Inhibition of Influenza Virus Replication by Phosphorothioate and Liposomally Endocapsulated Oligonucleotides

Abstract

We have demonstrated that antisense phosphorothioate oligonucleotides (S-ODNs) inhibit influenza virus A replication in MDCK cells. Phosphorothioate and liposomally encapsulated oligonucleotides with two target sites (PB1 and PB2) were synthesized and tested for virus-induced cytopathogenicity effects by a MTT assay using MDCK cells. The liposomally encapsulated S-ODNs complementary to the sites of the PB2-AUG initiation codon showed highly inhibitory effects. On the other hand, the inhibitory effect of the liposomally encapsulated S-ODNs targeted to PB1 was considerably decreased in comparison with the PB2 target sites. The liposomally encapsulated oligonucleotides exhibited higher inhibitory activity than the free oligonucleotides. The activities of the modified oligonucleotides are effectively enhanced by using the liposomal carrier.     

Dynamic Bis-Intercalation of a Homodimeric Thiazole Orange Dye in DNA: Evidence of Intercalator Creeping

Abstract

We have used one and two dimensional exchange ¹H NMR spectroscopy to characterize the dynamics of the binding of a homodimeric thiazole orange dye, 1,1′-(4,4,8,8-tetramethyl-4,8-diaza-undecamethylene)-bis-4-(3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)-quinolinium tetraiodide (TOTO), to double stranded DNA (dsDNA). The double stranded oligonucleotides used were d-(CGCTAGCG)₂ ( 1 ) and d(CGCTAGCTAGCG)₂ ( 2 ). TOTO binds preferentially to the (5′-CTAG-3′)₂ sites and forms mixtures of 1:1 and 1:2 dsDNA-TOTO complexes with 2 in ratios dependent on the relative amount of TOTO and the oligonucleotide in the sample. The dynamic exchange between preferential binding sites in the case of a 2:1 1 -TOTO mixture is an intermolecular exchange process between two binding sites on different oligonucleotides. In the case of the 1:1 2 -TOTO complex an intramolecular exchange process occur between two different binding sites on the same strand. Both processes were studied. The results demonstrate the ability of TOTO to migrate along a dsDNA strand in an intramolecular exchange process. The migration process (“creeping”) along the DNA strand is 6 times faster than the rate of intermolecular exchange between sites in two different oligonucleotides.     

The Concept of ‘Minimally Modified’ Antisense Oligonucleotides for Specific Inhibition of Gene Expression

Abstract

The design and use of minimally modified oligonucleotides for specific inhibition of gene expression is discussed. The “minimal” protection strategy is a combination of the end-capping technique and the protection of internal pyrimidine positions which are the major sites of endonuclease degradation. By reducing the number of phosphorothioate modifications needed to make the oligonucleotide resistant to nuclease degradation, non-sequence-specific effects, which are frequently observed with uniformly phosphorothioate-modified oligonucleotides, can be reduced.     

Synthesis of Circular Oligodeoxynucleotide Conjugates VIA Transient Abasic Sites

Abstract

New chemical ligation or cyclisation reactions, using high reactivity of abasic sites with amines, are reported for the synthesis of oligonucleotide clamps and singlestranded circular oligonucleotides. Thermal denaturation experiments show that these molecules display very high binding affinities for complementary DNA oligomer by forming triple-helical complexes.     

In Vitro and In Vivo Anti-influenza A Virus Activity of Antisense Oligonucleotides

Abstract

We have demonstrated that antisense phosphorothioate oligonucleotides (S-ODNs) inhibit influenza virus A replication in MDCK cells. The liposomally encapsulated and the free antisense phosphorothioate oligonucleotides with four target sites (PB1, PB2, PA, and NP) were tested for their abilities to inhibit virus-induced cytopathogenic effects by a MTT assay using MDCK cells. The liposomally encapsulated S-ODN complementary to the sites of the PB2-AUG initiation codon showed highly inhibitory effects. Therefore, the antiviral effects of S-ODN-PB2-AUG and PA-AUG were examined in a mouse model of influenza virus A infection. PB2-AUG oligomer treated i.v. significantly prolonged the mean survival time in day (MDS) and increased the survival rates with does dependent manner.     

