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Current Protocols in Nucleic Acid... Mar 2016Synthesis of oligonucleotide ending with an aldehyde functional group at their 5'-end (5'-AON) is possible for both DNA (5'-AODN) and RNA (5'-AORN) series irrespectively...
Synthesis of oligonucleotide ending with an aldehyde functional group at their 5'-end (5'-AON) is possible for both DNA (5'-AODN) and RNA (5'-AORN) series irrespectively of the nature of the last nucleobase. The 5'-alcohol of on-support ODN is mildly oxidized under Moffat conditions. Transient protection of the resulting aldehyde by N,N'-diphenylethylenediamine derivatives allows cleavage, deprotection, and RP-HPLC purification of the protected 5'-AON. Finally, 5'-AON is deprotected by usual acetic acid treatment. In the aggregates, 5'-AON can be now synthesized and purified as routinely as non-modified ODNs, following procedures similar to the well-known "DMT-On" strategy.
Topics: Aldehydes; Chromatography, High Pressure Liquid; Chromatography, Reverse-Phase; Oligonucleotides
PubMed: 26967469
DOI: 10.1002/0471142700.nc0470s64 -
Methods in Molecular Biology (Clifton,... 2019Across the pharmaceutical industry, there is increasing interest and need to investigate the biotransformation of oligonucleotide drugs. The method of choice is...
Across the pharmaceutical industry, there is increasing interest and need to investigate the biotransformation of oligonucleotide drugs. The method of choice is high-resolution mass spectrometry due to its unmet sensitivity and specificity.Here, we describe a method developed and applied in our laboratory studying the biotransformation of phosphorothioate-containing oligonucleotide drugs. This method is based on capillary flow liquid chromatography with column switching coupled to high-resolution mass spectrometry.
Topics: Biotransformation; Chromatography, Liquid; Data Analysis; Hepatocytes; Phosphorothioate Oligonucleotides; Tandem Mass Spectrometry
PubMed: 31410805
DOI: 10.1007/978-1-4939-9670-4_18 -
Chembiochem : a European Journal of... Jul 2010
Review
Topics: Animals; Drug Carriers; Drug Delivery Systems; Humans; Oligonucleotides; Peptides
PubMed: 20575132
DOI: 10.1002/cbic.201000138 -
Nature
Topics: Computer Simulation; DNA; Gene Expression Regulation; Genetic Therapy; Humans; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes; Oligonucleotides
PubMed: 1758492
DOI: 10.1038/354505a0 -
Nucleic Acids Research Jul 2018The success of widely used oligonucleotide-based experiments, ranging from PCR to microarray, strongly depends on an accurate design. The design process involves a...
The success of widely used oligonucleotide-based experiments, ranging from PCR to microarray, strongly depends on an accurate design. The design process involves a number of steps, which use specific parameters to produce high quality oligonucleotides. Oli2go is an efficient, user friendly, fully automated multiplex oligonucleotide design tool, which performs primer and different hybridization probe designs as well as specificity and cross dimer checks in a single run. The main improvement to existing oligonucleotide design web-tools is that oli2go combines multiple steps in an all-in-one solution, where other web applications only accomplish parts of the whole design workflow. Especially, the oli2go specificity check is not only performed against a single species (e.g. mouse), but against bacteria, viruses, fungi, invertebrates, plants, protozoa, archaea and sequences from whole genome shotgun sequence projects and environmental samples, at once. This allows the design of highly specific oligonucleotides in multiplex applications, which is further assured by performing dimer checks not only on the primers themselves, but in an all-against-all fashion. The software is freely accessible to all users at http://oli2go.ait.ac.at/.
Topics: Algorithms; DNA Primers; Internet; Oligonucleotides; Software
PubMed: 29718464
DOI: 10.1093/nar/gky319 -
Antisense Research and Development 1993
Topics: Humans; Oligonucleotides; Oligonucleotides, Antisense
PubMed: 8495103
DOI: 10.1089/ard.1993.3.1 -
Angewandte Chemie (International Ed. in... Jul 2013The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions.... (Review)
Review
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
Topics: Nucleic Acid Hybridization; Nucleic Acids; Oligonucleotides
PubMed: 23794204
DOI: 10.1002/anie.201208460 -
Oligonucleotides 2004
Topics: Artifacts; Genome; Oligonucleotides; Polymerase Chain Reaction; Substrate Specificity
PubMed: 15294078
DOI: 10.1089/1545457041526272 -
The Analyst May 2012We analyzed oligonucleotides by nanoparticle-assisted laser desorption/ionization (nano-PALDI) mass spectrometry (MS). To this end, we prepared several kinds of...
We analyzed oligonucleotides by nanoparticle-assisted laser desorption/ionization (nano-PALDI) mass spectrometry (MS). To this end, we prepared several kinds of nanoparticles (Cr-, Fe-, Mn-, Co-based) and optimized the nano-PALDI MS method to analyze the oligonucleotides. Iron oxide nanoparticles with diammonium hydrogen citrate were found to serve as an effective ionization-assisting reagent in MS. The mass spectra showed both [M - H](-) and [M + xMe(2+)- H](-) (Me: transition metal) peaks. The number of metal-adducted ion signals depended on the length of the oligonucleotide. This phenomenon was only observed using bivalent metal core nanoparticles, not with any other valency metal core nanoparticles. Our pilot study demonstrated that iron oxide nanoparticles could easily ionize samples such as chemical drugs and peptides as well as oligonucleotides without the aid of an oligonucleotide-specific chemical matrix (e.g., 3-hydroxypicolinic acid) used in conventional MS methods. These results suggested that iron-based nanoparticles may serve as the assisting material of ionization for genes and other biomolecules.
Topics: Base Sequence; DNA; Lasers; Mass Spectrometry; Nanoparticles; Oligonucleotides; Oxides; RNA; Transition Elements
PubMed: 22337326
DOI: 10.1039/c2an16237g -
Progress in Nucleic Acid Research and... 2003
Review
Topics: Base Pairing; Dinucleoside Phosphates; Hydrogen-Ion Concentration; Nucleic Acid Conformation; Oligonucleotides; Thermodynamics
PubMed: 14604016
DOI: 10.1016/s0079-6603(03)75009-0