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Nucleosides, Nucleotides & Nucleic Acids 2013A convenient synthetic strategy has been designed to prepare an alkyne-modified synthon for automated DNA synthesis. It is based on the key O-DMTr-protected...
A convenient synthetic strategy has been designed to prepare an alkyne-modified synthon for automated DNA synthesis. It is based on the key O-DMTr-protected 4-(2-hydroxyethyl)morpholin-2,3-dione and building blocks obtained by its functionalization by various aliphatic amines. A respective nonnucleosidic phosphoramidite monomer containing a terminal alkyne in the side-chain was synthesized, and corresponding oligothymidylates incorporating the modification in various positions were prepared. The presence of the alkyne group was confirmed by Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) between the functionalized oligonucleotide and an azide derivative of 7-nitro-2,1,3-benzoxadiazole.
Topics: Alkynes; Azides; Click Chemistry; Oligonucleotides; Organophosphorus Compounds; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 23638924
DOI: 10.1080/15257770.2013.787147 -
Organic Letters Nov 2007Se-(2-cyanoethyl)phthalimide was synthesized from di-(2-cyanoethyl) diselenide. This reagent was found to be an efficient selenium transfer reagent in the synthesis of...
Se-(2-cyanoethyl)phthalimide was synthesized from di-(2-cyanoethyl) diselenide. This reagent was found to be an efficient selenium transfer reagent in the synthesis of selenophosphates. Thus, nucleotide H-phosphonate diesters that are formed in situ through the H-phosphonate chemistry undergo quantitative reaction with Se-(2-cyanoethyl)phthalamide. The resulting Se-(2-cyanoethyl) oligonucleotide phosphoroselenoate triesters are subsequently deprotected to give oligonucleotide phosphoroselenoate diesters in excellent yields.
Topics: Chromatography, High Pressure Liquid; Magnetic Resonance Spectroscopy; Molecular Structure; Oligonucleotides; Organoselenium Compounds
PubMed: 17973486
DOI: 10.1021/ol702305v -
Biophysical Chemistry Oct 2010Detection and quantitation of biomolecules is one of the most commonly performed measurements in biomedical research and clinical diagnostics. There is high demand for... (Review)
Review
Detection and quantitation of biomolecules is one of the most commonly performed measurements in biomedical research and clinical diagnostics. There is high demand for convenient, rapid and sensitive biomolecule detection methodologies. In this review we discuss a family of sensors that have been developed in our laboratory that share a common simple biophysical mechanism of action and that are capable of rapid detection of a diverse range of biological targets. The sensors generate fluorescence signal in the presence of the target molecule through target-induced association of short fluorochrome-labeled complementary oligonucleotides that are attached to target recognition elements of the sensors (antibodies, aptamers, etc.) via nanometer scale flexible linkers. This sensor design can be used for detecting proteins, antibodies, nucleic acids and whole cells. The assays using these sensors require only adding a sample to the sensor mix followed by simple fluorescence intensity readout. The simplicity, the speed of detection and the potential for miniaturization are the main assets of these sensors.
Topics: Biophysics; Biosensing Techniques; Oligonucleotides; Time Factors
PubMed: 20542627
DOI: 10.1016/j.bpc.2010.05.008 -
Drugs Mar 2017Spinal muscular atrophy (SMA) is a rare autosomal recessive disorder characterized by muscle atrophy and weakness resulting from motor neuron degeneration in the spinal... (Review)
Review
Spinal muscular atrophy (SMA) is a rare autosomal recessive disorder characterized by muscle atrophy and weakness resulting from motor neuron degeneration in the spinal cord and brainstem. It is most commonly caused by insufficient levels of survival motor neuron (SMN) protein (which is critical for motor neuron maintenance) secondary to deletions or mutations in the SMN1 gene. Nusinersen (SPINRAZAâ„¢) is a modified antisense oligonucleotide that binds to a specific sequence in the intron, downstream of exon 7 on the pre-messenger ribonucleic acid (pre-mRNA) of the SMN2 gene. This modulates the splicing of the SMN2 mRNA transcript to include exon 7, thereby increasing the production of full-length SMN protein. Nusinersen is approved in the USA for intrathecal use in paediatric and adult patients with SMA. Regulatory assessments for nusinersen as a treatment for SMA are underway in the EU and several other countries. This article summarizes the milestones in the development of nusinersen leading to this first approval for SMA in paediatric and adult patients.
