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Journal articles on the topic 'Antisense Plasmids Nucleic acid hybridization'

Author: Grafiati

Published: 4 June 2021

Last updated: 13 February 2022

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1

Preston, David R., G. Rasul Chaudhry, and Samuel R. Farrah. "Detection and identification of poliovirus in environmental samples using nucleic acid hybridization." Canadian Journal of Microbiology 36, no. 9 (1990): 664–69. http://dx.doi.org/10.1139/m90-113.

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A procedure was developed to effectively extract viral RNA from poliovirus tissue-culture lysates while eliminating the hybridization background associated with tissue cultures uninfected with poliovirus. Poliovirus cDNA cloned into a pUC vector was used as probe. Both the recombinant plasmids and the cDNA showed great specificity towards poliovirus. However, both probes hybridized with the single-stranded DNA coliphage [Formula: see text]. Tissue culture was found to be an effective method to increase the number of viruses found in environmental samples to a level detectable by hybridization

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2

Southern, Edwin. "Microarrays for basic studies of nucleic acid hybridization and selection of antisense reagents." Nature Genetics 23, S3 (1999): 6. http://dx.doi.org/10.1038/14210.

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3

Prajapati, Rama, and Álvaro Somoza. "Albumin Nanostructures for Nucleic Acid Delivery in Cancer: Current Trend, Emerging Issues, and Possible Solutions." Cancers 13, no. 14 (2021): 3454. http://dx.doi.org/10.3390/cancers13143454.

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Cancer is one of the major health problems worldwide, and hence, suitable therapies with enhanced efficacy and reduced side effects are desired. Gene therapy, involving plasmids, small interfering RNAs, and antisense oligonucleotides have been showing promising potential in cancer therapy. In recent years, the preparation of various carriers for nucleic acid delivery to the tumor sites is gaining attention since intracellular and extracellular barriers impart major challenges in the delivery of naked nucleic acids. Albumin is a versatile protein being used widely for developing carriers for nu

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4

Ramasamy, Kanda S., and Wilfried Seifert. "Amino Acid Nucleic Acids: Synthesis and Hybridization Properties of a Novel Class of Antisense Oligonucleotides." Nucleosides and Nucleotides 16, no. 7-9 (1997): 1519–22. http://dx.doi.org/10.1080/07328319708006220.

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5

Ramasamy, Kanda S., and Wilfried Seifert. "Amino acid nucleic acids: synthesis and hybridization properties of a novel class of antisense oligonucleotides." Bioorganic & Medicinal Chemistry Letters 6, no. 15 (1996): 1799–804. http://dx.doi.org/10.1016/0960-894x(96)00320-4.

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6

Gifford, L. K. "Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules." Nucleic Acids Research 33, no. 3 (2005): e28-e28. http://dx.doi.org/10.1093/nar/gni024.

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7

Lundin, Karin E., Maroof Hasan, Pedro M. Moreno, et al. "Increased stability and specificity through combined hybridization of peptide nucleic acid (PNA) and locked nucleic acid (LNA) to supercoiled plasmids for PNA-anchored “Bioplex” formation." Biomolecular Engineering 22, no. 5-6 (2005): 185–92. http://dx.doi.org/10.1016/j.bioeng.2005.07.003.

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8

RAMASAMY, K. S., and W. SEIFERT. "ChemInform Abstract: Amino Acid Nucleic Acids: Synthesis and Hybridization Properties of a Novel Class of Antisense Oligonucleotides." ChemInform 27, no. 49 (2010): no. http://dx.doi.org/10.1002/chin.199649247.

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9

Romero-Palomo, Fernando, Matthias Festag, Barbara Lenz, et al. "Safety, Tissue Distribution, and Metabolism of LNA-Containing Antisense Oligonucleotides in Rats." Toxicologic Pathology 49, no. 6 (2021): 1174–92. http://dx.doi.org/10.1177/01926233211011615.

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Antisense oligonucleotides (ASOs) are chemically modified nucleic acids with therapeutic potential, some of which have been approved for marketing. We performed a study in rats to investigate mechanisms of toxicity after administration of 3 tool locked nucleic acid (LNA)-containing ASOs with differing established safety profiles. Four male rats per group were dosed once, 3, or 6 times subcutaneously, with 7 days between dosing, and sacrificed 3 days after the last dose. These ASOs were either unconjugated (naked) or conjugated with N-acetylgalactosamine for hepatocyte-targeted delivery. The ma

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10

Nass, Petra H., Leslie L. Domier, Birute P. Jakstys, and Cleora J. D'Arcy. "In Situ Localization of Barley Yellow Dwarf Virus-PAV 17-kDa Protein and Nucleic Acids in Oats." Phytopathology® 88, no. 10 (1998): 1031–39. http://dx.doi.org/10.1094/phyto.1998.88.10.1031.

