DNA binding properties of oligodeoxynucleotides containing pyrrolidino C-nucleosides

We have incorporated pyrrolidino-C-nucleosides (pyrrolidino-pseudonucleosides) containing the base uracil and N-1-methyl uracil into oligodeoxynucleotides and compared their thermal duplex and triplex stabilities with unmodified or pseudouridine-containing oligodeoxynucleotides. We find relative destabilizations of triplex formation by ca. -13 to -1 degrees C per modification (relative to thymidine) in a strongly sequence dependent mode. Duplex formation is less destabilizing and more homogeneous with -4 to -2 degrees C per modification

Synthesis of pyrrolidine C-nucleosides via Heck reaction

A novel method for the synthesis of pyrrolidine C-nucleosides has been developed. The key step of the synthesis is the palladium(0)-mediated coupling of a disubstituted N-protected 2-pyrroline and 5-iodouracil. C-Nucleoside 14 and its N-methyl derivative 15 can easily be converted to the corresponding phosphoramidite building blocks for DNA synthesis

Synthesis of Carbocyclic C-Nucleosides Containing Nonnatural Pyrimidine Bases

A series of new carbocyclic C-nucleosides with a cis-4′-(hydroxymethyl)cyclopent-2′-enyl sugar moiety and unnatural pyrimidine bases (2–6) were synthesized in racemic form in two steps starting from the easily accessible cyclic carbonate 1.

Synthesis and characterization of Pd(II) and Pt(II) complexes with triazolopyrimidine derivatives: The crystal structure of [Pd2L2Cl4] where L=5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine

The Pd(II) and Pt(II) complexes with triazolopyrimidine C-nucleosides L-1 (5,7-dimethyl-3-(2',3',5'-tri-O-benzoyl-beta-D-ribofuranosyl-s-triazolo)[4,3-a]pyrimidine), L-2 (5,7-dimethyl-3-beta-D-ribofuranosyl-s-triazolo [4,3-a]pyrimidine) and L-3 (5,7-dimethyl[1,5-a]-s-triazolopyrimidine), [Pd(en)(L-1)](NO3)(2), (Pd(bpy)(L-1)](NO3)(2), cis-Pd(L-3)(2)Cl-2, [Pd-2(L-3)(2)Cl-4]center dot H2O, cis-Pd(L-2)(2)Cl-2 and [Pt-3(L-1)(2)Cl-6] were synthesized and characterized by elemental analysis and NMR spectroscopy. The structure of the [Pd-2(L-3)(2)Cl-4]center dot H2O complex was established by Xray crystallography. The two L-3 ligands are found in a head to tail orientation, with a (PdPd)-Pd-... distance of 3.1254(17) angstrom.L-1 coordinates to Pd(II) through N8 and N1 forming polymeric structures. L-2 coordinates to Pd(II) through N8 in acidic solutions (0.1 M HCl) forming complexes of cis-geometry. The Pd(II) coordination to L-2 does not affect the sugar conformation probably due to the high stability of the C-C glycoside bond. (c) 2006 Elsevier B.V. All rights reserved.

5a-Butyl-1,3,8,10-tetra-chloro-7,13-bis-(4-nitro-benzo-yl)-5a,6a,12a,12b-tetra-hydro-7H,13H-thieno[2,3-b:4,5-b']bis-(1,4-benzoxazine)

The title compound, C(34)H(24)Cl(4)N(4)O(8)S, is a linear penta-cyclic system formed of two substituted benzoxazinyl groups fused to 2-n-butyl-tetra-hydro-thio-phene. The oxazine ring, which is fused to the n-butyl-substituted side of the thio-phene ring, is in a boat conformation. The other fused oxazine ring and the tetra-hydro-thiene ring are each in an envelope conformation. The bridgehead C atom alpha to both the S and N atoms forms the flap of each envelope. This results in a twist of the penta-cyclic system such that the dihedral angle between the terminal dichloro-benzene rings is 82.92 (8)°. In the crystal, inversion-related mol-ecules form a weakly hydrogen-bonded dimer, with two C-H⋯O inter-actions between an H atom on the oxazine ring and an amide O atom. Additionally, C-H⋯O inter-actions occur between an H atom on a screw-related nitro-benzene ring and an O atom on the nitro-benzene ring of one mol-ecule. One of the Cl atoms and the butyl group are disordered over two sets of sites with occupancy ratios of 0.94 (2):0.06 (2) and 0.624 (4):0.376 (4), respectively.

