ABSTRACT
Copper-free click chemistry between cyclooctynes and azide is a mild, fast and selective technology for conjugation of oligonucleotides. However, technology for site-specific introduction of the requisite probes by automated protocols is scarce, while the reported cyclooctynes are large and hydrophobic. In this work, it is demonstrated that the introduction of bicyclo[6.1.0]nonyne (BCN) into synthetic oligonucleotides is feasible by standard solid-phase phosphoramidite chemistry. A range of phosphoramidite building blocks is presented for incoporation of BCN or azide, either on-support or in solution. The usefulness of the approach is demonstrated by the straightforward and high-yielding conjugation of the resulting oligonucleotides, including biotinylation, fluorescent labeling, dimerization and attachment to polymer.
Subject(s)
Catalysis , Click Chemistry , Copper/chemistry , Oligonucleotides/chemistry , Azides/chemistry , Molecular Structure , StereoisomerismABSTRACT
Treatment of oximes with hypervalent iodine leads to substituted isoxazoles via rapid formation of nitrile oxides. Reaction with terminal alkynes led to a series of 3,5-disubstituted isoxazoles with complete regioselectivity and high yield, in a procedure mild enough to prepare a range of nucleoside and peptide conjugates. Exceptionally high reaction rates were found for the formation of 3,4,5-trisubstituted isoxazoles from a cyclic alkyne.
Subject(s)
Alkynes/chemistry , Iodine/chemistry , Isoxazoles/chemistry , Nitriles/chemistry , Oxides/chemistry , Cyclization , Isoxazoles/chemical synthesis , StereoisomerismABSTRACT
2'-O-(3-(Furan-2-yl)propyl)adenosine was synthesized and evaluated for interstrand crosslink (ICL) formation in DNA duplexes. In situ oxidation of the furan moiety with NIS showed rapid crosslink formation to dA and dC, while dT and dG were inactive.
Subject(s)
Adenosine/analogs & derivatives , Adenosine/chemistry , Adenosine/chemical synthesis , Cross-Linking Reagents/chemistry , Cross-Linking Reagents/chemical synthesis , DNA/chemistry , Furans/chemistry , Furans/chemical synthesis , Base Sequence , Bromosuccinimide/chemistry , DNA/genetics , Oxidation-Reduction , Succinimides/chemistryABSTRACT
A procedure is presented for copper(I)-catalyzed [3+2] cycloaddition of nucleosides and nucleotides in near-quantitative yield. Azido-alkyne cycloaddition was applied for the preparation of a range of adenosine dimers and derivatives with versatile functionality, as well as for the smooth condensation of two oligonucleotide strands. The described technology may find valuable application in the synthesis of oligonucleotide dimers and conjugates.
Subject(s)
Nucleosides/chemistry , Oligonucleotides/chemical synthesis , Alkynes/chemistry , Catalysis , Copper/chemistry , Cyclization , Molecular Structure , Oligonucleotides/chemistryABSTRACT
Apparent thermodynamics of association of DNA-modified gold nanoparticles has been characterized by UV spectroscopy and dynamic light scattering (DLS). Extinction coefficients of unlabelled and DNA-labelled gold nanoparticles have been determined to permit quantitative analysis of the absorption measurements. In contrast to previous studies the associating gold nanoparticles were furnished with complementary oligonucleotide DNA single strands. This resulted in direct complex formation between the nanoparticles on mixing without the requirement of a DNA linker sequence for initiation of cluster formation. Melting curves of the nanoparticle assemblies formed at different temperatures were subjected to two-state analysis. A comparison of the apparent thermodynamic parameters obtained for the dissociation of these aggregates suggests that both thermodynamically and structurally different nanoparticle clusters are obtained depending on the temperature at which assembly proceeds. The van't Hoff enthalpies permit an estimate of the DNA duplexes: gold nanoparticle ratio involved in network formation.
Subject(s)
DNA, Single-Stranded/chemistry , Gold/chemistry , Nanoparticles/chemistry , Thermodynamics , Molecular Structure , Spectrophotometry, Ultraviolet , Transition TemperatureABSTRACT
The stabilizing effect of 7-propynylated 7-deazapurine nucleosides on DNA-hairpins and DNA-duplexes containing d(GA) mismatches was investigated. The corresponding oligonucleotides were synthesized using solid-phase synthesis. For this purpose, the phosphoramidite of 7-deaza-7-propynyl-2'-deoxyadenosine (3c) was prepared. The incorporation of 3c instead of dA into the tandem d(GA) base pair of a DNA-hairpin alters the secondary structure, but has a positive effect on the duplex stability. A complete replacement of the canonical nucleosides of the tandem d(GA) base pair by 3c and 7-deaza-7-propynyl-2'-deoxyguanosine results in a significant base pair stabilization.
Subject(s)
Base Pairing , Deoxyadenosines/chemistry , Deoxyguanosine/analogs & derivatives , Base Sequence , Circular Dichroism , Deoxyguanosine/chemistry , Nucleic Acid Conformation , ThermodynamicsABSTRACT
The Oxytricha telomere DNA hairpin 5'-d(G4T4G4) immobilized on 13 nm gold nanoparticles forms a supramolecular assembly via dGC-quartets, as determined by the color change and by SEM. The aggregation is ion-dependent and selective for sodium ions. K+ is less efficient while Li+ and Cs+ do not drive the aggregation. This work is the first effort exploring the use of secondary structures of DNA (quadruplexes) for producing self-assemblies of gold nanoparticles.
