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Journal articles on the topic 'Oligonucleotide Oligonucleotide'

Author: Grafiati

Published: 4 June 2021

Last updated: 19 February 2022

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1

Dung, Tran Huu, Seung-Rok Lee, Suhk-Dong Han, et al. "Chitosan-TPP Nanoparticle as a Release System of Antisense Oligonucleotide in the Oral Environment." Journal of Nanoscience and Nanotechnology 7, no. 11 (2007): 3695–99. http://dx.doi.org/10.1166/jnn.2007.041.

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Antisense oligonucleotide loaded chitosan nanoparticles were prepared and the release of oligonucleotide from chitosan-TPP/oligonucleotide nanoparticles was investigated. Morphological property, zeta potential and particle size of the prepared chitosan/oligonucleotide nanoparticles were investigated using Field Emission-Scanning Electron Microscope (FE-SEM) and particle size analyzer. The interaction between chitosan and oligonucleotide was confirmed by using capillary zone electrophoresis (CZE), and the released oligonucleotides were determined by spectrophotometric method. Oligonucleotides f

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2

Juliano, Rudolph L. "Chemical Manipulation of the Endosome Trafficking Machinery: Implications for Oligonucleotide Delivery." Biomedicines 9, no. 5 (2021): 512. http://dx.doi.org/10.3390/biomedicines9050512.

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Antisense oligonucleotides (ASOs), siRNA and splice switching oligonucleotides (SSOs) all have immense potential as therapeutic agents, potential that is now being validated as oligonucleotides enter the clinic. However, progress in oligonucleotide-based therapeutics has been limited by the difficulty in delivering these complex molecules to their sites of action in the cytosol or nucleus of cells within specific tissues. There are two aspects to the delivery problem. The first is that most types of oligonucleotides have poor uptake into non-hepatic tissues. The second is that much of the olig

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3

Ravnik, Šimen, Ines Žabkar, Uršula Prosenc Zmrzljak, et al. "OligoPrime: An Information System for Oligonucleotide Management." Biomedical Engineering and Computational Biology 12 (January 2021): 117959722110419. http://dx.doi.org/10.1177/11795972211041983.

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With the increasing number of molecular biology techniques, large numbers of oligonucleotides are frequently involved in individual research projects. Thus, a dedicated electronic oligonucleotide management system is expected to provide several benefits such as increased oligonucleotide traceability, facilitated sharing of oligonucleotides between laboratories, and simplified (bulk) ordering of oligonucleotides. Herein, we describe OligoPrime, an information system for oligonucleotide management, which presents a computational support for all steps in an oligonucleotide lifecycle, namely, from

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4

Studzińska, Sylwia, Ewelina Zawadzka, Szymon Bocian, and Michał Szumski. "Synthesis and application of stationary phase for DNA-affinity chromatographic analysis of unmodified and antisense oligonucleotide." Analytical and Bioanalytical Chemistry 413, no. 20 (2021): 5109–19. http://dx.doi.org/10.1007/s00216-021-03473-7.

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AbstractThe goal of the research was the synthesis and application of an oligonucleotide immobilized stationary phase for the analysis of unmodified and antisense oligonucleotides. The method for attaching these molecules to aminopropyl silica modified with pentanedioic acid was developed. Each step of the synthesis was carefully controlled with the application of spectroscopic, elemental, and chromatographic analyses. The oligonucleotide-based stationary phase was applied for the retention studies. Unmodified oligonucleotides of different complementarity to the molecule attached as a stationa

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5

Milton, S., M. Murtola, J. Sandbrink, E. Yeheskiely, and R. Stromberg. "Making Oligonucleotide Conjugates and Breaking Oligonucleotides." Nucleic Acids Symposium Series 51, no. 1 (2007): 61. http://dx.doi.org/10.1093/nass/nrm031.

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6

Katsaloulis, P., T. Theoharis, and A. Provata. "Statistical Algorithms for Long DNA Sequences: Oligonucleotide Distributions and Homogeneity Maps." Scientific Programming 13, no. 3 (2005): 177–88. http://dx.doi.org/10.1155/2005/807304.

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The statistical properties of oligonucleotide appearances within long DNA sequences often reveal useful characteristics of the corresponding DNA areas. Two algorithms to statistically analyze oligonucleotide appearances within long DNA sequences in genome banks are presented. The first algorithm determines statistical indices for arbitrary length oligonucleotides within arbitrary length DNA sequences. The critical exponentμof the distance distribution between consecutive occurrences of the same oligonucleotide is calculated and its value is shown to characterize the functionality of the oligon

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7

Day, P. J., P. S. Flora, J. E. Fox, and M. R. Walker. "Immobilization of polynucleotides on magnetic particles. Factors influencing hybridization efficiency." Biochemical Journal 278, no. 3 (1991): 735–40. http://dx.doi.org/10.1042/bj2780735.

