Antisense inhibitory effect: a comparison between 3'-partial and full phosphorothioate antisense oligonucleotides.

Phosphorothioate (PS) antisense oligonucleotides are currently used to inhibit many cell functions both in vivo and in vitro. However, these modified oligos provide reasonable sequence specificity only within a narrow concentration range. To overcome such a limitation we synthesized antisense oligomers, partially phosphorothioated, targeted against the human N-myc mRNA. We utilized such modified oligomers in a human neuroblastoma cell line where the N-myc gene expression was very high, and compared them to full phosphorothioate oligonucleotides. Both full PS and partial PS antisense oligos produced a maximum reduction in target mRNA after 6 h of treatment. They were able to maintain a good level of inhibition for 20 h only at high concentration. While partial PS oligos produced a dose dependent and sequence specific inhibition of N-myc mRNA, full PS molecules suffer from some disadvantages at the highest concentration used. Our results showed that partial PS molecules were capable of reducing gene expression showing a greater sequence specificity over a far broader concentration range. For this reason we conclude that partial PS antisense oligos, with respect to full PS antisense oligos, might be particularly useful for studying gene function.     

Pharmacokinetics,Tissue Distribution,and Safety of P-Ethoxy Oligonucleotides Incorporated in Liposomes

Abstract

P-ethoxy oligonucleotides (oligos) are lipophilic analogs of phospho-diesters. We have used liposomes to increase the intracellular uptake of P-ethoxy oligos, and demonstrated that liposomal P-ethoxy antisense oligos specific for Bcr-Abl, Grb2, Crkl or Bcl-2 mRNA could selectively inhibit the production of the corresponding proteins, thereby inducing growth inhibition in leukemia and lymphoma cell lines. In support of studying the effectiveness of liposomal P-ethoxy antisense oligos in animal models, we had conducted a series of studies to evaluate the pharmacokinetics, tissue distribution and safety of intravenous injection of liposomal P-ethoxy oligos in normal mice. The pharmacokinetics and tissue distribution of liposomal P-ethoxy oligos are very similar to those of other liposomal compounds. The plasma clearance rate of liposomal P-ethoxy oligos was biphasic; the t_1/2 α and t_1/2 β were approximately 6.7 min and 7 h, respectively. The highest concentrations of liposomal P-ethoxy oligos were found in spleen and liver, with a t_1/2 of approximately 48 h. When up to 180 mg of P-ethoxy oligos per kg of mice's body weight were used, the administration of liposomal P-ethoxy oligos had no adverse effects on renal and hepatic functions, or on the hematological parameters studied. No major organ pathologic changes were observed. Our studies suggested that, at the doses studied, liposomal P-ethoxy oligos could be safely used in animal studies. Since liposomal P-ethoxy oligos were found to accumulate mainly in spleen and liver, which are the major organs of leukemic and lymphoma disease manifestation, we are currently investigating the use of liposomal P-ethoxy antisense oligos in experimental leukemia and lymphoma animal models.     

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation

Antisense oligodeoxynucleotides (oligos) are widely used for functional studies of both prokaryotic and eukaryotic genes. However, the identification of effective target sites is a major issue in antisense applications. Here, we study a number of thermodynamic and structural parameters that may affect the potency of antisense inhibition. We develop a cell-free assay for rapid oligo screening. This assay is used for measuring the expression of Escherichia coli lacZ, the antisense target for experimental testing and validation. Based on a training set of 18 oligos, we found that structural accessibility predicted by local folding of the target mRNA is the most important predictor for antisense activity. This finding was further confirmed by a direct validation study. In this study, a set of 10 oligos was designed to target accessible sites, and another set of 10 oligos was selected to target inaccessible sites. Seven of the 10 oligos for accessible sites were found to be effective (>50% inhibition), but none of the oligos for inaccessible sites was effective. The difference in the antisense activity between the two sets of oligos was statistically significant. We also found that the predictability of antisense activity by target accessibility was greatly improved for oligos targeted to the regions upstream of the end of the active domain for beta-galactosidase, the protein encoded by lacZ. The combination of the structure-based antisense design and extension of the lacZ assay to include gene fusions will be applicable to high-throughput gene functional screening, and to the identification of new drug targets in pathogenic microbes. Design tools are available through the Sfold Web server at http://sfold.wadsworth.org.     

Potent growth inhibition of leukemic cells by novel ribbon-type antisense oligonucleotides to c-myb1

We studied the effects of antisense oligonucleotides (AS oligos) with a novel structure. The AS oligos were covalently closed to avoid exonuclease activities by enzymatic ligation of two identical molecules. The AS oligos of a ribbon type (RiAS oligos) consist of two loops containing multiple antisense sequences and a stem connecting the two loops. Three antisense sequences targeting different binding sites were placed in a loop that was designed to form a minimal secondary structure by itself. RiAS oligos were found to be stable because they largely preserved their structural integrity after 24 h incubation in the presence of either exonuclease III or serums. When a human promyelocytic cell line, HL-60, was treated with RiAS oligos to c-myb, c-myb expression was effectively ablated. Cell growth was inhibited by >90% determined by both the 3-[4,5-dimethythiazol-2-yl]-2,5-diphenyltetrazolium bromide assay and [(3)H]thymidine incorporation. Further, when the leukemic cell line K562 was treated with c-myb RiAS oligos, colony formation on soft agarose was reduced by 92 +/- 2%. These results suggest that RiAS oligos may be employed for developing molecular antisense drugs as well as for the functional study of a gene.     

