Comparative Studies of Duplex and Triplex Formation of 2′-5′ and 3′-5′ Linked Oligoribonucleotides

Abstract

We have studied double and triple helix formation between 2′–5′ or 3–5′ linked oligoriboadenylates and oligoribouridylates with chain length 7 or 10 by CD spectrometry. The complex formation depends on the type of linkage of oligoribonucleotides, chain length, concentration and molar ratio of the strands, temperature and the cationic concentration. Mixture of any linkage isomers of oligo(rA) and oligo(rU) in 1:1 molar ratio form duplex at 0.1 M NaCl. The duplex stability largely depends on the type of the linkages and is in the following order; [35′] oligo(rA)·[3′-5′] oligo(rU) > [2′-5′] oligo(rA)'[3′-5′] oligo(rU) > [3′-5′] oligo(rA)·[2′-5′] oligo(rU) > [2–5′] oligo(rA)*[2′-5′] oligo(rU). The higher cationic concentrations, 0.5 M MgCl₂, stabilize the complex and either duplex or triplex is formed depending on the input strand ratio and the type of linkage. Thermodynamic parameters, DH and DS, for the complex formation between linkage isomers of oligo(rA) and oligo(rU) showed a linear relationship indicating an enthalpy-entropy compensation phenomena. The duplex and triplex composed of [2′-5′] oligo(rA) and [2′-5′] oligo(rU) exhibit different CD spectra compared to those of any others containing 3–5′ linkage, suggesting that the fully 2–5′ duplex and triplex may possess a unique conformation. We describe prebiological significance of the linkage isomers of RNA and selection of the 3–5′ linkage against 2′-5 linkage.     

Conjugates of Oligo(2′-O-Methylribonucleotides) with Minor Groove Binders as New Sequence-Specific Agents Recognizing Both Grooves of Double-Stranded DNA

Abstract

Design, synthesis and physico-chemical studies of new pyrimidine oligo(2′-O-methylribonucleotide) conjugates with one or two oligo(pyrrolecarboxamide) minor groove binders (MGB) are described.     

TWO EFFICIENT POLYMERIC CHEMICAL PLATFORMS FOR OLIGONUCLEOTIDE MICROARRAY PREPARATION

ABSTRACT

In this report we describe two robust procedures for oligonucleotide microarray preparation based on polymeric coatings. The proposed chemical approaches include: 1) a glass functionalisation step with appropriate silanes (γ-aminopropyltriethoxysilane-APTES or 3-glycid-oxypropyltrimethoxysilane-GOPS), 2) a coating step using polymers (poly-L-Lysine or poly(acrylic acid-co-acrylamide) copolymer) covalently bound to the modified glass and 3) a surface activation step to allow for the attachment of amino-modified oligonucleotides. Results obtained using these chemistries in oligo microarray preparation show: 1) an overall high loading capacity and availability to hybridisation against targets, 2) a good uniformity, 3) resistance to consecutive probing/stripping cycles, 4) stability to thermal cycles, 5) effectiveness in hybridisation-mediated mutation detection procedures and 6) the possibility to perform enzymatic reactions, such as ligation.     

Delivery of shRNA using gold nanoparticle-DNA oligonucleotide conjugates as a universal carrier

The efficient delivery of nucleic acids into mammalian cells is a central aspect of research involving cell biology and medical applications, including the clinical treatment of genetic disorders. We report an efficient small hairpin RNA (shRNA) delivery system that utilizes a single species of gold nanoparticle-DNA oligonucleotide conjugate (AuNP-DNA oligo) as a universal carrier. In vitro synthesized shRNA that is specific to the p53 gene was efficiently delivered into HEK293 and HeLa human cell lines using an AuNP-DNA oligo. The delivery resulted in an 80-90% knockdown of p53 expression. The same AuNP-DNA oligo was also efficient for the delivery of another shRNA, which is specific to the Mcl-1 gene, as well as the repression of MCL-1 expression. The knockdown efficiency of shRNA that was delivered using an AuNP-DNA oligo was comparable with that of a liposome-based shRNA delivery method. Our results offer an alternate delivery system for shRNA that can be used on any gene of interest.     