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Immobilization of oligonucleotides containing 5′-terminal thiol groups on thiol-terminated paramagnetic Biomag beads via disulphide bond formation was investigated. Oligonucleotides are demonstrated to couple at high yields, the linkage is stable at 90 degrees C and is reversible, and the immobilized oligonucleotide is available for complementary, but not non-complementary, hybridization. Specific hybridization capacity per micrograms of immobilized oligonucleotide exceeds that achieved with other forms of immobilization chemistries employing random attachment and/or specific end attachment of

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8

Zhang, Hui Yong. "Solid-Phase Synthesis of DNA Chemical Sensor." Advanced Materials Research 815 (October 2013): 305–11. http://dx.doi.org/10.4028/www.scientific.net/amr.815.305.

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Oligonucleotides are essential components of many applications in molecular biology. The synthesis chemistry is robust and commercial oligonucleotide synthesizers have taken advantage of the chemistry to provide oligonucleotides of high quality and purity. This paper established nucleic acid synthesis platform to carry out the synthesis of the labeled nucleic acid probes based on the DNA synthesizer and solid-phase synthesis technology. We chose to study the automated synthesis starting from DMT protected FAM labeled amidite attached to controlled pore glass (CPG) support and the standard trit

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9

Kilanowska, Anna, Łukasz Nuckowski, and Sylwia Studzińska. "Studying in vitro metabolism of the first and second generation of antisense oligonucleotides with the use of ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry." Analytical and Bioanalytical Chemistry 412, no. 27 (2020): 7453–67. http://dx.doi.org/10.1007/s00216-020-02878-0.

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Abstract The aim of the present investigation was the analysis and identification of antisense oligonucleotide metabolism products after incubation with human liver microsomes regarding four different oligonucleotide modifications. Separation and detection methods based on the use of liquid chromatography coupled with quadrupole time-of-flight mass spectrometry were developed for this purpose. Firstly, the optimization of mass spectrometer parameters was done to select those which ensure the highest possible sensitivity of oligonucleotide analysis. This step was conducted for two chromatograph

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10

Zhao, Q., X. Song, T. Waldschmidt, E. Fisher, and AM Krieg. "Oligonucleotide uptake in human hematopoietic cells is increased in leukemia and is related to cellular activation." Blood 88, no. 5 (1996): 1788–95. http://dx.doi.org/10.1182/blood.v88.5.1788.1788.

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Abstract The use of antisense oligonucleotides as tools for modulating gene expression represents a novel strategy for designing drugs to treat a variety of diseases. Several factors, including cellular uptake and internalization of the oligonucleotides, are important parameters in determining the effectiveness of antisense agents such as therapeutic drugs. We have studied oligonucleotides uptake in normal and leukemic human hematopoietic cells, such as peripheral blood, bone marrow (BM), and HL-60 cell line; and have found that, in normal human blood and BM, myeloid cells and B cells preferab

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11

Zhao, Q., X. Song, T. Waldschmidt, E. Fisher, and AM Krieg. "Oligonucleotide uptake in human hematopoietic cells is increased in leukemia and is related to cellular activation." Blood 88, no. 5 (1996): 1788–95. http://dx.doi.org/10.1182/blood.v88.5.1788.bloodjournal8851788.

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The use of antisense oligonucleotides as tools for modulating gene expression represents a novel strategy for designing drugs to treat a variety of diseases. Several factors, including cellular uptake and internalization of the oligonucleotides, are important parameters in determining the effectiveness of antisense agents such as therapeutic drugs. We have studied oligonucleotides uptake in normal and leukemic human hematopoietic cells, such as peripheral blood, bone marrow (BM), and HL-60 cell line; and have found that, in normal human blood and BM, myeloid cells and B cells preferably took u

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12

Pérez-Rentero, Sónia, Alvaro Somoza, Santiago Grijalvo, et al. "Biophysical and RNA Interference Inhibitory Properties of Oligonucleotides Carrying Tetrathiafulvalene Groups at Terminal Positions." Journal of Chemistry 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/650610.

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Oligonucleotide conjugates carrying a single functionalized tetrathiafulvalene (TTF) unit linked through a threoninol molecule to the 3′ or 5′ ends were synthesized together with their complementary oligonucleotides carrying a TTF, pyrene, or pentafluorophenyl group. TTF-oligonucleotide conjugates formed duplexes with higher thermal stability than the corresponding unmodified oligonucleotides and pyrene- and pentafluorophenyl-modified oligonucleotides. TTF-modified oligonucleotides are able to bind to citrate-stabilized gold nanoparticles (AuNPs) and produce stable gold AuNPs functionalized wi

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13

Lesnikowski, Zbigniew J., Marzena Przepiórkiewicz, Yutaka Tamura, Hideko Kaji, and Eric Wickstrom. "P-Chiral Oligonucleotides. Effect of Configuration at Phosphorus on Transport of Tetra(thymidine Methylphosphonate)s Across Organic Liquid Membrane." Collection of Czechoslovak Chemical Communications 66, no. 6 (2001): 912–22. http://dx.doi.org/10.1135/cccc20010912.