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Barley yellow dwarf virus strain PAV (BYDV-PAV) RNA and the 17-kDa protein were localized in BYDV-PAV-infected oat cells using in situ hybridization and in situ immunolocalization assays, respectively. The in situ hybridization assay showed labeling of filamentous material in the nucleus, cytoplasm, and virus-induced vesicles with both sense and antisense nucleic acid probes, suggesting that the filamentous material found in BYDV-PAV-infected cells contains viral RNA. BYDV-PAV negative-strand RNA was detected before virus particles were observed, which indicates that RNA replication is initiat

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11

Moats-Staats, B. M., H. W. Jarvis, A. J. D'Ercole, and A. D. Stiles. "Cloning and characterization of a novel RNA involved in cellular growth regulation." Molecular and Cellular Biology 14, no. 5 (1994): 2936–45. http://dx.doi.org/10.1128/mcb.14.5.2936.

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During the course of antisense oligodeoxynucleotide (oligo) inhibition experiments investigating the role of insulin-like growth factor I (IGF-I) in the WI-38 cell cycle, we found that a sense-strand oligo (S oligo), used as a control, inhibited DNA synthesis 90 to 95%. S1 nuclease protection assays demonstrated that this S oligo formed intracellular duplexes with WI-38 RNA, and Northern (RNA) hybridization analyses demonstrated specific hybridization of this 32P-labeled S oligo to 1.8-, 2.3-, and 3.2-kb RNAs. We have cloned and sequenced a 2,251-bp cDNA, designated BB1, corresponding to the 2

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12

Moats-Staats, B. M., H. W. Jarvis, A. J. D'Ercole, and A. D. Stiles. "Cloning and characterization of a novel RNA involved in cellular growth regulation." Molecular and Cellular Biology 14, no. 5 (1994): 2936–45. http://dx.doi.org/10.1128/mcb.14.5.2936-2945.1994.

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During the course of antisense oligodeoxynucleotide (oligo) inhibition experiments investigating the role of insulin-like growth factor I (IGF-I) in the WI-38 cell cycle, we found that a sense-strand oligo (S oligo), used as a control, inhibited DNA synthesis 90 to 95%. S1 nuclease protection assays demonstrated that this S oligo formed intracellular duplexes with WI-38 RNA, and Northern (RNA) hybridization analyses demonstrated specific hybridization of this 32P-labeled S oligo to 1.8-, 2.3-, and 3.2-kb RNAs. We have cloned and sequenced a 2,251-bp cDNA, designated BB1, corresponding to the 2

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13

Semple, Kathleen M., James L. Doran, and D. W. S. Westlake. "DNA relatedness of oil-field isolates of Shewanella putrefaciens." Canadian Journal of Microbiology 35, no. 10 (1989): 925–31. http://dx.doi.org/10.1139/m89-153.

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Classification of several oil-field isolates of Shewanella putrefaciens was assessed by nucleic acid hybridization techniques. The results of DNA – DNA hybridization analysis generally confirmed the phenetic characterization of these isolates and supported the classification of oil-field isolates of S. putrefaciens groups 1, 3, and 4. However, two group 2 isolates were considered to be mistakenly classified. Strain ESSO 1-1 appeared to belong to group 3, a result which was supported by the pattern of 5S rRNA hybridization to restriction digests of genomic DNA, and strain 213 appeared to be a m

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14

Stedman, N. L., T. P. Brown, and C. C. Brown. "Localization of Avian Leukosis Virus Subgroup J in Naturally Infected Chickens by RNA In Situ Hybridization." Veterinary Pathology 38, no. 6 (2001): 649–56. http://dx.doi.org/10.1354/vp.38-6-649.

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The novel subgroup J of avian leukosis virus (ALV-J) has emerged as a significant cause of myeloid neoplasia and weight suppression in broiler chickens. We investigated viral tropism using RNA in situ hybridization (ISH) in naturally infected chickens. Formalin-fixed tissues were collected from 12-day-old embryos (seven infected, two control) and from 0-week-old (four infected, one control), 3-week-old (five infected, one control), 6-week-old (five infected, one control), and 9-week-old (10 infected, two control) chickens naturally infected with ALV-J in ovo. A 636-base antisense riboprobe com

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15

Maruyama, Fumito, Takehiko Kenzaka, Nobuyasu Yamaguchi, Katsuji Tani, and Masao Nasu. "Visualization and Enumeration of Bacteria Carrying a Specific Gene Sequence by In Situ Rolling Circle Amplification." Applied and Environmental Microbiology 71, no. 12 (2005): 7933–40. http://dx.doi.org/10.1128/aem.71.12.7933-7940.2005.

