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Bioconjugate Chemistry Jun 2009Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics,... (Review)
Review
Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics, inefficient cellular uptake and subsequent release from endosomes to cytoplasm appear to be the most severe ones. Covalent conjugation of oligonucleotides to molecules that expectedly facilitate the internalization, targets the conjugate to a specific cell-type or improves the parmacokinetics offers a possible way to combat against these shortcomings. Since workable chemistry is a prerequisite for biological studies, development of efficient and reproducible methods for preparation of various types of oligonucleotide conjugates has become a subject of considerable importance. The present review summarizes the advances made in the solid-supported synthesis of oligonucleotide conjugates aimed at facilitating the delivery and targeting of nucleic acid drugs.
Topics: Animals; Drug Carriers; Glycoconjugates; Humans; Nucleic Acids; Oligonucleotides; Peptides; Polyamines
PubMed: 19175328
DOI: 10.1021/bc800406a -
Nucleosides, Nucleotides & Nucleic Acids 2020An Ir(III) polypyridyl complex-conjugated 14-mer oligonucleotide (Ir-DNA) was synthesized and its hybridization properties with single-stranded DNA (ssDNA) and...
An Ir(III) polypyridyl complex-conjugated 14-mer oligonucleotide (Ir-DNA) was synthesized and its hybridization properties with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) were evaluated by UV-melting experiments. The stabilities of the duplexes of Ir-DNA with 14-, 20-, and 26-mer ssDNAs were higher than those of the unconjugated oligonucleotides. The triplex of Ir-DNA with 14-mer dsDNA was also stabilized. However, the triplexes of Ir-DNA with 20- and 26-mer dsDNAs, flanked by 3 and 6 base pairs at the both ends of 14-mer dsDNA target, were destabilized. This is presumably because of steric repulsion between the Ir(III) complex and the protruding 3- and 6-mer dsDNA moieties which are inflexible compared to ssDNA.
Topics: Chemistry Techniques, Synthetic; DNA Probes; Iridium; Magnetic Resonance Spectroscopy; Molecular Structure; Nucleic Acid Conformation; Nucleic Acid Hybridization; Oligonucleotides
PubMed: 31983279
DOI: 10.1080/15257770.2019.1690150 -
Biochemistry Sep 1988A few different methods for the preparation of oligonucleotide N-alkylphosphoramidates were compared directly. One of these, involving the use of protected nucleoside...
A few different methods for the preparation of oligonucleotide N-alkylphosphoramidates were compared directly. One of these, involving the use of protected nucleoside phosphites as building blocks, provided the requisite N-alkylphosphoramidates via oxidation of the intermediate dinucleoside methyl phosphites with iodine in the presence of the appropriate alkylamine. This method was found to have several attractive features, including the use of building blocks identical with those employed for the synthesis of DNA and compatibility with procedures and instruments employed for the stepwise synthesis of oligonucleotides by solution and solid-phase methods. This procedure was used to make several di-, tri-, and tetranucleotide N-alkylphosphoramidates derived from deoxyadenosine and thymidine; alkyl substituents included N,N-dimethyl, N-butyl, N-octyl, N-dodecyl, and N-(5-aminopentyl). The aminoalkyl derivative of d(TpT) (24) was used to demonstrate the feasibility of introducing an intercalative agent to the alkylphosphoramidate moiety of such derivatives. The oligonucleotide N-alkylphosphoramidates were separated into their component diastereomers and characterized structurally by a number of techniques including circular dichroism, high-field 1H NMR spectroscopy, FAB mass spectrometry, and enzymatic digestion to authentic nucleosides and nucleotides. Physicochemical characterization of several di- and trinucleotide alkyl-phosphoramidates revealed that the adenine nucleotide analogues formed stable complexes with poly-(thymidylic acid). The stabilities of these complexes were found to increase with increasing chain length of the N-alkylphosphoramidate substituents. The finding that N-alkylphosphoramidate substituents can enhance the binding of certain oligonucleotides to their complementary polynucleotides suggests the existence of a novel source of polynucleotide affinity.
Topics: Chemical Phenomena; Chemistry; Chromatography, High Pressure Liquid; Circular Dichroism; Deoxyadenosines; Magnetic Resonance Spectroscopy; Mass Spectrometry; Molecular Structure; Nucleic Acid Probes; Oligonucleotides; Organophosphorus Compounds; Polynucleotides; Stereoisomerism; Thymidine
PubMed: 3264723
DOI: 10.1021/bi00419a010 -
BMC Bioinformatics Feb 2013DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that...
BACKGROUND
DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind only to the intended target, (ii) cover the highest possible number of genes, that is, all genes that allow such unique regions, and (iii) are computed fast. None of the existing programs meet all these criteria.
RESULTS
We introduce a new approach with our software program BOND (Basic OligoNucleotide Design). According to Kane's criteria for oligo design, BOND computes highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. The same approach enables us to introduce also an evaluation procedure that correctly measures the quality of the oligonucleotides. Extensive comparison is performed to prove our claims. BOND is flexible, easy to use, requires no additional software, and is freely available for non-commercial use from http://www.csd.uwo.ca/∼ilie/BOND/.
CONCLUSIONS
We provide an improved solution to the important problem of oligonucleotide design, including a thorough evaluation of oligo design programs. We hope BOND will become a useful tool for researchers in biological and medical sciences by making the microarray procedures faster and more accurate.