Topics: Animals; Drug Approval; Humans; Muscular Atrophy, Spinal; Oligonucleotides; Oligonucleotides, Antisense; United States
PubMed: 28229309
DOI: 10.1007/s40265-017-0711-7 -
Methods in Molecular Biology (Clifton,... 2019Molecular dynamics simulations with a state-of-the-art force field provide an atomistic detailed description of the structural and thermodynamic features of...
Molecular dynamics simulations with a state-of-the-art force field provide an atomistic detailed description of the structural and thermodynamic features of biomolecules. Effects of chemical modifications and of the environment such as sequence, solvent, and ionic strength can explicitly be taken into account. Molecular simulation techniques can also provide insight in change in binding affinity, in protonation (pK shift) and tautomeric propensity due to changes in the environment or in the molecular system. The quality and reliability of a simulation depend on the quality of the force field and on the reproducibility of the data, and validation depends on the availability of suitable experimental data. Here, we describe the workflow to investigate oligonucleotide hybrids using molecular simulation including hardware and software information.
Topics: Models, Chemical; Molecular Dynamics Simulation; Molecular Structure; Nucleic Acid Conformation; Oligonucleotides; Thermodynamics
PubMed: 31410793
DOI: 10.1007/978-1-4939-9670-4_6 -
Nucleic Acids Research Apr 2000A new procedure for rapid deprotection of synthetic oligodeoxynucleotides has been developed. While all known deprotection methods require purification to remove the...
A new procedure for rapid deprotection of synthetic oligodeoxynucleotides has been developed. While all known deprotection methods require purification to remove the residual protective groups (e.g. benzamide) and insoluble silicates, the new procedure based on the use of an ammonia-free reagent mixture allows one to avoid the additional purification steps. The method can be applied to deprotect the oligodeoxynucleotides synthesized by using the standard protected nucleoside phosphoramidites dG(iBu), dC(Bz)and dA(Bz).
Topics: Genetic Techniques; Oligodeoxyribonucleotides; Oligonucleotide Array Sequence Analysis; Oligonucleotides
PubMed: 10734206
DOI: 10.1093/nar/28.8.e29 -
Methods in Molecular Biology (Clifton,... 2019Oligonucleotide conjugates have already reached considerable importance in life science research and oligonucleotide drug development. Since the preparation of...
Oligonucleotide conjugates have already reached considerable importance in life science research and oligonucleotide drug development. Since the preparation of oligonucleotide conjugates depends critically on the chemical nature of the used ligand and linker, there is no general and universal procedure. Here, we present a detailed, quick, and facile protocol for attaching fluorescent dyes or cross-linkers of variable chemical stability to oligonucleotides at 3'- or 5'-aminoalkyl handles. Purification and removal of educts and side-products and structural verification by gel electrophoresis and mass spectrometry are presented. Aspects for adapting this protocol for other reaction sites at the oligonucleotide are discussed. We highlight important issues for generating oligonucleotide conjugates with other molecules, including peptide, proteins, and small molecules for receptor-targeting applications. The methodology is suitable for oligonucleotides with various modifications, including stabilized antisense, siRNAs, and miRNAs.
Topics: Cross-Linking Reagents; Electrophoresis, Polyacrylamide Gel; Fluorescent Dyes; Mass Spectrometry; Oligonucleotides; Staining and Labeling
PubMed: 30838609
DOI: 10.1007/978-1-4939-9092-4_4 -
Organic Letters Feb 2016A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal...