Bipyridyl- and biphenyl-DNA: A recognition motif based on interstrand aromatic stacking

The synthesis and incorporation into oligonucleotides of C-nucleosides containing the two aromatic, non-hydrogen-bonding nucleobase substitutes biphenyl (I) and bipyridyl (Y) are described. Their homo- and hetero-recognition properties in different sequential arrangements were then investigated via UV-melting curve analysis, gel mobility assays, CD- and NMR spectroscopy. An NMR analysis of a dodecamer duplex containing one biphenyl pair in the center, as well as CD data on duplexes with multiple insertions provide further evidence for the zipper-like interstrand stacking motif that we proposed earlier based on molecular modeling. UV-thermal melting experiments with duplexes containing one to up to seven I- or Y base pairs revealed a constant increase in T(m) in the case of I and a constant decrease for Y. Mixed I/Y base pairs lead to stabilities in between the homoseries. Insertion of alternating I/abasic site- or Y/abasic site pairs strongly decreases the thermal stability of duplexes. Asymmetric distribution of I- or Y residues on either strand of the duplex were also investigated in this context. Duplexes with three natural base pairs at both ends and 50 % of I pairs in the center are still readily formed, while duplexes with blunt ended I pairs tend to aggregate unspecifically. Duplexes with one natural overhang at the end of a I-I base pair tract can both aggregate or form ordered duplexes, depending on the nature of the natural bases in the overhang

Synthesis and triplex forming properties of pyrrolidino pseudoisocytidine containing oligodeoxynucleotides

Pyrrolidino pseudo-C-nucleosides are isosteres of natural deoxynucleosides which are protonated at the pyrrolidino ring nitrogen under physiological conditions. As constituents of a triplex forming oligodeoxynucleotide (TFO), the positive charge is expected to stabilise DNA triple helices via electrostatic interactions with the phosphodiester backbone of the target DNA. We describe the synthesis of the pyrrolidino isocytidine pseudonucleoside and the corresponding phosphoramidite building block and its incorporation into TFOs. Such TFOs show substantially increased DNA affinity compared to unmodified oligodeoxynucleotides. The increase in affinity is shown to be due to the positive charge at the pyrrolidino subunit

Pyrrolidino-DNA

We synthesized pyrrolidino-C-nucleosides, incorporated them into oligodeoxynucleotides and investigated their pairing properties. The thermal duplex and triplex stabilities were measured. While triplex formation is destabilized in the case of pyrrolidino-pseudo-U and -T, pyrrolidino-pseudo-iso-C leads to an increase of the Tm value for third strand dissociation. Duplexes are destabilized with all pyrrolidino-C-nucleosides

Bridgehead arylation: A direct route to advanced intermediates for the synthesis of C-20 diterpene alkaloids

[GRAPHICS] Rapid access to the ABCE ring system of the C-20 diterpene alkaloids was achieved by silver(I)-promoted intramolecular Friedel-Crafts arylation of a functional group-specific 5-bromo-3-azabicyclo[3.3.1]nonane derivative.

Pd-catalysed amidation of 2,6-dihalopurine nucleosides. Replacement of iodine at 0 ºC

Pd-catalysed reactions of 2-Cl, 2-Br and 2-I derivatives of a 6-chloropurine nucleoside with benzamide have been compared, using Pd2dba3, Xantphos and Cs2CO3 in toluene, between 20 and 80 °C. The reactivity order was 2-I > 2-Br > 6-Cl ≫ 2-Cl. The 2-I substituent could be replaced even at 0 °C, under conditions disclosed here for the first time. On the other hand, the replacement of the chlorine atom at position 2 (2-Cl) required 110 °C.