应用CRISPR/Cas9系统构建MTHFD1基因敲除的HEK-293细胞系

目的:利用成簇的、规律间隔的短回文重复序列/Cas9核酸酶(CRISPR/Cas9)基因编辑技术构建亚甲基四氢叶酸脱氢酶1(methylenetetrahydrofolate dehydrogenase 1, MTHFD1))基因敲除人胚肾(HEK-293)稳定细胞系。方法:利用在线软件筛选出评分最高的3条针对MTHFD1基因的单向导RNA (sg RNA),然后合成sg RNA序列并将其插入到含有GFP标签的质粒中;重组质粒转染HEK-293细胞后通过流式细胞仪分选出已被转入sg RNA的单细胞,通过测序确认单克隆细胞系中MTHFD1的DNA序列突变状态;最后应用实时荧光定量多聚核苷酸链式反应(real-time quantitative Polymerase Chain Reaction, RT-q PCR)和蛋白质印迹(Western blot)方法检测单克隆细胞中MTHFD1的m RNA和蛋白表达水平。结果:重组载体中含有正确的sg RNA序列;测序结果显示该细胞系中MTHFD1基因发生了单个碱基插入突变和6个碱基的缺失突变;RT-qPCR结果显示单克隆细胞系中MTHFD1在m RNA水平显著降低;Western blot检测成功构建MTHFD1蛋白缺失的HEK-293细胞。结论:本研究利用CRISPR/Cas9技术成功构建的MTHFD1敲除HEK-293细胞系。     

The binding of exogenous DNA fragments to bovine spermatozoa

Abstract

The ability of mature, freeze‐thawed bovine sperm to bind exogenous end‐labelled or oligo‐labelled λ Hind III DNA restriction fragments was examined. Following 30 min. incubation of bovine sperm with P³² end‐labelled λ Hind III DNA and five washes with medium, approximately 5.8 ng DNA were bound to 10⁷ sperm. Agarose gel autoradiography revealed that all of the λ Hind III DNA bands were present following sperm washes except for the smaller 0.5 Kb and 0.125 Kb bands. Incubation of sperm with ³H oligo‐labelled λ Hind III DNA gave a much higher level of binding (138 ng/10⁷ sperm) than that found with end‐labelled DNA. This binding was entirely eliminated by DNase I. The separation of live and dead sperm fractions on Percoll gradients revealed that more oligo‐labelled λ Hind III DNA was found to be associated with the dead sperm fraction (31.2 ng/10⁷ sperm) rather than the live sperm fraction (2.7 ng/10⁷ sperm). Analysis of supravital stained, light microscopic autoradiographs confirmed that oligo‐labelled λ Hind III DNA bound to dead sperm in the post‐acrosomal region of the sperm head although other minor distribution patterns were observed.     

The spike protein of SARS-CoV-2 induces heme oxygenase-1: Pathophysiologic implications

BackgroundAcute kidney injury (AKI) is both a consequence and determinant of outcomes in COVID-19. The kidney is one of the major organs infected by the causative virus, SARS-CoV-2. Viral entry into cells requires the viral spike protein, and both the virus and its spike protein appear in the urine of COVID-19 patients with AKI. We examined the effects of transfecting the viral spike protein of SARS-CoV-2 in kidney cell lines.MethodsHEK293, HEK293-ACE2⁺ (stably overexpressing ACE2), and Vero E6 cells having endogenous ACE2 were transfected with SARS-CoV-2 spike or control plasmid. Assessment of gene and protein expression, and syncytia formation was performed, and the effects of quercetin on syncytia formation examined.FindingsSpike transfection in HEK293-ACE2⁺ cells caused syncytia formation, cellular sloughing, and focal denudation of the cell monolayer; transfection in Vero E6 cells also caused syncytia formation. Spike expression upregulated potentially nephrotoxic genes (TNF-α, MCP-1, and ICAM1). Spike upregulated the cytoprotective gene HO-1 and relevant signaling pathways (p-Akt, p-STAT3, and p-p38). Quercetin, an HO-1 inducer, reduced syncytia formation and spike protein expression.InterpretationThe major conclusions of the study are: 1) Spike protein expression in kidney cells provides a relevant model for the study of maladaptive and adaptive responses germane to AKI in COVID-19; 2) such spike protein expression upregulates HO-1; and 3) quercetin, an HO-1 inducer, may provide a clinically relevant/feasible protective strategy in AKI occurring in the setting of COVID-19.FundingR01-DK119167 (KAN), R01-AI100911 (JPG), P30-DK079337; R01-DK059600 (AA).     

Tips for improving the quality and quantity of the extracted DNA from exhaled breath condensate samples

Abstract

There is a growing interest in the tracking of genetic and epigenetic alterations in exhaled breath condensate (EBC) samples. The effects of different procedures on the quality and quantity of DNA in EBC were studied. The results demonstrated that sodium acetate precipitation and oligo (dT) improved the quality of the extracted DNA significantly (p?<?0.01). Also, sodium acetate precipitation, using oligo (dT), incubation at 70?°C and SDS treatment increased the quantity of DNA significantly (p?<?0.01). These results showed the advantages of the chemical and physical manipulations for improving the quality and quantity of the extracted DNA from EBC samples.     