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The stereodependent transport of a P-stereoregular oligonucleotide through a model organic liquid membrane is described. The electroneutral tetra(thymidine methylphosphonate) was used as oligonucleotide. The transportability increased in the order: all-RP > random distribution of P-diastereomers > all-SP. These findings extend our knowledge of the physicochemical properties of single-stranded methylphosphonate oligonucleotides in solution, and might facilitate cellular uptake of future antisense oligonucleotide drugs.

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14

Yamashita, Shoko, Kodai Nishida, Takashi Osawa, Ayumi Nakanishi, Yuta Ito, and Yoshiyuki Hari. "Synthesis of Oligonucleotides Containing 2′-N-alkylaminocarbonyl-2′-amino-LNA (2′-urea-LNA) Moieties Using Post-Synthetic Modification Strategy." Molecules 25, no. 2 (2020): 346. http://dx.doi.org/10.3390/molecules25020346.

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The post-synthetic modification of an oligonucleotide is a powerful strategy for the synthesis of various analogs of the oligonucleotide, aiming to achieve the desired functions. In this study, we synthesized the thymidine phosphoramidite of 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA, which was introduced into oligonucleotides. Oligonucleotides containing a 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA unit could be isolated under ultra-mild deprotection conditions (50 mM K2CO3 in MeOH at room temperature for 4 h). Moreover, by treatment with various amines as a post-synthetic modification, t

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15

Pavlova, Anna S., Ilya S. Dovydenko, Maxim S. Kupryushkin, Alina E. Grigor’eva, Inna A. Pyshnaya, and Dmitrii V. Pyshnyi. "Amphiphilic “Like-A-Brush” Oligonucleotide Conjugates with Three Dodecyl Chains: Self-Assembly Features of Novel Scaffold Compounds for Nucleic Acids Delivery." Nanomaterials 10, no. 10 (2020): 1948. http://dx.doi.org/10.3390/nano10101948.

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The conjugation of lipophilic groups to oligonucleotides is a promising approach for improving nucleic acid-based therapeutics’ intracellular delivery. Lipid oligonucleotide conjugates can self-aggregate in aqueous solution, which gains much attention due to the formation of micellar particles suitable for cell endocytosis. Here, we describe self-association features of novel “like-a-brush” oligonucleotide conjugates bearing three dodecyl chains. The self-assembly of the conjugates into 30–170 nm micellar particles with a high tendency to aggregate was shown using dynamic light scattering (DLS

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16

Kool, Eric T. "Circular Oligonucleotides: New Concepts in Oligonucleotide Design." Annual Review of Biophysics and Biomolecular Structure 25, no. 1 (1996): 1–28. http://dx.doi.org/10.1146/annurev.bb.25.060196.000245.

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17

Kumar, Ajay. "Binding of Dumbbell Oligonucleotides to MoMuLV Reverse Transcriptase: Inhibitory Properties of RNase H Activity." E-Journal of Chemistry 7, no. 3 (2010): 701–8. http://dx.doi.org/10.1155/2010/616512.

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Dumbbell oligonucleotides with loops of various chemistry were synthesized. Incubation of dumbbell oligonucleotides containing phosphorothioate bonds or trimethylene phosphate linkages in loops with S1 nuclease did not result in significant cleavage under conditions which led to the degradation of dumbbell oligonucleotide containing phophodiester bonds in the loops. The binding of reverse transcriptase of Moloney Murine Leukemia Virus (MoMuLV) was evaluated with all the five oligonucleotides. The protein binds to all the dumbbell oligonucleotides with similar affinity. The dissociation constan

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18

Schleicher, Martina, Jan Hansmann, Bentsian Elkin, et al. "Oligonucleotide and Parylene Surface Coating of Polystyrene and ePTFE for Improved Endothelial Cell Attachment and Hemocompatibility." International Journal of Biomaterials 2012 (2012): 1–14. http://dx.doi.org/10.1155/2012/397813.

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In vivoself-endothelialization by endothelial cell adhesion on cardiovascular implants is highly desirable. DNA-oligonucleotides are an intriguing coating material with nonimmunogenic characteristics and the feasibility of easy and rapid chemical fabrication. The objective of this study was the creation of cell adhesive DNA-oligonucleotide coatings on vascular implant surfaces. DNA-oligonucleotides immobilized by adsorption on parylene (poly(monoaminomethyl-para-xylene)) coated polystyrene and ePTFE were resistant to high shear stress (9.5 N/m2) and human blood serum for up to 96 h. Adhesion o

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19

Patutina, Olga A., Svetlana K. Gaponova (Miroshnichenko), Aleksandra V. Sen’kova, et al. "Mesyl phosphoramidate backbone modified antisense oligonucleotides targeting miR-21 with enhanced in vivo therapeutic potency." Proceedings of the National Academy of Sciences 117, no. 51 (2020): 32370–79. http://dx.doi.org/10.1073/pnas.2016158117.

