Automated synthesis of 3'-metalated oligonucleotides

Synthesis of Phosphorodiamidate Oligonucleotide Dimers

Azido nucleosides couple with phosphoramidites via an initial iminophosphorane, which eliminates acrylonitrile to generate the coupled dimer P(V) product. The vulnerable phosphite triester intermediate is bypassed entirely, making the methodology very suitable to solution-phase synthesis. This new coupling protocol requires no protection of the 5'-OH function and provides a new method of installing internucleosidic phosphorodiamidate bonds with near quantitative yields.

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

Solid-phase synthesis of tris-heteroleptic ruthenium(II) complexes and application to acetylcholinesterase inhibition

A synthetic route with two consecutive coordination chemistry steps on a solid support affords tris-heteroleptic ruthenium(II) polypyridyl complexes with high purity and in good yields. As an application we report the identification of a nanomolar acetylcholinesterase inhibitor from a small ruthenium complex library synthesized on Lanterns.

Porphyrin conjugated to DNA by a 2'-amido-2'-deoxyuridine linkage

A porphyrin that contains a single carboxylic acid group was synthesized and coupled to 2'-amino-2'-deoxyuridine. The resultant product contained a free 3' hydroxyl group and a 4,4'-dimethoxytrityl (DMT) protecting group on the 5' hydroxyl of the uridine, making it suitable for use in oligonucleotide synthesis. The 3' H-phosphonate derivative of this molecule was synthesized and used to form a conjugate with a 19 nucleotide sequence of DNA (5'-CCTCCAGTGGAAATCAAGG-3'). This was carried out with the DNA attached at the 3' end to a control pore glass (CPG) substrate, allowing for rapid purification. After removal of the DMT group, an additional three nucleotides were added, leaving the porphyrin as an internal modification. This is the first report of porphyrin attached internally to an oligonucleotide using a hydrogen-bonding nucleoside analog. This allows oligonucleotides to be used as a scaffold for precise positioning of multiple porphyrins within biomimetic arrays.

Far-red luminescent ruthenium pyridylimine complexes; building blocks for multinuclear arrays

Ruthenium(II) pyridylimine complexes are explored for their potential as units that might be incorporated into electronic or photonic arrays. The complexes [Ru(bipy)2(L)][PF6]2 (1) and [Ru(tpy)(L)Cl][BF4] (2) with L = phenylpyridin-2-ylmethylene-amine are synthesized and fully characterised using X-ray diffraction analysis and (2D) NMR spectroscopy. 1 displays emission in the far-red area of the spectrum at room temperature. The emission is significantly shifted to longer wavelength with respect to [Ru(bpy)3]2+ indicating that the lowest MLCT state is localised on the pyridylimine ligand. 2 is non-emissive at room temperature and at 77 K.

Developing the {M(CO)3}+ Core for Fluorescence Applications: Rhenium Tricarbonyl Core Complexes with Benzimidazole, Quinoline, and Tryptophan Derivatives

Tridentate ligands derived from benzimidazole, quinoline, and tryptophan have been synthesized, and their reactions with [NEt4]2[Re(CO)3Br3] have been investigated. The complexes 1-4 and 6 and 7 exhibit fac-{Re(CO)3N3} coordination geometry in the cationic molecular units, while 5 exhibits fac-{Re(CO)3N2O} coordination for the neutral molecular unit, where N3 and N2O refer to the ligand donor groups. The ligands bis(1-methyl-1H-benzoimidazol-2-ylmethyl)amine (L1), [bis(1-methyl-1H-benzoimidazol-2-ylmethyl)amino]acetic acid ethyl ester (L2), [bis(1-methyl-1H-benzoimidazol-2-ylmethy)amino]acetic acid methyl ester (L3), [bis(quinolin-2-ylmethyl)amino]acetic acid methyl ester (L4), 3-(1-methyl-1H-indol-3-yl)-2-[(pyridin-2-ylmethyl)amino]propionic acid (L5), 2-[bis(pyridin-2-ylmethyl)amino]-3-(1-methyl-1H-indol-3-yl)propionic acid (L6), and 2-[bis(quinolin-2-ylmethyl)amino]-3-(1-methyl-1H-indol-3-yl)propionic acid (L7) were obtained in good yields and characterized by elemental analysis, 1D and 2D NMR, and high-resolution mass spectrometry (HRMS). The rhenium complexes were obtained in 70-85% yields and characterized by elemental analysis, 1D and 2D NMR, HRMS, IR, UV, and luminescence spectroscopy, as well as X-ray crystallography for [Re(CO)3(L1)]Br (1), {[Re(CO)3(L2)]Br}2.NEt4Br . 8.5H2O (3(2).NEt4Br . 8.5H2O), [Re(CO)3(L4)]Br (4), and [Re(CO)3(L6)]Br (6). Crystal data for C21H19BrN5O3Re (1): monoclinic, P2(1)/c, a = 13.1851(5) A, b = 16.1292(7) A, c = 10.2689(4) A, beta = 99.353(1) degrees , V = 2154.8(2) A3, Z = 4. Crystal data for C56H73Br3N11O18.50 Re2 (3(2).NEt4Br . 8.5H2O): monoclinic, C2/c, a = 34.7760(19) A, b = 21.1711(12) A, c = 20.3376(11) A, beta = 115.944(1) degrees , V = 13464.5(1) A3, Z = 8. Crystal data for C26H21BrN3O5Re (4): monoclinic, P2(1)/c, a = 16.6504(6) A, b = 10.1564(4) A, c = 14.6954(5) A, beta = 96.739(1) degrees , V = 2467.9(2) A3, Z = 4. Crystal data for C27H24BrN4O5Re (6): monoclinic, P2(1), a = 8.7791(9) A, b = 16.312(2) A, c = 8.9231(9) A, beta = 90.030(1) degrees , V = 1277.8(2) A3, Z = 2.

