranded RNA viruses.ResultsRecent studies have revealed the possible binding sites present on SARS-CoV-2 and studied their interactions with tea polyphenols. EGCG and theaflavins, especially theaflavin-3,3′-digallate (TF3) have shown a significant interaction with the receptors under consideration in this review. Some docking studies further emphasize on the activity of these polyphenols against COVID-19.ConclusionThis review summarizes the available reports and evidences which support the use of tea polyphenols as potential candidates in prophylaxis and treatment of COVID-19.     

Ribonuclease T1 cleaves RNA after guanosines within single-stranded gaps of any length

RNA-oligonucleotides with defined single-stranded stretches were designed to investigate the minimal requirements of a ribonuclease T1 substrate. It could be shown, that RNase T1 cleaves single-stranded RNA after a unique guanosine flanked by two double-stranded areas. However, the turnover of such a G-gap is significantly lower than that of a gap of two, three or four nucleotides.     

Preparation and Properties of a New Type of Acyclic,Achiral Nucleoside Analogue

Abstract

Preparation of the nucleoside analogues 1 and incorporation of 1, B = T, in deoxyribooligonucleotides by the phosphoramidite method is described. A two-step deprotection procedure was developed to reduce cleavage of the modified allylic unit. The binding properties of the modified oligonucleotides towards complementary DNA and RNA has been evaluated by T_m measurements showing a ΔT_m of ?2 to ?6.5°C per modification. An oligonucleotide with two modifications at the 3′-end showed considerable resistance towards cleavage by a 3′-exonuclease. No antiviral activity against HIV-1 or HSV-1 was found for 1, B = G or T, or for any of the trihydroxy derivatives 5.     

喉上神经阻滞复合瑞芬太尼和右美托咪定用于经皮气管切开术的临床效果

目的:探讨喉上神经阻滞复合瑞芬太尼和右美托咪定应用于经皮气管切开术(PT)的临床效果。方法:将60例因呼吸困难行PT的患者随机分为两组。所有患者均喉上神经阻滞,对照组(30例)采用丙泊酚复合瑞芬太尼,实验组(30例)采用右美托咪定复合瑞芬太尼。观察并比较两组患者术前(T1)、麻醉药物注射结束后(T2)、气管切开置入套管时(T3)、手术结束时(T4)收缩压(SBP)、舒张压(DBP)、心率(HR)、血氧饱和度(SpO_2)及平均动脉压(MAP)、警觉/镇静(OAA/S)评分的变化及术中并发症的发生情况。结果:对照组T3、T4时刻SBP、DBP、HR、MAP均较T1时明显升高,且明显高于实验组同时点(P0.05),而实验组T2、T3、T4时SBP、DBP、HR、MAP与T1时刻比较差异无明显统计学意义(P0.05)。实验组术中呛咳、呼吸抑制的发生率显著低于对照组(P0.05)。两组T2～T4时刻OAA/S评分均明显低于T1时刻,且实验组OAA/S评分均明显低于对照组同时刻(P0.05)。结论:喉上神经阻滞复合右美托咪啶和瑞舒芬太尼应用于PT中可维持血流动力学的稳定,减少应激反应,降低术中并发症的发生率。     

Macrocyclic zinc(II) complexes for selective recognition of nucleobases in single- and double-stranded polynucleotides

 As an extension of our earlier discoveries that Zn^II-cyclen complex (1) (cyclen=1,4,7,10-tetraazacyclododecane) and Zn^II-acridine-pendant cyclen complex Zn^II-N-(9-acridin)ylmethyl-cyclen (3) are the first compounds to selectively recognize thymidine and uridine nucleosides in aqueous solution at physiological pH, the interaction of these and a relevant complex, bis(Zn^II-cyclen) (7), has been investigated with a series of polynucleotides, single-stranded poly(U) and poly(G), and double-stranded poly(A)·poly(U), poly(dA)·poly(dT) and poly(dG)·poly(dC). These Zn^II-cyclen complexes interact with the imide-containing nucleobases in the single-stranded poly(U), unperturbed by the presence of the anionic phosphodiester backbone. The affinity constant of 1 for each N(3)-deprotonated uracil base in poly(U) is determined to be log K= 5.1 by a kinetic measurement, which is almost the same as log K=5.2 for the interaction of 1 with uridine. Thus, they disrupt the A-U (or A-T) hydrogen bonds to unzip the duplex of poly(A)·poly(U) or poly(dA)·poly(dT), as demonstrated by lowering of the melting temperatures (T _m) of poly(A)·poly(U) and poly(dA)·poly(dT) in 5 mM Tris-HCl buffer (pH 7.6, 10 mM NaCl) with increase in their concentrations. The order of the denaturing efficiency is well correlated with that of the 1 : 1 affinity constants for each complex with uracil or thymine;7>3>1. The comparison of circular dichroism (CD) spectra for poly(A)·poly(U), poly(A), and poly(U) in the presence of 3 has revealed a structural change from poly(A)·poly(U) to two single strands, poly(A) and poly(U), caused by 3 binding exclusively to uracils in poly(U). On the other hand, the acridine-pendant cyclen complex 3, which earlier was found to associate with guanine by the Zn^II coordinating with guanine N(7), in addition to the π-π stacking, interacts with guanine in the double helix of poly(dG)·poly(dC) from outside and stabilized the double-stranded structure, as indicated by higher T _m. Received: 31 December 1997 / Accepted: 23 February 1998     