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The design of modified oligonucleotides that combine in one molecule several therapeutically beneficial properties still poses a major challenge. Recently a new type of modified mesyl phosphoramidate (or µ-) oligonucleotide was described that demonstrates high affinity to RNA, exceptional nuclease resistance, efficient recruitment of RNase H, and potent inhibition of key carcinogenesis processes in vitro. Herein, using a xenograft mouse tumor model, it was demonstrated that microRNA miR-21–targeted µ-oligonucleotides administered in complex with folate-containing liposomes dramatically inhibit

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20

Dowaidar, Moataz, Hani Nasser Abdelhamid, Mattias Hällbrink, Ülo Langel, and Xiaodong Zou. "Chitosan enhances gene delivery of oligonucleotide complexes with magnetic nanoparticles–cell-penetrating peptide." Journal of Biomaterials Applications 33, no. 3 (2018): 392–401. http://dx.doi.org/10.1177/0885328218796623.

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Gene-based therapies, including the delivery of oligonucleotides, offer promising methods for the treatment of cancer cells. However, they have various limitations including low efficiency. Herein, cell-penetrating peptides (CPPs)-conjugated chitosan-modified iron oxide magnetic nanoparticles (CPPs-CTS@MNPs) with high biocompatibility as well as high efficiency were tested for the delivery of oligonucleotides such as plasmid pGL3, splice correction oligonucleotides, and small-interfering RNA. A biocompatible nanocomposite, in which CTS@MNPs was incorporated in non-covalent complex with CPPs-ol

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21

Annenkov, Vadim, Uma Krishnan, Viktor Pal’shin, Stanislav Zelinskiy, Gayathri Kandasamy, and Elena Danilovtseva. "Design of Oligonucleotide Carriers: Importance of Polyamine Chain Length." Polymers 10, no. 12 (2018): 1297. http://dx.doi.org/10.3390/polym10121297.

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Amine containing polymers are extensively studied as special carriers for short-chain RNA (13–25 nucleotides), which are applied as gene silencing agents in gene therapy of various diseases including cancer. Elaboration of the oligonucleotide carriers requires knowledge about peculiarities of the oligonucleotide–polymeric amine interaction. The critical length of the interacting chains is an important parameter which allows us to design sophisticated constructions containing oligonucleotide binding segments, solubilizing, protective and aiming parts. We studied interactions of (TCAG)n, n = 1–6

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22

Meng, Melissa, Boris Schmidtgall, and Christian Ducho. "Enhanced Stability of DNA Oligonucleotides with Partially Zwitterionic Backbone Structures in Biological Media." Molecules 23, no. 11 (2018): 2941. http://dx.doi.org/10.3390/molecules23112941.

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Deficient stability towards nuclease-mediated degradation is one of the most relevant tasks in the development of oligonucleotide-derived biomedical agents. This hurdle can be overcome through modifications to the native oligonucleotide backbone structure, with the goal of simultaneously retaining the unique hybridization properties of nucleic acids. The nucleosyl amino acid (NAA)-modification is a recently introduced artificial cationic backbone linkage. Partially zwitterionic NAA-modified oligonucleotides had previously shown hybridization with DNA strands with retained base-pairing fidelity

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23

Tanaka, T., C. C. Chu, and W. E. Paul. "An antisense oligonucleotide complementary to a sequence in I gamma 2b increases gamma 2b germline transcripts, stimulates B cell DNA synthesis, and inhibits immunoglobulin secretion." Journal of Experimental Medicine 175, no. 2 (1992): 597–607. http://dx.doi.org/10.1084/jem.175.2.597.

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An antisense phosphorothioate (S)-oligonucleotide to a sequence in the intervening (I) region of the gamma 2b immunoglobulin (Ig) heavy chain gene inhibits Ig secretion by B cells stimulated with lipopolysaccharide (LPS) or LPS plus interleukin 4. It is also a striking stimulant of DNA synthesis by resting B cells. The antisense S-oligonucleotide causes a 10-20-fold increase in the expression of the gamma 2b germline transcript. Among mutants of the antisense S-oligonucleotide, some show all the effects whereas others are inactive. A similar hierarchy exists in the quantitative biological acti

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24

Božič, Tim, Matja Zalar, Boris Rogelj, Janez Plavec, and Primož Šket. "Structural Diversity of Sense and Antisense RNA Hexanucleotide Repeats Associated with ALS and FTLD." Molecules 25, no. 3 (2020): 525. http://dx.doi.org/10.3390/molecules25030525.