A Systematic Study of Patterns of Hydration in Nucleic Acids:(I) Guanine and Cytosine

Abstract

The hydration sites of guanine and cytosine are defined by examination of the crystal structures of bases, nucleosides, nucleotides, and three dinucleoside phosphate salts. The patterns of hydration for two guanine and cytosine containing oligonucleotides are then predicted. The relationship between these structural motifs and thermodynamic parameters is discussed.     

基于荧光染料Cy5.5标记的引物延伸法鉴定细菌RNA剪切加工位点

【背景】传统引物延伸法常与放射性标记结合使用,但由于放射性元素半衰期短、危害人体健康及严格的操作要求等限制了其在一般实验室的广泛使用。因此,开发新型非放射性引物延伸法成为当前研究的热点。【目的】建立非放射性的引物延伸法,并利用该方法实现对细菌RNA剪切加工位点的鉴定。【方法】将包含RNA剪切位点的序列克隆至双荧光报告系统,然后利用荧光染料Cy5.5标记的特异性靶向mcherry寡核苷酸引物进行延伸,并辅以Northern blotting、RT-qPCR等技术,确定RNA剪切加工的精确位点。【结果】鉴定了来自解纤维梭菌cip-cel mRNA中的2个剪切加工位点均位于颈环结构下游的单链区域,且在剪切位点附近未发现保守序列。【结论】基于Cy5.5标记的引物延伸法能够精确鉴定RNA剪切加工位点,且与传统的放射性引物延伸法相比,该方法具有更高的安全性和更快的检测速度,能够满足一般实验室的实验要求。     

Elucidation of the Hydrolytical Properties of α-Hydroxybenzylphosphonates as a New Potential Pro-Oligonucleotide Concept

Abstract

The synthesis of Fpmp-protected α-hydroxybenzylphosphonate modified oligonucleotides as potential new pro-oligonucleotides is described. The proposed hydrolytic pathways of the oligonucleotides were studied using two dimers 2 and 4 and the tetramer 6 containing one α-hydroxybenzyl modification as model compounds.     

Novel Hoogsteen-like Bases for Recognition of the C-G Base Pair by DNA Triplex Formation

Effective sequence-specific recognition of duplex DNA is possible by triplex formation with natural oligonucleotides via Hoogsteen H-bonding. However, triplex formation is in practice limited to pyrimidine oligonucleotides that bind duplex A-T or G-C base pair DNA sequences specifically at homopurine sites in the major groove as T·A-T and C⁺ ·G-C triplets. Here we report the successful modelling of novel unnatural nucleosides that recognize the C-G DNA base pair by Hoogsteen-like major groove interaction. These novel Hoogsteen nucleotides are examined within model A-type and B-type conformation triplex structures since the DNA triplex can be considered to incorporate A-type and/or B-type configurational properties. Using the same deoxyribose-phosphodiester and base-deoxyribose dihedral angle configuration, a triplet comprised of a C-G base pair and the novel Hoogsteen nucleotide, Y2, replaces the central T·A-T triplet in the triplex. The presence of any structural or energetic perturbations due to the central triplet in the energy-minimized triplex is assessed with respect to the unmodified energy minimized (T·A-T)₁₁ starting structures. Incorporation of this novel triplet into both A-type and B-type natural triplex structures provokes minimal change in the configuration of the central and adjacent triplets.     

Carbohydrate Modifications in Antisense Oligonucleotide Therapy: New Kids on the Block

Abstract

Chemical modifications to improve the efficacy of an antisense oligonucleotide are designed to increase the binding affinity to target RNA, to enhance the nuclease resistance, and to improve cellular delivery. Among the different sites available for chemical modification in a nucleoside building block, the 2′-position of the carbohydrate moiety¹ has proven to be the most valuable for various reasons: (1) 2′-modification can confer an RNA-like 3′-endo conformation to the antisense oligonucleotide. Such a preorganization for an RNA like conformation^2,3,4,5 greatly improves the binding affinity to the target RNA; (2) 2′-modification provides nuclease resistance to oligonucleotides; (3) 2′-modification provides chemical stability against potential depurination conditions pharmacology evaluations and correlation with pharmacokinetic changes are emerging from these novel chemical modifications. Analytical chemistry of modified oligonucleotides before and after biological administration of antisense oligonucleotides with techniques such as capillary gel electrophoresis (CGE) and mass spectrometry help to determine the purity as well as the in vivo fate of these complex molecules. Large-scale synthesis is becoming a tangible reality for antisense oligonucleotides. Nucleic acid chemists and biologists alike are beginning to understand the structure-biological activity in terms of basic physical-organic parameters such as the gauche effect, the charge effect and conformational constraints. Synthesis of chimeric designer oligonucleotides bringing the attractive features of different modifications to a given antisense oligonucleotide sequence to generate synergistic interactions is forthcoming³⁰. These advances along with the potential availability of complete human genome sequence information promise a bright future for the widespread use of nucleic acid based therapeutics.     

