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Antisense & Nucleic Acid Drug... Feb 199731P NMR is an extremely valuable tool for oligonucleotide research and development. This brief commentary, which is directed to scientists who do not regularly use 31P... (Review)
Review
31P NMR is an extremely valuable tool for oligonucleotide research and development. This brief commentary, which is directed to scientists who do not regularly use 31P NMR in their work, attempts to outline some of the principles, considerations, and representative applications of 31P NMR spectroscopy in oligonucleotide research and development.
Topics: Drug Stability; Isotope Labeling; Magnetic Resonance Spectroscopy; Oligonucleotides; Phosphorus Isotopes; Quality Control
PubMed: 9055040
DOI: 10.1089/oli.1.1997.7.55 -
Farmaco (Societa Chimica Italiana :... Mar 2000The application of synthetic oligonucleotide combinatorial libraries is described in the studies of triplex DNA. A new method of selection of dispersed (beaded)... (Review)
Review
The application of synthetic oligonucleotide combinatorial libraries is described in the studies of triplex DNA. A new method of selection of dispersed (beaded) oligonucleotide combinatorial libraries based on the use of streptavidin magnetic beads is presented. A combinatorial chemistry approach is also proposed for studies of polyaminooligonucleotides.
Topics: Carbohydrate Sequence; DNA; Molecular Sequence Data; Oligonucleotides
PubMed: 10919074
DOI: 10.1016/s0014-827x(00)00014-8 -
Proceedings of the National Academy of... Jun 1995Synthetic oligonucleotides and their analogs have attracted considerable interest recently. These compounds may lead to highly specific therapeutic agents, as well as to... (Comparative Study)
Comparative Study
Synthetic oligonucleotides and their analogs have attracted considerable interest recently. These compounds may lead to highly specific therapeutic agents, as well as to powerful diagnostic tools. Here, we present the synthesis of uniformly modified oligodeoxyribonucleotide N3'-->P5' phosphoramidates containing 3'-NHP(O)(O-)O-5' internucleoside linkages and the study of their hybridization properties. Thermal dissociation experiments show that these compounds form very stable duplexes with single-stranded DNA, RNA, and with themselves following Watson-Crick base pairing. The duplex thermal stability was enhanced by 2.2-2.6 degrees C per modified linkage compared with phosphodiesters. The structure of complexes formed by phosphoramidates closely resembles that of RNA oligomers and corresponds to an A form, as judged by CD spectroscopy. N3'-->P5' phosphoramidates also form stable triplexes with double-stranded DNA under near-physiological conditions when natural phosphodiesters fail to do so. Physicochemical characteristics of the amidates are similar to those of RNA oligomers, even though they are composed of 2'-deoxyfuranose-based nucleosides.
Topics: Amides; Base Sequence; Circular Dichroism; DNA; Drug Stability; Indicators and Reagents; Molecular Sequence Data; Molecular Structure; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Oligonucleotides; Oligoribonucleotides; Phosphoric Acids; RNA
PubMed: 7541136
DOI: 10.1073/pnas.92.13.5798 -
Bioanalysis Jun 2019Reliable quantitative LC-MS methodology has been established and validated for an oligonucleotide in plasma in a fresh and unique fashion, free of ion-pairing reagents...
Reliable quantitative LC-MS methodology has been established and validated for an oligonucleotide in plasma in a fresh and unique fashion, free of ion-pairing reagents and the various associated deleterious effects from primary solution preparation through sample preparation and extraction to the LC-MS analytical end point, offering a highly selective mixed-mode solid-phase extraction with hydrophilic-interaction liquid chromatography as the chromatographic element prior to SRM detection. Inter- and intra-assay accuracy and precision ranged from 97.9 to 111% and 2.75 to 9.66%, respectively. Recoveries of 50% were attained, and there was no significant matrix effect manifestation. The method demonstrated rugged performance and reliability under the optimized conditions, indicating a possible exciting new avenue, free of ion-pairing, for general application in oligonucleotide quantitative LC-MS.