Topics: Algorithms; Genes; Oligonucleotide Array Sequence Analysis; Oligonucleotide Probes; Oligonucleotides; Software
PubMed: 23444904
DOI: 10.1186/1471-2105-14-69 -
Nucleosides, Nucleotides & Nucleic Acids Jan 2011Oligonucleotide analogs containing one or a few glycine, L-, and D-alanine or L-and D-phenylalanine residues instead of phosphodiesterinternucleotide linkages were...
Oligonucleotide analogs containing one or a few glycine, L-, and D-alanine or L-and D-phenylalanine residues instead of phosphodiesterinternucleotide linkages were synthesized. The stability of the duplexes formed by modified oligonucleotides and their wildtype complements was studied. Oligonucleotides with D-alanine residues in internucleotide linkages form duplexes more stable than native ones (ΔT(m) +0.2 °C per modification), whereas other modifications destabilize the duplexes.
Topics: Alanine; Glycine; Nucleic Acid Hybridization; Oligonucleotides; Peptide Nucleic Acids; Phenylalanine
PubMed: 21259162
DOI: 10.1080/15257770.2010.542790 -
Current Protocols in Nucleic Acid... Jun 2013This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified...
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
Topics: Nucleic Acids; Oligonucleotides; Solid-Phase Synthesis Techniques
PubMed: 23775808
DOI: 10.1002/0471142700.nc0301s53 -
Bioorganic & Medicinal Chemistry Jul 2018Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5'-thio or...
Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which the 5'-bridging oxygen atom is replaced with a sulfur atom, are attracting attention and gaining importance in oligonucleotide-based research. In our present study, we synthesized 5'-thio-2',4'-BNA/LNA monomers bearing thymine or 5-methylcytosine nucleobase. The 5'-thio-2',4'-BNA/LNA monomers were successfully incorporated into target oligonucleotides, and their nuclease stability and binding affinity with complementary strands were evaluated.
Topics: Bridged-Ring Compounds; Exonucleases; Nucleic Acid Conformation; Oligonucleotides; Sulfhydryl Compounds; Transition Temperature
PubMed: 29886084
DOI: 10.1016/j.bmc.2018.05.040 -
Nucleic Acid Therapeutics Oct 2020A risk-based approach for routine identity testing of therapeutic oligonucleotide drug substances and drug products is described. Risk analysis of solid-phase...
A risk-based approach for routine identity testing of therapeutic oligonucleotide drug substances and drug products is described. Risk analysis of solid-phase oligonucleotide synthesis indicates that intact mass measurement is a powerful technique for confirming synthesis of the intended oligonucleotide. Further risk assessment suggests that the addition of a second, sequence-sensitive identity test, which relies on a comparison of some property of the sample to a reference standard of proven identity, results in a sufficient test of identity for most oligonucleotide drug substances and products. Alternative strategies for drug product identity testing are presented. The analysis creates a common way to communicate risk and should result in a harmonized approach to identity testing that avoids the unnecessary analytical burden associated with routine sequencing, without compromising quality or patient safety.
Topics: Humans; Oligonucleotides; Pharmaceutical Preparations; Risk Assessment; Sequence Analysis, DNA
PubMed: 32857010
DOI: 10.1089/nat.2020.0878 -
Recent Patents on Inflammation &... Jan 2011RNA-protein interactions have been characterized often. Above all, the proteins which are associated with the studied RNA should be precisely identified. The... (Review)
Review
RNA-protein interactions have been characterized often. Above all, the proteins which are associated with the studied RNA should be precisely identified. The pharmaceutical compositions containing nucleic acids and/or other compounds can be administered by any suitable route for administering medications. The immunostimulatory oligonucleotides play the role of antisense drugs which are being researched to treat cancers (including lung cancer, colorectal carcinoma, pancreatic carcinoma, malignant glioma and malignant melanoma), diabetes, Amyotrophic lateral sclerosis (ALS), and diseases such as asthma and arthritis with an inflammatory component. The immunostimulatory oligonucleotides may contain one or more natural or unnatural amino acid residues which are connected to the polymer by peptide (amide) linkages. The vaccine against cancer which has been produced during this work can be prophylactic or therapeutic. Since most studies so far have been performed with first-generation antisense oligonucleotides (ODNs), it is interesting to observe how second-generation immune stimulatory drug candidates with enhanced potency and efficacy can further improve the utility of this class of therapeutic agents. The aim of this article is to review most significant patents on immunostimulatory oligonucleotides.
Topics: Adjuvants, Immunologic; Animals; Humans; Oligodeoxyribonucleotides; Oligonucleotides; Patents as Topic
PubMed: 21158735
DOI: 10.2174/187221311794474856 -
Biological Chemistry Oct 2004Recent developments including pulse and multi-frequency techniques make the combination of site-directed spin labeling and electron paramagnetic resonance (EPR)... (Review)
Review
Recent developments including pulse and multi-frequency techniques make the combination of site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy an attractive approach for the study of protein-protein or protein-oligonucleotide interaction. Analysis of the spin label side chain mobility, its solvent accessibility, the polarity of the spin label micro-environment and distances between spin label side chains allow the modeling of protein domains or protein-protein interaction sites and their conformational changes with a spatial resolution at the level of the backbone fold. Structural changes can be detected with millisecond time resolution. Inter- and intra-molecular distances are accessible in the range from approximately 0.5 to 8 nm by the combination of continuous wave and pulse EPR methods. Recent applications include the study of transmembrane substrate transport, membrane channel gating, gene regulation and signal transfer.
Topics: Animals; Electron Spin Resonance Spectroscopy; Humans; Oligonucleotides; Protein Binding; Protein Interaction Mapping; Spin Labels
PubMed: 15551865
DOI: 10.1515/BC.2004.119