Effective solvent systems for separation and an improved detection method for amino acids by paper chromatoghraphy

Binding of poly(A)-containing RNP to oligo(dT)-cellulose has been investigated as a function of mono- and divalent ion concentration. 80–90% binding was obtained either in high (500 mM) or in moderate NaCl concentrations in the presence of 5 mM MgCl₂. At 40 mM NaCl and 5 mM MgCl₂ poly(A)⁺-RNP exhibit approximately t he same stability as poly(A)⁺-RNA in binding to oligo(dT)-cellulose with a melting temperature of 41 and 45°C, respectively, indicating that the protein moeity has no effect on the ribonucleoprotein binding in these conditions. Differences were observed int he elution of poly(A)⁺-RNA and poly(A)⁺-RNP from oligo(dT)-cellulose in buffer without salts. Poly(A)⁺-RNA was completely removed at 4°C whereas the melting temperature of poly(A)⁺-RNP was only decreased to 34°C. The isolation of poly(A)⁺-RNP by thermal elution from oligo(dT)-cellulose is described.     

Modification of Oligo (Poly) Nucleotide Phosphomonoester Groups in Aqueous Solutions

Abstract

Selective modification of oligo (poly) nucleotide phosphomonoester groups in an aqueous medium by N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide in the presence of various nucleophilic agents has been investigated. Optimal conditions of the modification by amino- and hydroxycompounds have been found. Based on these studies a general efficient method for preparation of oligo (poly) nucleotide phosphoamidates and phosphodiesters in an aqueous solution has been developed. The method allows to prepare both oligodeoxyribonucleotide derivatives at 3′- and 5′-terminal phosphate groups and oligoribonucleotide derivatives at 5′-terminal phosphate groups with 80–100% yields.     

Use of antisense oligodeoxynucleotide to determine δ-opioid receptor involvement in [d-Ala2]deltorphin II-induced locomotor hyperactivity

Intracerebroventricularly (i.c.v.)-administered [d-Ala²]deltorphin II (20 μg) produced a marked locomotor hyperactivity in male ICR mice. The locomotor hyperactivity induced in response to i.c.v. [d-Ala²]deltorphin II (20 μg) was suppressed by pretreatment with naltriben (NTB, 10 μg) but not 7-benzylidene naltrexone (BNTX, 1 μg) and d-Phe-Cys-Tyr-d-Try-Orn-Thr-Phe-Thr-NH₂ (CTOP, 100 ng). The influence of antisense oligodeoxynucleotide to δ-opioid receptor mRNA (δ-AS oligo) or a mismatch oligodeoxynucleotide (MM oligo) on the locomotor hyperactivity induced by [d-Ala²]deltorphin II was determined. Groups of mice pretreated i.c.v. with δ-AS oligo (1 μg), MM oligo (1 μg) or saline (4 μl) once a day for 3 days, were injected i.c.v. [d-Ala²]deltorphin II (10 or 20 μg) and the locomotor response to [d-Ala²]deltorphin II was measured. The locomotor hyperactivity of i.c.v. [d-Ala²]deltorphin II (10 or 20 μg) were significantly suppressed by i.c.v. pretreatment with δ-AS oligo but not MM oligo. The present results indicate that pretreatment with δ-AS oligo suppresses mouse locomotor hyperactivity produced by stimulation of δ₂-opioid receptors in the brain.     

Theory of oligonucleotide stabilization. I. The effect of single-strand stacking

Certain theoretical difficulties present in the analysis of thermal transition properties of short complementary double-stranded RNA oligomers can be resolved in part by introducing the stability of the component single-stranded systems explicitly into the model. The stability constant S of the usual theories is redefined so as to contain double-stranded pairing (τt) and single-stranded stacking (ρ) contributions, and we analyze the statistics of two experimental systems—acid oligo(A) and oligo (A_n·U_n) dimers—to exhibit the underlying stability parameters. We present a fitting procedure to extract values of the heats and entropies of the separated components when the required single-strand data is unreliable or not available. The theory leads to length dependent heats and entropies for short single strands in a natural way, and permits a more accurate assessment of the contribution of partially bonded states in thermal transitions than has previously been possible.     

Construction of Europium (Eu3+)-Labelled Oligo DNA Hybridization Probes

Abstract

Three different oligo DNA probes were synthesized and their value as hybridization probes was tested.     