Cloning and determination of the nucleotide sequence of the Mn-containing superoxide dismutase gene from Halobacterium halobium

A group of synthetic 17-mer oligodeoxynucleotides (oligos) was constructed to correspond to a sequence of amino acids situated near the N terminus of the manganese-containing superoxide dismutase (Mn-SOD) purified from the halophilic bacterium, Halobacterium halobium. A cosmid library of a Sau3AI partial digest of halobium DNA, cloned into the BamHI site of pHC79, was probed with the radiolabeled oligos. Cosmid DNA was purified from the clone that showed hybridization at the highest stringency. A 1.8-kb PstI fragment of this DNA which hybridized the probes was subcloned into bacteriophage M13 and transfected into Escherichia coli JM101. The entire insert containing a 600-bp sequence coding for Mn-SOD and its 5'- and 3'-flanking regions was sequenced. The derived amino acid sequence of the structural gene showed a similarity to other manganese and iron-containing SODs in normally conserved regions.     

EC_oligos: automated and whole-genome primer design for exons within one or between two genomes

SUMMARY: EC_oligos designs oligonucleotides (oligos) from exons of annotated genomic sequence information. It can automatically and rapidly select oligos that are conserved between two sets of sequence data, and can pair up oligos for use as PCR primers. It can do this on a whole-genome scale and according to user-defined criteria. AVAILABILITY: The source code, executable program and user manual are available at ftp://ftp.ebi.ac.uk/pub/software/dos/EC_oligos/.     

Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming

MOTIVATION: Both small interfering RNAs (siRNAs) and antisense oligonucleotides can selectively block gene expression. Although the two methods rely on different cellular mechanisms, these methods share the common property that not all oligonucleotides (oligos) are equally effective. That is, if mRNA target sites are picked at random, many of the antisense or siRNA oligos will not be effective. Algorithms that can reliably predict the efficacy of candidate oligos can greatly reduce the cost of knockdown experiments, but previous attempts to predict the efficacy of antisense oligos have had limited success. Machine learning has not previously been used to predict siRNA efficacy. RESULTS: We develop a genetic programming based prediction system that shows promising results on both antisense and siRNA efficacy prediction. We train and evaluate our system on a previously published database of antisense efficacies and our own database of siRNA efficacies collected from the literature. The best models gave an overall correlation between predicted and observed efficacy of 0.46 on both antisense and siRNA data. As a comparison, the best correlations of support vector machine classifiers trained on the same data were 0.40 and 0.30, respectively.     

Precise discrimination among homologous sequences by DNA probe column chromatography.

Synthesized oligo probes were immobilized to a HPLC gel in high concentrations (30-40 O.D. per gram dry gel), packed in a column (2mm x 10cm) and incorporated into a conventional HPLC system. The system was applied to the discrimination among homologous sequences. Two probes different in sequence and length (16mer and 24mer) were investigated under isothermal and isocratic conditions. For each probe, 4 oligos of similar sequences, one perfectly matched to the probe and others containing one mismatch in the center of the chain, were synthesized. The chromatogram obtained as the results of high performance liquid affinity chromatography (HPLAC) considerably varied with the column temperature and the type of mismatches. The dependency of the deformation of elution profile upon mismatch seemed to reflect the stability of the hybrid composed of samples and immobilized probe.     

筛选神经系统基因功能的行为学检测平台的探索

为大规模鉴定哺乳动物神经系统新基因的功能,利用反义核酸技术建立了一个小鼠行为学检测平台。从大鼠脑低丰度表达基因的cDNA亚库中挑选出在大鼠脑内表达的20个基因,设计并合成了这些基因的小鼠同源基因的特异性反义核酸。用Hamilton微量注射器将反义核酸注射到小鼠的侧脑室,并以注射生理盐水和随机序列核酸组作为对照。小鼠的行为学检测模型为;考察日常代谢能力的摄食量,考察Locomotion activity(移动）的旷场行为,考察疼痛阈值的甩尾试验和记忆能力的步下法实验,结果显示,上述20个基因中的14个在不同行为学模型中与对照组有显著性差异。     