New Synthesis of 5-Carboxy-2′-deoxyuridine and Its Incorporation into Synthetic Oligonucleotides

Abstract

5-Carboxy-2′-deoxyuridine is a methyl oxidation product of thymidine. It can be formed by the menadione-mediated photosensitization of thymidine in aerated aqueous solution. Here in we present a new four-step synthesis of the 5-carboxy-2′-deoxyuridine phosphoramidite building block based on the alkaline hydrolysis of 5-trifluoromethyl-2′-deoxyuridine. The phosphoramidite derivative has been incorporated at defined sites into oligonucleotides using the solid phase synthesis approach.     

Quantitative One Step Derivatization of Oligonucleotides by a Fluorescent Label Through Abasic Site Formation

Abstract

Reaction of abasic site-containing oligonucleotides with an oxyamino fluorescent label is described. The reaction represents an efficient method to functionalize oligonucleotides at preselected positions.     

Comparison of Physicochemical and Biological Properties of (o-Carboran-1-YL)methylphosphonate and Methylphosphonate Oligonucleotides

Abstract

(o-Carboran-1-yl)methylphosphonate (CBMP) oligonucleotides demonstrate advantages in their physicochemical and biological characteristics over the corresponding methylphosphonate oligonucleotides.     

Inhibition of Tumor Necrosis Factor Alpha (TNFα) Expression and Function In Vitro by Modified Antisense Oligonucleotides

Abstract

Antisense oligonucleotides containing C-5 hexynyl/propynyl modified pyrimidines were synthesized using solid phase phosphoramidite chemistry. These modified oligonucleotides were found to have significant inhibitory activity against TNFα production in vitro.     

Biological Activities of Oligonucleotides Linked to Poly(L-Lysine)

Abstract

We have developped a method to couple oligonucleotides to poly(L-lysine). This tool has been tested with anti m-RNA synthetic oligodeoxyribonucleotides and 2′-5′(A)_n and allows oligonucleotides to enter intact cells.     

Specific Inhibition of Hepatitis C Viral Gene Expression by Non-polar (Phenylalkyl)phosphonates

Abstract

Different phenylalkyl backbone modified antisense oligonucleotides complementary to the Hepatitis C virus (HCV) RNA nucleotides 326–342 were synthesized. The lipohilic character of modified oligonucleotides was determined from RP-HPLC retention times. The inhibitory effect of these antisense oligonucleotides on HCV gene expression was analyzed in an in vitro test system.     

Synthesis and Properties of 2′-O-Methylribonucleotide Methylphosphonate Containing Chimeric Oligonucleotides

Abstract

2′-O-methylribonucleoside methylphosphonamidites are synthesized and incorporated into oligonucleotides to obtain chimeric antisense oligonucleotides. The resulting oligonucleotide binds to their target RNA/DNA sequences efficiently and stable in a medium containing bovine serum.     

Synthesis and Biophysical Studies of Modified Oligonucleotides Containing Acyclic Amino Alcohol Nucleoside Analogs

Abstract

Novel serine derivative of thymine was prepared and incorporated into oligonucleotides. These modified oligonucleotides were studied for their binding affinity with complementary DNA/RNA.     

Fluorescent Labelling of Oligodeoxyribonucleotides by the Oxyamino-Aldehyde Coupling Reaction

Abstract

We describe the reaction of oligonucleotides containing an aldehydic group at the 5′-end or inside the sequence with an oxyamino label. The reaction was found to be highly selective and represents an efficient method for derivatization of oligonucleotides.     

Synthesis and Properties of Some (2′-5′) Linked Dinucleoside Monophosphates Modified with 3′-Difluoromethylene Groups

Abstract

The title dimers were prepared to investigate conditions required for the synthesis of 3′-difluoromethylene modified oligonucleotides on solid support. As a result a new synthetic cycle was developed that enabled the solid phase synthesis of the modified oligonucleotides.