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The hexanucleotide expansion GGGGCC located in C9orf72 gene represents the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). Since the discovery one of the non-exclusive mechanisms of expanded hexanucleotide G4C2 repeats involved in ALS and FTLD is RNA toxicity, which involves accumulation of pathological sense and antisense RNA transcripts. Formed RNA foci sequester RNA-binding proteins, causing their mislocalization and, thus, diminishing their biological function. Therefore, structures adopted by pathological RNA transcripts could hav

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Zhao, Q., T. Waldschmidt, E. Fisher, CJ Herrera, and AM Krieg. "Stage-specific oligonucleotide uptake in murine bone marrow B-cell precursors." Blood 84, no. 11 (1994): 3660–66. http://dx.doi.org/10.1182/blood.v84.11.3660.bloodjournal84113660.

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Fluorescein isothiocyanate (FITC)-conjugated phosphodiester and phosphorothioate oligonucleotides were used in four-color flow cytometry with murine bone marrow cells stained with monoclonal antibody specific for the differentiation markers B220, S7 (CD43), and BP-1 to show possible stage-specific oligonucleotide uptake. Relatively low uptake was observed among pre-Pro- and early Pro-B cells. Late Pro- B- and pre-B cells had increased oligonucleotide uptake, whereas B cells had a lower level. Cell membrane binding of oligonucleotides varied during B-cell differentiation in parallel with intern

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26

He, Zhili, Liyou Wu, Matthew W. Fields, and Jizhong Zhou. "Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression." Applied and Environmental Microbiology 71, no. 9 (2005): 5154–62. http://dx.doi.org/10.1128/aem.71.9.5154-5162.2005.

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ABSTRACT Microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole-genome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal intensity, numbers of genes detected, specificity, sensitivity, and differential gene expression under experimental conditions. Hybridizations conducted at 42°C, 45°C, 50°C, and 60°C indicated th

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27

SHARPE, CLAIRE C., MARK E. C. DOCKRELL, MAZHAR I. NOOR, BRETT P. MONIA, and BRUCE M. HENDRY. "Role of Ras Isoforms in the Stimulated Proliferation of Human Renal Fibroblasts in Primary Culture." Journal of the American Society of Nephrology 11, no. 9 (2000): 1600–1606. http://dx.doi.org/10.1681/asn.v1191600.

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Abstract. The proliferation of renal fibroblasts is implicated in the pathophysiologic processes of renal fibrosis. Many of the growth factors involved in proliferation are known to activate intracellular signaling pathways that converge on Ras monomeric GTPases. Although three ras family genes exist, their functional specificity is not yet known. Using antisense oligonucleotides, a role for Kirsten (Ki)-Ras in the stimulated proliferation of a primate renal fibroblast cell line was previously demonstrated. This study examines Ras in primary cultures of adult human renal fibroblasts. Using rev

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28

Winkler, Johannes, and Christian R. Noe. "Oligonucleotide Charge Reversal: 2′-O-Lysylaminohexyl Modified Oligonucleotides." Nucleosides, Nucleotides & Nucleic Acids 26, no. 8-9 (2007): 939–42. http://dx.doi.org/10.1080/15257770701507978.

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CARUTHERS, M. H. "ChemInform Abstract: Synthesis of Oligonucleotides and Oligonucleotide Analogs." ChemInform 23, no. 16 (2010): no. http://dx.doi.org/10.1002/chin.199216340.

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Lei, Yi, and Ryan Hili. "Structure–activity relationships of the ATP cofactor in ligase-catalysed oligonucleotide polymerisations." Organic & Biomolecular Chemistry 15, no. 11 (2017): 2349–52. http://dx.doi.org/10.1039/c6ob02792j.

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Guzzo-Pernell, Nancy, and Geoffrey W. Tregear. "Triple helical DNA formation by a hydrophobic oligonucleotide-peptide hybrid molecule." Australian Journal of Chemistry 53, no. 8 (2000): 699. http://dx.doi.org/10.1071/ch00114.

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Stable triple helical DNA formation with triplex forming oligonucleotide–peptide hybrids, containing hydrophobic peptides, has previously been difficult to achieve. We report hereon stable triplexation with an oligonucleotide–peptide hybrid containing a hydrophobic peptide. The peptide of interest is the gp41b peptide, which is derived from the hydrophobic terminal domain of the HIV transmembrane glycoprotein gp41. Triplex forming oligonucleotides conjugated to the gp41b peptide were prepared with and without intramolecular spacer linkers. Hybrids with appropriate spacers formed stable triplex

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Goddard, Layla R., Charlotte E. Mardle, Hassan Gneid, et al. "An Investigation into the Potential of Targeting Escherichia coli rne mRNA with Locked Nucleic Acid (LNA) Gapmers as an Antibacterial Strategy." Molecules 26, no. 11 (2021): 3414. http://dx.doi.org/10.3390/molecules26113414.