Pd-catalysed amidation of 2,6-dihalopurine nucleosides. Replacement of iodine at 0 ºC

Pd-catalysed reactions of 2-Cl, 2-Br and 2-I derivatives of a 6-chloropurine nucleoside with benzamide have been compared, using Pd2dba3, Xantphos and Cs2CO3 in toluene, between 20 and 80 °C. The reactivity order was 2-I > 2-Br > 6-Cl ≫ 2-Cl. The 2-I substituent could be replaced even at 0 °C, under conditions disclosed here for the first time. On the other hand, the replacement of the chlorine atom at position 2 (2-Cl) required 110 °C.

Introduction of vinyl and hydroxymethyl functionalities at C-4 of glucose-derived substrates: synthesis of spirocyclic, bicyclic, and tricyclic nucleosides

Installing hydroxymethyl and hydroxyethyl substitutions at C-4 through vinylation and hydroboration-oxidation reactions of the C-4 bis-hydroxymethyl derivative of D-glucose based substrate, and inserting heteroatoms thereafter permitted formation of N-, O-, or S-heterocycles leading to [4,5]or [5,5]-spirocycles and a bicyclo[3.3.0]octane product. Some of the spirocycles were converted to spironucleosides under Vorbruggen glycosidation reaction conditions. Similarly, the bicyclic product was elaborated to the corresponding bicyclic nucleoside as well as an unexpected tricyclic nucleoside.

Novel approaches for the synthesis of C-5 modified pyrimidine nucleosides

The antiviral or anticancer activities of C-5 modified pyrimidine nucleoside analogues validate the need for the development of their syntheses. In the first half of this dissertation, I explore the Pd-catalyzed cross-coupling reaction of allylphenylgermanes with aryl halides in the presence of SbF 5/TBAF to give various biaryls by transferring multiple phenyl groups, which has also been applied to the 5-halo pyrimidine nucleosides for the synthesis of 5-aryl derivatives. To avoid the use of organometallic reagents, I developed Pd-catalyzed direct arylation of 5-halo pyrimidine nucleosides. It was discovered that 5-aryl pyrimidine nucleosides could be synthesized by Pd-catalyzed direct arylation of N3-free 5-halo uracil and uracil nucleosides with simple arenes or heteroaromatics in the presence of TBAF within 1 h. Both N3-protected and N3-free uracil and uracil nucleosides could undergo base-promoted Pd-catalyzed direct arylation, but only with electron rich heteroaromatics. ^ In the second half of this dissertation, 5-acetylenic uracil and uracil nucleosides have been employed to investigate the hydrogermylation, hydrosulfonylation as well as hydroazidation for the synthesis of various functionalized 5-vinyl pyrimidine nucleosides. Hydrogermylation of 5-alkynyl uracil analogues with trialkylgermane or tris(trimethylsilyl)germane hydride gave the corresponding vinyl trialkylgermane, or tris(trimethylsilyl)germane uracil derivatives. During the hydrogermylation with triphenylgermane, besides the vinyl triphenylgermane uracil derivatives, 5-[2-(triphenylgermyl)acetyl]uracil was also isolated and characterized and the origin of the acetyl oxygen was clarified. Tris(trimethylsilyl)germane uracil derivatives were coupled to aryl halides but with decent yield. Iron-mediated regio- and stereoselective hydrosulfonylation of the 5-ethynyl pyrimidine analogues with sulfonyl chloride or sulfonyl hydrazine to give 5-(1-halo-2-tosyl)vinyluracil nucleoside derivatives has been developed. Nucleophilic substitution of the 5-(β-halovinyl)sulfonyl nucleosides with various nucleophiles have been performed to give highly functionalized 5-vinyl pyrimidine nucleosides via the addition-elimination mechanism. The 5-(β-keto)sulfonyluracil derivative has also been synthesized via the aerobic difunctionalization of 5-ethynyluracil analogue with sulfinic acid in the presence of catalytic amount of pyridine. Silver catalyzed hydroazidation of protected 2'-deoxy-5-ethynyluridine with TMSN3 in the presence of catalytic amount of water to give 5-(α-azidovinyl)uracil nucleoside derivatives was developed. Strain promoted Click reaction of the 5-(α-azidovinyl)uracil with cyclooctyne provide the corresponding fully conjugated triazole product.^