A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal nucleosides was developed. The Z-ACSS allowed for the preparation of fully protected deoxyribo- and ribo-oligonucleotides without chromatographic purification and released dimer- to tetramer-size oligonucleotide blocks via hydrogenation using a Pd/C catalyst without significant loss or migration of protective groups such as 5'-end 4,4'-dimethoxtrityl, 2-cyanoethyl on internucleotide bonds, or 2'-TBS.
Topics: Molecular Structure; Nuclear Magnetic Resonance, Biomolecular; Nucleosides; Oligonucleotides
PubMed: 26845521
DOI: 10.1021/acs.orglett.6b00077 -
Bioconjugate Chemistry 2006A facile and efficient method for direct immobilization of phosphorylated oligonucleotides on an epoxy-activated glass surface is described. The new immobilization...
A facile and efficient method for direct immobilization of phosphorylated oligonucleotides on an epoxy-activated glass surface is described. The new immobilization strategy has been analyzed for its performance in DNA microarray under both microwave and thermal conditions. It reflects high immobilization efficiency ( approximately 23%), and signal-to-noise ratio ( approximately 98) and resulted in high hybridization efficiency ( approximately 36%) in comparison to those obtained with standard methods, viz., NTMTA ( approximately 9.76%) and epoxide-amine ( approximately 9.82%). The probes immobilized through the new strategy were found to be heat-stable, since the performance of microarray decreased by only approximately 7% after subjecting it to 20 PCR-like heat cycles, suggesting that the chemistry could be used in integrated PCR/microarray devices. The immobilization of probes following the proposed chemistry resulted in spots of superior quality in terms of spot morphology, spot homogeneity, and signal reproducibility. The constructed microarrays have been successfully used for the discrimination of nucleotide mismatches. In conclusion, these features make the new immobilization strategy ideal for facile, efficient, and cost-effective manufacturing of DNA microarrays.
Topics: Epoxy Compounds; Hot Temperature; Hydrogen-Ion Concentration; Materials Testing; Molecular Structure; Oligonucleotide Array Sequence Analysis; Oligonucleotides; Sensitivity and Specificity; Surface Properties
PubMed: 16984127
DOI: 10.1021/bc0601065 -
Clinical Pharmacokinetics Jan 1995Antisense oligonucleotides are promising therapeutic agents for the treatment of life-threatening diseases. Intravenous injection of phosphodiester oligonucleotide... (Review)
Review
Antisense oligonucleotides are promising therapeutic agents for the treatment of life-threatening diseases. Intravenous injection of phosphodiester oligonucleotide analogue (P-oligonucleotide) in monkeys shows that the oligonucleotide is degraded rapidly in the plasma with a half-life of about 5 minutes. Administration of a single dose of the phosphorothioate (S-oligonucleotide) in animals by the intravenous route reveals biphasic plasma elimination. An initial short half-life (0.53 to 0.83 hours) represents distribution out of the plasma compartment and a second long half-life (35 to 50 hours) represents elimination from the body. This elimination half-life was similar when the oligonucleotide was administered subcutaneously. In contrast, methylphosphonate oligonucleotides have an elimination half-life of 17 minutes in mice. S-Oligonucleotide was distributed into most of organs of rats and mice. Liver and kidney were the 2 organs with highest uptake of the oligonucleotide. The S-oligonucleotide was primarily excreted in urine. Up to 30% was excreted in the first 24 hours. Repeated daily intravenous injections of a 25-mer S-oligonucleotide into rats showed that the concentrations in the plasma are at steady-state during the 8 days' administration. The data represented here support the potential utility of phosphorothioate and methylphosphonate oligonucleotides as therapeutic agents in vivo.
Topics: Animals; Antiviral Agents; Base Sequence; Clinical Trials as Topic; Esters; Humans; Molecular Sequence Data; Oligodeoxyribonucleotides, Antisense; Oligonucleotides; Oligonucleotides, Antisense; Organophosphorus Compounds; Thionucleotides; Tissue Distribution
PubMed: 7712663
DOI: 10.2165/00003088-199528010-00002