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The increase in antibacterial resistance is a serious challenge for both the health and defence sectors and there is a need for both novel antibacterial targets and antibacterial strategies. RNA degradation and ribonucleases, such as the essential endoribonuclease RNase E, encoded by the rne gene, are emerging as potential antibacterial targets while antisense oligonucleotides may provide alternative antibacterial strategies. As rne mRNA has not been previously targeted using an antisense approach, we decided to explore using antisense oligonucleotides to target the translation initiation regi

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Hao, Fei, Yuhuan Li, Jing Zhu, et al. "Polyethylenimine-based Formulations for Delivery of Oligonucleotides." Current Medicinal Chemistry 26, no. 13 (2019): 2264–84. http://dx.doi.org/10.2174/0929867325666181031094759.

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Polyethyleneimine (PEI) is well-known as a non-viral gene delivery vector, especially for oligonucleotide delivery. However, its clinical applications are significantly limited due to its high cationic charge, lack of specificity, and interaction with the proteins and nontarget cells in the biological fluids, resulting in high cytotoxicity, poor stability and low transfection efficiency for oligonucleotides transporting. It has been shown that the molecular weight (MW) of PEI, degree of branching, N/P ratio, buffer capacity, oligonucleotide structure, culture medium pH, serum, presence or abse

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Farooqi, Kanwal, Marjan Ghazvini, Leah D. Pride, et al. "A Protein in the Yeast Saccharomyces cerevisiae Presents DNA Binding Homology to the p53 Checkpoint Protein and Tumor Suppressor." Biomolecules 10, no. 3 (2020): 417. http://dx.doi.org/10.3390/biom10030417.

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Saccharomyces cerevisiae does not contain a p53 homolog. Utilizing this yeast as an in vivo test tube model, our aim was to investigate if a yeast protein would show p53 DNA binding homology. Electrophoretic mobility shift analyses revealed the formation of specific DNA-protein complexes consisting of S. cerevisiae nuclear protein(s) and oligonucleotides containing p53 DNA binding sites. A S. cerevisiae p53 binding site factor (Scp53BSF) bound to a p53 synthetic DNA-consensus sequence (SCS) and a p53 binding-site sequence from the MDM2 oncogene. The complexes were of comparable size. Like mamm

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Zhang, R., Z. Lu, X. Zhang, et al. "In vivo stability and disposition of a self-stabilized oligodeoxynucleotide phosphorothioate in rats." Clinical Chemistry 41, no. 6 (1995): 836–43. http://dx.doi.org/10.1093/clinchem/41.6.836.

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Abstract The use of antisense oligonucleotides represents a novel, genetically based therapy. The biostability and pharmacokinetics of a 33-mer self-stabilized oligodeoxynucleotide with significant anti-HIV activity was determined in rats after intravenous administration of [35S]oligodeoxynucleotide. Plasma disappearance of the labeled oligodeoxynucleotide could be described by a two-compartment model, with half-lives of 0.54 and 41.44 h. The oligodeoxynucleotide in plasma remained mainly intact. Urinary excretion represented the major elimination pathway, with approximately 27% of the adminis

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Takakura, Kazuki, Atsushi Kawamura, Yuichi Torisu, Shigeo Koido, Naohisa Yahagi, and Masayuki Saruta. "The Clinical Potential of Oligonucleotide Therapeutics against Pancreatic Cancer." International Journal of Molecular Sciences 20, no. 13 (2019): 3331. http://dx.doi.org/10.3390/ijms20133331.

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Although many diagnostic and therapeutic modalities for pancreatic cancer have been proposed, an urgent need for improved therapeutic strategies remains. Oligonucleotide therapeutics, such as those based on antisense RNAs, small interfering RNA (siRNA), microRNA (miRNA), aptamers, and decoys, are promising agents against pancreatic cancer, because they can identify a specific mRNA fragment of a given sequence or protein, and interfere with gene expression as molecular-targeted agents. Within the past 25 years, the diversity and feasibility of these drugs as diagnostic or therapeutic tools have

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Meng, Zhaojing, and Patrick A. Limbach. "Shotgun Sequencing Small Oligonucleotides by Nozzle-Skimmer Dissociation and Electrospray Ionization Mass Spectrometry." European Journal of Mass Spectrometry 11, no. 2 (2005): 221–29. http://dx.doi.org/10.1255/ejms.736.

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Nozzle-skimmer dissociation in combination with de novo sequencing was investigated as an approach for increasing the throughput of oligonucleotide analysis attainable by electrospray ionization mass spectrometry. An experimental method allowing for the sequential generation of precursor and fragment ion data during direct infusion of samples was developed. These data can then be used with readily available de novo sequencing software to characterize small oligonucleotides. When this approach was applied to mixtures of oligonucleotides, it was found that de novo sequencing becomes limited due

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Gissot, Arnaud, Khalid Oumzil, Amit Patwa, and Philippe Barthélémy. "A hybrid lipid oligonucleotide: a versatile tool for supramolecular chemistry." New J. Chem. 38, no. 11 (2014): 5129–34. http://dx.doi.org/10.1039/c4nj00850b.