Selection of oligonucleotide probes for protein coding sequences

MOTIVATION: Large arrays of oligonucleotide probes have become popular tools for analyzing RNA expression. However to date most oligo collections contain poorly validated sequences or are biased toward untranslated regions (UTRs). Here we present a strategy for picking oligos for microarrays that focus on a design universe consisting exclusively of protein coding regions. We describe the constraints in oligo design that are imposed by this strategy, as well as a software tool that allows the strategy to be applied broadly. RESULT: In this work we sequentially apply a variety of simple filters to candidate sequences for oligo probes. The primary filter is a rejection of probes that contain contiguous identity with any other sequence in the sample universe that exceeds a pre-established threshold length. We find that rejection of oligos that contain 15 bases of perfect match with other sequences in the design universe is a feasible strategy for oligo selection for probe arrays designed to interrogate mammalian RNA populations. Filters to remove sequences with low complexity and predicted poor probe accessibility narrow the candidate probe space only slightly. Rejection based on global sequence alignment is performed as a secondary, rather than primary, test, leading to an algorithm that is computationally efficient. Splice isoforms pose unique challenges and we find that isoform prevalence will for the most part have to be determined by analysis of the patterns of hybridization of partially redundant oligonucleotides. AVAILABILITY: The oligo design program OligoPicker and its source code are freely available at our website.     

Fast large scale oligonucleotide selection using the longest common factor approach

We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within four days, a speedup of one to two orders of magnitude compared to previous approaches. This speed is attained by using the longest common substring as a specificity measure for candidate oligos. We present a space- and time-efficient algorithm, based on a suffix array with additional information, to compute matching statistics (lengths of longest matches) between all candidate oligos and all remaining sequences. With the matching statistics available, we show how to incorporate constraints such as oligo length, melting temperature, and self-complementarity into the selection process at a postprocessing stage. As a result, we can now design custom oligos for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.     

Fas基因mRNA反义靶点筛选和体外验证

应用PARASS(poly-A anchored RNA accessible sites screening) 技术筛选Fas基因mRNA 获得3个潜在反义作用靶点,靶点1、2、3分别位于Fas基因297nt-317nt、619nt-639nt和662nt-682nt。设计了对应靶点的反义寡核苷酸A1、A2、A3,和10-23型DNAzyme D1、D2和D3。将反义寡核苷酸和Fas基因RNA结合再加入RNase H进行反应,10-23型DNAzyme则直接与Fas基因RNA作用,结果表明：3个靶点的反义寡核苷酸组及DNAzyme均能降解Fas基因RNA,为有效靶点,其靶点反应优势次序为靶点3>靶点1>靶点2;而非靶点对照组和有效靶点突变了2个碱基的对照组均没有反应。靶点2和靶点3与ISIS公司经过多次实验筛选到的Fas反义作用靶点位置基本相同,表明PARASS技术的有效性和可靠性。获得的有效反义寡核苷酸和DNAzyme为后续研究打下基础。     

Hoxb-5 control of early airway formation during branching morphogenesis in the developing mouse lung

Hox proteins control structural morphogenesis, pattern formation and cell fate in the developing embryo. To determine if Hoxb-5 participates in patterning of early airway branching during lung morphogenesis, gestational day 11.5 embryonic lung cultures were treated with retinoic acid (RA) to up-regulate and antisense oligonucleotides to down-regulate Hoxb-5 protein expression. RA (10^?6 M) and Hoxb-5 antisense oligonucleotide (20 μM) treatment each significantly decreased branching morphogenesis (P<0.001), but the morphology of branching under these conditions was very different. RA-treated lungs had elongated primary branches but decreased further branching with increased Hoxb-5 immunostaining in subepithelial regions underlying these elongated airways. Western blots confirmed that Hoxb-5 protein was increased by 189±20% (mean±S.E.M., P<0.05) in RA-treated lungs compared to controls. In contrast, lungs treated with Hoxb-5 antisense oligos plus RA had foreshortened primary branches with rudimentary distal clefts resulting in decreased numbers of primary and subsequent branches. Immunohistochemistry confirmed that Hoxb-5 antisense oligos inhibited Hoxb-5 protein expression even in the presence of RA. We conclude that regional and quantitative changes in Hoxb-5 protein expression influence morphogenesis of the first airway divisions from the mainstem bronchi. RA-induced alterations in branching are mediated in part through regulated Hoxb-5 expression.     

Oligo replication advantage driven by GC content and Gibbs free energy

Large scale DNA oligo pools are emerging as a novel material in a variety of advanced applications. However, GC content and length cause significant bias in amplification of oligos. We systematically explored the amplification of one oligo pool comprising of over ten thousand distinct strands with moderate GC content in the range of 35–65%. Uniqual amplification of oligos result to the increased Gini index of the oligo distribution while a few oligos greatly increased their proportion after 60 cycles of PCR. However, the significantly enriched oligos all have relatively high GC content. Further thermodynamic analysis demonstrated that a high value of both GC content and Gibbs free energy could improve the replication of specific oligos during biased amplification. Therefore, this double-G (GC content and Gibbs free energy) driven replication advantage can be used as a guiding principle for the sequence design for a variety of applications, particularly for data storage.