Rhenium Tricarbonyl Core Complexes of Thymidine and Uridine Derivatives

Thymidine and uridine were modified at the C2' and C5' ribose positions to form amine analogues of the nucleosides (1 and 4). Direct amination with NaBH(OAc)3 in DCE with the appropriate aldehydes yielded 1-{5-[(bis(pyridin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L1), 1-{5-[(bis(quinolin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L2), and 1-[3-(bis(pyridin-2-ylmethyl)amino)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1H-pyrimidine-2,4-dione (L5), while standard coupling procedures of 1 and 4 with 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid (2) and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid (3) in the presence of HOBT-EDCI in DMF provided a second novel series of bifunctional chelators: 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L3), 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L4), 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L6), and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L7). The rhenium tricarbonyl complexes of L1-L4, L6, and L7, [Re(CO)3(LX)]Br (X=1-4, 6, 7: compounds 5-10, respectively), have been prepared by reacting the appropriate ligand with [NEt4][Re(CO)3Br3] in methanol. The ligands and their rhenium complexes were obtained in good yields and characterized by common spectroscopic techniques including 1D and 2D NMR, HRMS, IR, cyclic voltammetry, UV, and luminescence spectroscopy and X-ray crystallography. The crystal structure of complex 6.0.5NaPF6 displays a facial geometry of the carbonyl ligands. The nitrogen donors of the tridentate ligand complete the distorted octahedral spheres of the complex. Crystal data: monoclinic, C2, a = 24.618(3) A, b = 11.4787(11) A, c = 15.5902(15) A, beta = 112.422(4) degrees , Z = 4, D(calc) = 1.562 g/cm3.

5' modification of duplex DNA with a ruthenium electron donor-acceptor pair using solid-phase DNA synthesis

Incorporation of metalated nucleosides into DNA through covalent modification is crucial to measurement of thermal electron-transfer rates and the dependence of these rates with structure, distance, and position. Here, we report the first synthesis of an electron donor-acceptor pair of 5' metallonucleosides and their subsequent incorporation into oligonucleotides using solid-phase DNA synthesis techniques. Large-scale syntheses of metal-containing oligonucleotides are achieved using 5' modified phosporamidites containing [Ru(acac)(2)(IMPy)](2+) (acac is acetylacetonato; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (3) and [Ru(bpy)(2)(IMPy)](2+) (bpy is 2,2'-bipyridine; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (4). Duplexes formed with the metal-containing oligonucleotides exhibit thermal stability comparable to the corresponding unmetalated duplexes (T(m) of modified duplex = 49 degrees C vs T(m) of unmodified duplex = 47 degrees C). Electrochemical (3, E(1/2) = -0.04 V vs NHE; 4, E(1/2) = 1.12 V vs NHE), absorption (3, lambda(max) = 568, 369 nm; 4, lambda(max) = 480 nm), and emission (4, lambda(max) = 720 nm, tau = 55 ns, Phi = 1.2 x 10(-)(4)) data for the ruthenium-modified nucleosides and oligonucleotides indicate that incorporation into an oligonucleotide does not perturb the electronic properties of the ruthenium complex or the DNA significantly. In addition, the absence of any change in the emission properties upon metalated duplex formation suggests that the [Ru(bpy)(2)(IMPy)](2+)[Ru(acac)(2)(IMPy)](2+) pair will provide a valuable probe for DNA-mediated electron-transfer studies.