Subject(s)
Nanostructures , Base Sequence , DNA/chemistry , Gold/chemistry , Guanine/chemistry , Ions , Macromolecular Substances , Microscopy, Electron, Scanning , Molecular Conformation , Molecular Sequence Data , Nanostructures/chemistry , Nucleic Acid Conformation , Nucleic Acid Denaturation , Nucleic Acid Heteroduplexes , Potassium/chemistry , Sodium/chemistry , Telomere/ultrastructure , Ultraviolet RaysABSTRACT
Oligonucleotides containing 7-deazapurines or 9-deazapurines with propynyl groups at the 7- or 9-position were prepared. The stabilizing effect of the propynyl group was studied on DNA duplexes, hairpins and triplexes.
Subject(s)
DNA/chemistry , Nucleic Acid Heteroduplexes/chemistry , Purines/chemistry , Base Sequence , Models, Chemical , Molecular Biology/methods , Molecular Sequence Data , Oligonucleotides/chemistry , Oligonucleotides, Antisense/chemistry , Organophosphorus Compounds/chemistry , Purines/pharmacology , Temperature , ThermodynamicsABSTRACT
Joining the thrombin-binding aptamer 5-d(GGTTGGTGTGGTTGG) and the minihairpin 5-d(GCGAAGC) leads to new DNA nanoparticles, which are different from rod-like helical double-stranded DNA. Covalent interstrand cross-links in DNA duplexes generated by bifunctional alkadiyne chains were used to build-up the DNA networks.
Subject(s)
DNA/chemistry , Molecular Biology/methods , Nanotechnology/methods , Aptamers, Nucleotide/chemistry , Base Pairing , Binding Sites , Biosensing Techniques , Gene Transfer Techniques , Models, Chemical , Nucleic Acid Conformation , Polymers/chemistry , Temperature , Thermodynamics , Thrombin/chemistryABSTRACT
In the title compound, 4-amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-6-methylsulfanyl-1H-pyrazolo[3,4-d]pyrimidine, C11H16N5O3S, the conformation of the glycosidic bond is between anti and high anti. The 2'-deoxyribofuranosyl moiety adopts the C3'-exo-C4'-endo conformation (3T4, S-type sugar pucker), and the conformation at the exocyclic C-C bond is +sc (+gauche). The exocyclic 6-amine group and the 2-methylsulfanyl group lie on different sides of the heterocyclic ring system. The molecules form a three-dimensional hydrogen-bonded network that is stabilized by O-H...N, N-H...O and C-H...O hydrogen bonds.
Subject(s)
Adenosine/analogs & derivatives , Aza Compounds/chemistry , Adenosine/chemistry , Hydrogen Bonding , Models, MolecularABSTRACT
Ion-selective self-assembly of Au nanoparticles is described. The Oxytricha telomere DNA hairpin 5'-d(G4T4G4) immobilized on 13-nm Au nanoparticles forms a supramolecular assembly via dG-quartets, as determined by the color change and by scanning electron microscopy (SEM). The aggregation is ion-dependent and selective for Na+ ions. K+ is less efficient, while Li+ and Cs+ do not drive the aggregation. This work is the first effort to explore the use of secondary structures of DNA (quadruplexes) for producing self-assemblies of Au nanoparticles. It can be utilized to generate novel devices and materials, potentially useful for sensing and other applications in medicinal or engineering science.
Subject(s)
DNA/chemistry , Gold/chemistry , Metal Nanoparticles/chemistry , Animals , Base Sequence , DNA/genetics , DNA/ultrastructure , Ions , Metal Nanoparticles/ultrastructure , Molecular Conformation , Oxytricha/genetics , TelomereABSTRACT
The synthesis of the 2'-deoxyadenosine analogues 1b, 2b, and 3c modified at the 7- and/or 2-position is described. The effect of 7-chloro and 2-methylthio groups on the duplex stability is evaluated. For that, the nucleosides 1b, 2b, and 3c were converted to the corresponding phosphoramidites 15, 19, and 22, which were employed in the solid-phase oligonucleotide synthesis. In oligonucleotide duplexes, compound 1b forms stable base pairs with dT, of which the separated 1b-dT base pairs contribute stronger than that of the consecutive base pairs. Compound 2b shows universal base pairing properties while its N8 isomer 3c forms duplexes with lower stability.
Subject(s)
Adenine/chemistry , Oligodeoxyribonucleotides/chemical synthesis , Adenine/analogs & derivatives , Base Pairing , Oligodeoxyribonucleotides/chemistry , Pyrazoles , PyrimidinesABSTRACT
In the title compound, C(12)H(13)N(3)O(5), the conformation of the glycosylic bond is anti [torsion angle = -105.3 (2) degrees ]. The 2'-deoxyribofuranose moiety adopts an S-type sugar pucker and the orientation of the exocyclic C-C bond is -sc (trans).