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Kiviniemi, Anu, Petri Heinonen, and Harri Lönnberg. "Oligonucleotides bearing pentaerythritol-derived mass tags." Open Chemistry 5, no. 1 (2007): 191–200. http://dx.doi.org/10.2478/s11532-006-0046-9.

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AbstractFive different di-O-alkylated pentaerythritol phosphoramidite building blocks (2a–e) were synthesized and introduced into oligonucleotides to obtain mass-tagged probes (6a–f) useful in RNA transcription profiling. These non-nucleosidic mass tags allow categorization of oligonucleotide probes having identical nucleoside content and, hence, identification of the probe hybridized to RNA by mass spectrometry analysis. Hybridization properties of the oligonucleotide conjugates were elucidated by melting temperature measurements.

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Agramunt, Jordi, Enrique Pedroso, Silvia Kreda, Rudolph Juliano, and Anna Grandas. "Retro-1-Oligonucleotide Conjugates. Synthesis and Biological Evaluation." Molecules 24, no. 3 (2019): 579. http://dx.doi.org/10.3390/molecules24030579.

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Addition of small molecule Retro-1 has been described to enhance antisense and splice switching oligonucleotides. With the aim of assessing the effect of covalently linking Retro-1 to the biologically active oligonucleotide, three different derivatives of Retro-1 were prepared that incorporated a phosphoramidite group, a thiol or a 1,3-diene, respectively. Retro-1–oligonucleotide conjugates were assembled both on-resin (coupling of the phosphoramidite) and from reactions in solution (Michael-type thiol-maleimide reaction and Diels-Alder cycloaddition). Splice switching assays with the resultin

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Yantsevich, Aleksei V., Veronika V. Shchur, and Sergey A. Usanov. "Oligonucleotide Preparation Approach for Assembly of DNA Synthons." SLAS TECHNOLOGY: Translating Life Sciences Innovation 24, no. 6 (2019): 556–68. http://dx.doi.org/10.1177/2472630319850534.

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An effective oligonucleotide preparation approach for the thermodynamically balanced, inside-out (TBIO) PCR-based assembly of long synthetic DNA molecules (synthons) is described in the current work. We replaced the necessity to purify individual oligonucleotides with just one purification procedure per approximately 500 base pairs (bp) of duplex DNA. So for an enhanced green fluorescent protein (EGFP) gene of 717 bp, we synthesized 24 oligonucleotides with a length of 50 bases and performed just two solid-phase extraction (SPE) purification procedures. It was found that the capacity of ZipTip

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Verri, A., P. Mazzarello, S. Spadari, and F. Focher. "Uracil-DNA glycosylases preferentially excise mispaired uracil." Biochemical Journal 287, no. 3 (1992): 1007–10. http://dx.doi.org/10.1042/bj2871007.

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We have investigated the substrate specificity of human, viral and bacterial uracil-DNA glycosylases employing as substrate double-stranded oligonucleotides containing in the same position of the 5′-32P-labelled strand an uracil residue facing, on the complementary strand, guanine (mimicking cytosine deamination) or adenine (mimicking dUTP misincorporation). The enzyme removal of uracil was monitored and quantified by the generation of alkali-sensitive apyrimidinic sites. All three uracil-DNA glycosylases excise uracil from mispaired oligonucleotides (U/G) more efficiently than from paired oli

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Brachman, Erin E., and Eric B. Kmiec. "Targeted Nucleotide Repair of cyc1 Mutations in Saccharomyces cerevisiae Directed by Modified Single-Stranded DNA Oligonucleotides." Genetics 163, no. 2 (2003): 527–38. http://dx.doi.org/10.1093/genetics/163.2.527.

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Abstract Modified single-stranded DNA oligonucleotides have been used to direct base changes in the CYC1 gene of Saccharomyces cerevisiae. In this process, the oligonucleotide is believed to hybridize to the target site through the action of a DNA recombinase and, once bound, DNA repair enzymes act to excise the nucleotide, replace it, and revert the gene to wild-type status. Nucleotide exchange exhibits a strand bias as, in most cases, a higher level of base reversal appears in cells in which the oligonucleotide is designed to hybridize to the nontemplate strand. But, in one case, a higher le

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Studzińska, Sylwia, Magdalena Skoczylas, Szymon Bocian, Anna Dembska, and Bogusław Buszewski. "Attachment of hybridizable oligonucleotides to a silica support and its application for selective extraction of unmodified and antisense oligonucleotides from serum samples." RSC Advances 10, no. 28 (2020): 16221–30. http://dx.doi.org/10.1039/d0ra01620a.

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SIPES, TAMARA B., and SUSAN M. FREIER. "PREDICTION OF ANTISENSE OLIGONUCLEOTIDE EFFICACY USING AGGREGATE MOTIFS." Journal of Bioinformatics and Computational Biology 06, no. 05 (2008): 919–32. http://dx.doi.org/10.1142/s0219720008003795.