Topics: Analytic Sample Preparation Methods; Base Sequence; Calibration; Chromatography, Liquid; Humans; Hydrophobic and Hydrophilic Interactions; Oligonucleotides
PubMed: 31241345
DOI: 10.4155/bio-2019-0031 -
Nucleic Acid Therapeutics Oct 2023This white paper summarizes the recommendations of the absorption, distribution, metabolism, and excretion (ADME) Subcommittee of the Oligonucleotide Safety Working...
This white paper summarizes the recommendations of the absorption, distribution, metabolism, and excretion (ADME) Subcommittee of the Oligonucleotide Safety Working Group for the characterization of absorption, distribution, metabolism, and excretion of oligonucleotide (ON) therapeutics in nonclinical studies. In general, the recommended approach is similar to that for small molecule drugs. However, some differences in timing and/or scope may be warranted due to the greater consistency of results across ON classes as compared with the diversity among small molecule classes. For some types of studies, a platform-based approach may be appropriate; once sufficient data are available for the platform, presentation of these data should be sufficient to support development of additional ONs of the same platform. These recommendations can serve as a starting point for nonclinical study design and foundation for discussions with regulatory agencies.
Topics: Oligonucleotides
PubMed: 37590469
DOI: 10.1089/nat.2023.0011 -
Nucleic Acid Therapeutics Oct 2014This white paper summarizes the current consensus of the Reproductive Subcommittee of the Oligonucleotide Safety Working Group on strategies to assess potential... (Review)
Review
This white paper summarizes the current consensus of the Reproductive Subcommittee of the Oligonucleotide Safety Working Group on strategies to assess potential reproductive and/or developmental toxicities of therapeutic oligonucleotides (ONs). The unique product characteristics of ONs require considerations when planning developmental and reproductive toxicology studies, including (a) chemical characteristics, (b) assessment of intended and unintended mechanism of action, and (c) the optimal exposure, including dosing regimen. Because experience across the various classes of ONs as defined by their chemical backbone is relatively limited, best practices cannot be defined. Rather, points to consider are provided to help in the design of science-based reproductive safety evaluation programs based upon product attributes.
Topics: Animals; Biomarkers, Pharmacological; Drug Administration Routes; Drug Administration Schedule; Drug Dosage Calculations; Drug Evaluation, Preclinical; Genetic Fitness; Guidelines as Topic; Humans; Models, Animal; Oligonucleotides; Reproduction
PubMed: 25137397
DOI: 10.1089/nat.2014.0490 -
Journal of Pharmaceutical Sciences Aug 2003Oligonucleotides (ONs) are a new class of therapeutic compounds under investigation for the treatment of a variety of disease states, such as cancer and HIV, and for FDA... (Review)
Review
Oligonucleotides (ONs) are a new class of therapeutic compounds under investigation for the treatment of a variety of disease states, such as cancer and HIV, and for FDA approval of an anti-CMV retinitis antisense molecule (Vitravene trade mark, Isis Pharmaceuticals). However, these molecules are limited not only by poor cellular uptake, but also by a general lack of understanding regarding the mechanism(s) of ON cellular uptake. As a result, various delivery vehicles have been developed that circumvent the proposed mechanism of uptake, endocytosis, while improving target specific delivery and/or drug stability. This review describes various traditional and novel delivery mechanisms that have been employed to improve ON cellular delivery, cost effectiveness, and therapeutic efficacy.
Topics: Animals; Drug Delivery Systems; Humans; Oligonucleotides
PubMed: 12884243
DOI: 10.1002/jps.10399 -
Bioanalysis Nov 2019Advancements in RNA interference therapeutics have triggered development of improved bioanalytical methods for oligonucleotide metabolite profiling and high-throughput...