Treatment with Antisense Oligodeoxynucleotide to a Conserved Sequence of Opioid Receptors Inhibits Antinociceptive Effects of Delta Subtype Selective Ligands

Abstract

Previous work has suggested the existence of subtypes of the delta opioid receptor (DOR) which have been termed δ₁ and δ₂. [D-Ala², Glu⁴]deltorphin has been suggested to selectively elicit antinociception via the δ₂ receptor while [D-Pen², D-Pen⁵]enkephalin (DPDPE) is thought to act via the δ₁ receptor. Treatment with an antisense oligodeoxynucleotide (oligo) directed towards the N-terminal portion of the cloned DOR has been demonstrated to selectively inhibit the antinociceptive actions of [D-Ala², Glu⁴]deltorphin, but not of DPDPE, suggesting that the cloned DOR corresponds to that pharmacologically defined as δ₂. Here, an antisense oligo (or a mismatch sequence) was designed to target a conserved region of the cloned μ δ and opioid receptor. These oligos were employed in order to determine whether the antinociceptive effects of [DAla², Glu⁴]deltorphin, as well as DPDPE, could be inhibited. The data indicate that the antinociceptive actions of both ligands were inhibited by treatment with this antisense, but not with the mismatch oligo. Taken together, the results of the treatments with oligos directed towards the N-terminal portion of the cloned DOR and with that directed to the conserved region of the opioid receptors suggest that (a) DPDPE effects are mediated by a subtype of the DOR which shares a domain common to the cloned opioid receptors, and (b) the N-terminal region differs between these putative DOR subtypes.     

HPLC and Synthesis Strategy in Nucleoside and (Oligo)Nucleotide Chemistry

Abstract

A judicious use of HPLC allows to simplify the synthetic approach of an (oligo)nucleotide. As an example, is reported a preparation of an antiviral (3′-5′)dinucleotide with simultaneous isolation of its (3′-3′) isomer.     

CRISPR/Cas9介导的USP30基因敲除细胞系的建立及其对塞内卡病毒增殖的影响

【目的】利用规律成簇的间隔短回文重复序列/Cas9核酸酶（clustered regularly interspaced short palindromic repeats/Cas9 nuclease,CRISPR/Cas9）技术建立USP30基因敲除的人胚胎肾细胞（human embryonic kidney 293T cells,HEK-293T）细胞系,为开展宿主泛素特异性蛋白酶30（ubiquitin-specific protease 30,USP30）蛋白的功能研究建立了细胞模型;同时,初步探究USP30蛋白在病毒感染过程中的作用。【方法】根据Ensemble数据库查询USP30基因序列,定位USP30在基因组中不同转录本重叠区的第一个外显子段,设计并合成2对引导RNA （single guide RNAs,sgRNA）,分别构建在pX459载体中;将pX459-USP30-sgRNA质粒转染HEK-293T细胞,并用嘌呤霉素处理,筛选出转染阳性的细胞,然后通过有限稀释法筛选单克隆细胞,通过Western blotting及测序检测USP30基因的敲除。通过Western blotting及实时荧光定量PCR分析比较塞内卡病毒（Senecavirus A,SVA）在野生型和USP30基因敲除HEK-293T细胞中的复制差异。【结果】Western blotting及测序证实USP30基因敲除单克隆细胞系构建成功。进一步实验发现,SVA在USP30基因敲除细胞中的复制水平显著低于野生型细胞。【结论】成功构建USP30基因敲除的HEK-293T细胞系,首次证明USP30对SVA的复制具有促进作用,为进一步揭示USP30相关免疫反应和SVA感染过程的作用机制提供了良好的细胞模型,也为开展宿主USP30蛋白调控病毒复制的机制研究提供了关键工具和一定的理论依据。     

Impaired trafficking and intracellular retention of mutant kidney anion exchanger 1 proteins (G701D and A858D) associated with distal renal tubular acidosis

Abstract

Novel compound heterozygous mutations, G701D, a recessive mutation, and A858D, a mild dominant mutation, of human solute carrier family 4, anion exchanger, member 1 (SLC4A1) were identified in two pediatric patients with distal renal tubular acidosis (dRTA). To examine the interaction, trafficking, and cellular localization of the wild-type and two mutant kidney AE1 (kAE1) proteins, we expressed the proteins alone or together in human embryonic kidney (HEK) 293T and Madin-Darby canine kidney (MDCK) epithelial cells. In individual expressions, wild-type kAE1 was localized at the cell surface of HEK 293T and the basolateral membrane of MDCK cells. In contrast, kAE1 G701D was mainly retained intracellularly, while kAE1 A858D was observed intracellularly and at the cell surface. In co-expression experiments, wild-type kAE1 formed heterodimers with kAE1 G701D and kAE1 A858D, and promoted the cell surface expression of the mutant proteins. The co-expressed kAE1 G701D and A858D could also form heterodimers but showed predominant intracellular retention in HEK 293T and MDCK cells. Thus impaired trafficking of the kAE1 G701D and A858D mutants would lead to a profound decrease in functional kAE1 at the basolateral membrane of α-intercalated cells in the distal nephron of the patients with dRTA.