T cells redirected to interleukin-13Rα2 with interleukin-13 mutein–chimeric antigen receptors have anti-glioma activity but also recognize interleukin-13Rα1

Background aimsOutcomes for patients with glioblastoma remain poor despite aggressive multimodal therapy. Immunotherapy with genetically modified T cells expressing chimeric antigen receptors (CARs) targeting interleukin (IL)13Rα2, human epidermal growth factor receptor 2, epidermal growth factor variant III or erythropoietin-producing hepatocellular carcinoma A2 has shown promise for the treatment of glioma in preclinical models. On the basis of IL13Rα2 immunotoxins that contain IL13 molecules with one or two amino acid substitutions (IL13 muteins) to confer specificity to IL13Rα2, investigators have constructed CARS with IL13 muteins as antigen-binding domains. Whereas the specificity of IL13 muteins in the context of immunotoxins is well characterized, limited information is available for CAR T cells.MethodsWe constructed four second-generation CARs with IL13 muteins with one or two amino acid substitutions, and evaluated the effector function of IL13-mutein CAR T cells in vitro and in vivo.ResultsT cells expressing all four CARs recognized IL13Rα1 or IL13Rα2 recombinant protein in contrast to control protein (IL4R) as judged by interferon-γ production. IL13 protein produced significantly more IL2, indicating that IL13 mutein–CAR T cells have a higher affinity to IL13Rα2 than to IL13Rα1. In cytotoxicity assays, CAR T cells killed IL13Rα1- and/or IL13Rα2-positive cells in contrast to IL13Rα1- and IL13Rα2-negative controls. Although we observed no significant differences between IL13 mutein–CAR T cells in vitro, only T cells expressing IL13 mutein–CARs with an E13K amino acid substitution had anti-tumor activity in vivo that resulted in a survival advantage of treated animals.ConclusionsOur study highlights that the specificity/avidity of ligands is context-dependent and that evaluating CAR T cells in preclinical animal model is critical to assess their potential benefit.     

五灵胶囊联合富马酸丙酚替诺福韦片对慢性乙型肝炎患者氧化应激、CD4+CD25+调节性T细胞和血清MMP-1、MMP-2、TIMP-1的影响

摘要 目的：探讨五灵胶囊联合富马酸丙酚替诺福韦片对慢性乙型肝炎（CHB）患者氧化应激、CD4⁺CD25⁺调节性T细胞和血清基质金属蛋白酶-1（MMP-1）、基质金属蛋白酶-2（MMP-2）、基质金属蛋白酶组织抑制因子-1（TIMP-1）的影响。方法：纳入苏州大学附属传染病医院2021年6月~2022年12月期间收治的CHB患者122例,采用随机数字表法分为对照组（n=61,富马酸丙酚替诺福韦片）和研究组（n=61,五灵胶囊联合富马酸丙酚替诺福韦片）。对比两组疗效、氧化应激指标、CD4⁺CD25⁺调节性T细胞、肝功能指标[总胆红素（TBIL）、谷丙转氨酶（ALT）、谷氨酰转肽酶（GGT）]、血清MMP-1、MMP-2、TIMP-1水平和不良反应发生情况。结果：研究组的临床总有效率高于对照组（P<0.05）。两组治疗后丙二醛（MDA）下降,且研究组低于对照组同时间点;超氧化物歧化酶（SOD）升高,且研究组高于对照组同时间点（P<0.05）。两组治疗后CD4⁺CD25⁺调节性T细胞下降,且研究组低于对照组同时间点（P<0.05）。两组治疗后MMP-1、MMP-2、TIMP-1下降,且研究组低于对照组同时间点（P<0.05）。两组治疗后TBIL、ALT、GGT下降,且研究组低于对照组同时间点（P<0.05）。两组不良反应总发生率组间对比未见差异（P>0.05）。结论：五灵胶囊联合富马酸丙酚替诺福韦片治疗CHB患者,可有效减轻机体氧化应激,调节CD4⁺CD25⁺调节性T细胞和血清MMP-1、MMP-2、TIMP-1水平。