Advancements in RNA interference therapeutics have triggered development of improved bioanalytical methods for oligonucleotide metabolite profiling and high-throughput quantification in biological matrices. HPLC coupled with high-resolution mass spectrometry (LC-HRMS) methods were developed to investigate the metabolism of a REVERSIR™ molecule Plasma and tissue samples were extracted using solid-phase extraction followed by LC-HRMS analysis for metabolite profiling and quantification. The method was qualified from 10 to 5000 ng/ml (plasma) and 100 to 50000 ng/g (liver and kidney). In rat liver, intra and interday accuracy ranged from 80.9 to 118.5% and 88.4 to 111.9%, respectively, with acceptable precision (<20% CV). The LC-HRMS method can be applied for metabolite profiling and quantification of oligonucleotides in biological matrices.
Topics: Animals; Base Sequence; Chromatography, Liquid; Liver; Macaca fascicularis; Mass Spectrometry; Metabolomics; Oligonucleotides
PubMed: 31829056
DOI: 10.4155/bio-2019-0137 -
Nucleic Acid Therapeutics Oct 2023We describe here the design, synthesis, physicochemical properties, and hepatitis B antiviral activity of new 2'-O-alkyl ribonucleotide N3'→P5' phosphoramidate...
We describe here the design, synthesis, physicochemical properties, and hepatitis B antiviral activity of new 2'-O-alkyl ribonucleotide N3'→P5' phosphoramidate (2'-O-alkyl-NPO) and (thio)-phosphoramidite (2'--alkyl-NPS) oligonucleotide analogs. Oligonucleotides with different 2'-O-alkyl modifications such as 2'-O-methyl, -O-ethyl, -O-allyl, and -O-methoxyethyl combined with 3'-amino sugar-phosphate backbone were synthesized and evaluated. These molecules form stable duplexes with complementary DNA and RNA strands. They show an increase in duplex melting temperatures of up to 2.5°C and 4°C per linkage, respectively, compared to unmodified DNA. The results agree with predominantly C3'-endo sugar pucker conformation. Moreover, 2'-O-alkyl phosphoramidites demonstrate higher hydrolytic stability at pH 5.5 than 2'-deoxy NPOs. In addition, the relative lipophilicity of the 2'-O-alkyl-NPO and NPS oligonucleotides is higher than that of their 3'-O- counterparts. The 2'-O-alkyl-NPS oligonucleotides were evaluated as antisense (ASO) compounds and using Hepatitis B virus as a model system. Subcutaneous delivery of GalNAc conjugated 2'-O-MOE-NPS gapmers demonstrated higher activity than the 3'-O-containing 2'-O-MOE counterpart. The properties of 2'-O-alkyl-NPS constructs make them attractive candidates as ASO suitable for further evaluation and development.
Topics: Oligonucleotides; Oligonucleotides, Antisense; Phosphoric Acids; Amides
PubMed: 37638793
DOI: 10.1089/nat.2023.0014 -
Chemistry & Biodiversity Oct 2004Nowadays, oligonucleotide-carbohydrate conjugates are used in antisense biotechnology and in the study of glycosylated DNA functioning in vitro. The application of mono-... (Review)
Review
Nowadays, oligonucleotide-carbohydrate conjugates are used in antisense biotechnology and in the study of glycosylated DNA functioning in vitro. The application of mono- and disaccharide phosphoramidites, solid-phase supports with immobilized carbohydrates, glycosylated nucleoside phosphoramidites, and postsynthetic conjugation of reactive sugar derivatives with oligonucleotides for preparation of oligonucleotide-carbohydrate conjugates have been systematically studied. The advantages and disadvantages of these approaches are considered. Possible strategies for synthesis of glycoclusters with different topologies conjugated to DNA are discussed. Applications of oligonucleotide-carbohydrate conjugates are highlighted. Studies of interactions of glycosylated oligonucleotides with proteins and effective cell-specific delivery of oligonucleotide-carbohydrate conjugates are discussed.
Topics: Carbohydrates; DNA; Drug Delivery Systems; Glycosylation; Oligonucleotides
PubMed: 17191787
DOI: 10.1002/cbdv.200490104