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Antisense oligonucleotide technology allows the targeted reduction of mRNA expression through the in vitro application of short (~20 nt) DNA molecules. Oligonucleotides are valuable both in the study of gene regulation and for having potential therapeutic effects. In theory, a base sequence complementary to a region of the transcript would hybridize to its mRNA target. Nevertheless, in practice some complementary antisense oligonucleotides are more active and more potent than others in suppressing specific gene expression. We present a novel computational approach to modeling oligonucleotide e

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Nguyen, Jennifer M., Martin Gilar, Brooke Koshel, et al. "Assessing the impact of nonspecific binding on oligonucleotide bioanalysis." Bioanalysis 13, no. 16 (2021): 1233–44. http://dx.doi.org/10.4155/bio-2021-0115.

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Aim: Accurate and reliable quantification of oligonucleotides can be difficult, which has led to an increased focus on bioanalytical methods for more robust analyses. Recent advances toward mitigating sample losses on liquid chromatography (LC) systems have produced recovery advantages for oligonucleotide separations. Results & methodology: LC instruments and columns constructed from MP35N metal alloy and stainless steel columns were compared against LC hardware modified with hybrid inorganic-organic silica surfaces. Designed to minimize metal-analyte adsorption, these surfaces demonstrate

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Gunneberg, A., G. Scobie, K. Hayes, and N. Kalsheker. "Competitive assay to improve the specificity of detection of single-point mutations in alpha 1-antitrypsin deficiency." Clinical Chemistry 39, no. 10 (1993): 2157–62. http://dx.doi.org/10.1093/clinchem/39.10.2157.

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Abstract Allele-specific oligonucleotides are used widely for the detection of single point mutations in genes. A modification of this assay based on competition has been developed for detection of the Z mutation of alpha 1-antitrypsin (alpha 1-AT). The normal alpha 1-AT allele is referred to as M, and the Z mutation arises from a single base substitution. Amplified DNA products corresponding to homozygous M, heterozygous MZ, and homozygous Z obtained by the polymerase chain reaction were incubated with a twofold molar excess of unlabeled oligonucleotide prior to hybridization with a radiolabe

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CHAKRABORTY, Rila, Dalia DASGUPTA, Samit ADHYA, and Mukul K. BASU. "Cationic liposome-encapsulated antisense oligonucleotide mediates efficient killing of intracellular Leishmania." Biochemical Journal 340, no. 2 (1999): 393–96. http://dx.doi.org/10.1042/bj3400393.

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Antisense oligonucleotides have been considered as inhibitors of growth of intracellular parasites such as Leishmania, but only limited inhibition has been observed in vitro. We have encapsulated an antisense oligonucleotide, complementary to the Leishmania universal miniexon sequence, in cationic liposomes. Low concentrations (4 μM) of encapsulated oligonucleotides specifically reduced the amastigote burden within cultured macrophages by 80%. This result illustrates the importance of effective delivery for efficient antiparasitic activity of antisense oligonucleotides.

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Xiong, Haoyu, Rakesh N. Veedu, and Sarah D. Diermeier. "Recent Advances in Oligonucleotide Therapeutics in Oncology." International Journal of Molecular Sciences 22, no. 7 (2021): 3295. http://dx.doi.org/10.3390/ijms22073295.

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Cancer is one of the leading causes of death worldwide. Conventional therapies, including surgery, radiation, and chemotherapy have achieved increased survival rates for many types of cancer over the past decades. However, cancer recurrence and/or metastasis to distant organs remain major challenges, resulting in a large, unmet clinical need. Oligonucleotide therapeutics, which include antisense oligonucleotides, small interfering RNAs, and aptamers, show promising clinical outcomes for disease indications such as Duchenne muscular dystrophy, familial amyloid neuropathies, and macular degenera

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WU, AIGUO, TATJANA PAUNESKU, ERIC M. B. BROWN, et al. "TITANIUM DIOXIDE NANOPARTICLES ASSEMBLED BY DNA MOLECULES HYBRIDIZATION AND LOADING OF DNA INTERACTING PROTEINS." Nano 03, no. 01 (2008): 27–36. http://dx.doi.org/10.1142/s1793292008000836.

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This work demonstrates the assembly of TiO 2 nanoparticles with attached DNA oligonucleotides into a 3D mesh structure by allowing base pairing between oligonucleotides. A change of the ratio of DNA oligonucleotide molecules and TiO 2 nanoparticles regulates the size of the mesh as characterized by UV-visible light spectra, transmission electron microscopy (TEM) and atomic force microscopy (AFM) images. This type of 3D mesh, based on TiO 2-DNA oligonucleotide nanoconjugates, can be used for studies of nanoparticle assemblies in materials science, energy science related to dye-sensitized solar

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