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ABSTRACT Rolling circle amplification (RCA) generates large single-stranded and tandem repeats of target DNA as amplicons. This technique was applied to in situ nucleic acid amplification (in situ RCA) to visualize and count single Escherichia coli cells carrying a specific gene sequence. The method features (i) one short target sequence (35 to 39 bp) that allows specific detection; (ii) maintaining constant fluorescent intensity of positive cells permeabilized extensively after amplicon detection by fluorescence in situ hybridization, which facilitates the detection of target bacteria in vari

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16

Kalota, Anna, Lidia Karabon, Cezary S. Swider, et al. "A Novel 2′-Deoxy-2′-Fluoro (2′F-ANA) Ribose Modification Significantly Enhances the Duration, and Efficiency, of Nucleic Acid Mediated Gene Silencing." Blood 106, no. 11 (2005): 3062. http://dx.doi.org/10.1182/blood.v106.11.3062.3062.

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Abstract The field of nucleic acid mediated gene silencing has been reinvigorated with the widespread adoption of RNA interference using siRNA. Since issues of delivery, stability, and duration of effect remain relevant to siRNA, and all other types of gene silencing nucleic acids, we are studying chemical modifications that may enhance the efficiency of molecules employed for this purpose. To this end, we synthesized 2′-deoxy-2′-fluoro-d-arabinonucleic acid (2′F-ANA) modifications of DNA as our prior work suggested that they would simultaneously raise the Tm of mRNA:DNA hybrids, increase resi

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17

Luger, Selina M., Stephen G. O'Brien, Janina Ratajczak, et al. "Oligodeoxynucleotide-mediated inhibition of c-myb gene expression in autografted bone marrow: a pilot study." Blood 99, no. 4 (2002): 1150–58. http://dx.doi.org/10.1182/blood.v99.4.1150.

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Antisense oligodeoxynucleotide (ODN) drugs might be more effective if their delivery was optimized and they were targeted to short-lived proteins encoded by messenger RNA (mRNA) species with equally short half-lives. To test this hypothesis, an ODN targeted to the c-mybproto-oncogene was developed and used to purge marrow autografts administered to allograft-ineligible chronic myelogenous leukemia patients. CD34+ marrow cells were purged with ODN for either 24 (n = 19) or 72 (n = 5) hours. After purging, Myb mRNA levels declined substantially in approximately 50% of patients. Analysis of bcr/a

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18

Pham, Dien G., Guillermo E. Madico, Thomas C. Quinn, Mark J. Enzler, Thomas F. Smith, and Charlotte A. Gaydos. "Use of Lambda Phage DNA as a Hybrid Internal Control in a PCR-Enzyme Immunoassay To Detect Chlamydia pneumoniae." Journal of Clinical Microbiology 36, no. 7 (1998): 1919–22. http://dx.doi.org/10.1128/jcm.36.7.1919-1922.1998.

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An inherent problem in the diagnostic PCR assay is the presence of ill-defined inhibitors of amplification which may cause false-negative results. Addition of an amplifiable fragment of foreign DNA in the PCR to serve as a hybrid internal control (HIC) would allow for a simple way to identify specimens containing inhibitors. Two oligonucleotide hybrid primers were synthesized to contain nucleic acid sequences of the Chlamydia pneumoniae 16S rRNA primers in a position flanking two primers that target the sequences of a 650-bp lambda phage DNA segment. By using the hybrid primers, hybrid DNA com

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19

Haynes, J. S., P. G. Halbur, T. Sirinarumitr, P. S. Paul, X. J. Meng, and E. L. Huffman. "Temporal and Morphologic Characterization of the Distribution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) by In Situ Hybridization in Pigs Infected with Isolates of PRRSV that Differ in Virulence." Veterinary Pathology 34, no. 1 (1997): 39–43. http://dx.doi.org/10.1177/030098589703400106.

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Three groups of 5-week-old cesarian-derived, colostrum-deprived pigs were inoculated intranasally with either a high-virulence isolate (VR2385) or a low-virulence isolate (VR2431) of porcine reproductive and respiratory syndrome virus (PRRSV) or with uninfected cell culture and media. Formalin-fixed, paraffin-embedded tissues from pigs euthanatized at 10, 21, and 28 days post-inoculation were examined by in situ hybridization for PRRSV nucleic acid using a digoxigenin-labeled antisense RNA probe approximately 1,000 nucleotides in length. Alveolar macrophages were positive in the lungs of 9/9,

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20

Wu, Shizhou, Yunjie Liu, Lei Lei, and Hui Zhang. "Virulence of methicillin-resistant Staphylococcus aureus modulated by the YycFG two-component pathway in a rat model of osteomyelitis." Journal of Orthopaedic Surgery and Research 14, no. 1 (2019). http://dx.doi.org/10.1186/s13018-019-1508-z.

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Abstract Objectives Methicillin-resistant Staphylococcus aureus (MRSA) strains present an urgent medical problem in osteomyelitis cases. Our previous study indicated that the YycFG two-component regulatory pathway is associated with the bacterial biofilm organization of MRSA strains. The aim of this study was to investigate the regulatory roles of ASyycG in the bacterial biofilm formation and the pathogenicity of MRSA strains using an antisense RNA strategy. Methods An ASyycG-overexpressing MRSA clinical isolate was constructed. The bacterial growth was monitored, and the biofilm biomass on bo

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