Pyrazolo[3,4-d]pyrimidine nucleic acids: adjustment of dA-dT to dG-dC base pair stability.

Oligonucleotides incorporating 8-aza-7-deazapurin-2,6-diamine (pyrazolo[3,4-d]pyrimidin-4,6-diamine) nucleoside 2a or its 7-bromo derivative 2b show enhanced duplex stability compared to those containing dA. While incorporation of 2a opposite dT increases the T(m) value only slightly, the 7-bromo compound 2b forms a very stable base pair which is as strong as the dG-dC pair. Compound 2b shows a similar base discrimination in duplex DNA as dA. The base-modified nucleosides 2a,b have a significantly more stable N-glycosylic bond than the rather labile purin-2,6-diamine 2'-deoxyribonucleoside 1. Base protection with acyl groups, with which we had difficulties in the case of purine nucleoside 1, was effective with pyrazolo[3,4-d]-pyrimidine nucleosides 2a,b. Oligonucleotides containing 2a,b were obtained by solid phase synthesis employing phosphoramidite chemistry. Compound 2b harmonizes the stability of DNA duplexes. Their stability is no longer dependent on the base pair composition while they still maintain their sequence specificity. Thus, they have the potential to reduce the number of mispairs when hybridized in solution or immobilized on arrays.

The N(8)-(2'-deoxyribofuranoside) of 8-aza-7-deazaadenine: a universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents.

The 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin-4-amine) N(8)-(2'-deoxyribonucleoside) (2) which has an unusual glycosylation position was introduced as a universal nucleoside in oligonucleotide duplexes. These oligonucleotides were prepared by solid-phase synthesis employing phosphoramidite chemistry. Oligonucleotides incorporating the universal nucleoside 2 are capable of forming base pairs with the four normal DNA nucleosides without significant structural discrimination. The thermal stabilities of those duplexes are very similar and are only moderately reduced compared to those with regular Watson-Crick base pairs. The universal nucleoside 2 belongs to a new class of compounds that form bidentate base pairs with all four natural DNA constituents through hydrogen bonding. The base pair motifs follow the Watson-Crick or the Hoogsteen mode. Also an uncommon motif is suggested for the base pair of 2 and dG. All of the new base pairs have a different shape compared to those of the natural DNA but fit well into the DNA duplex as the distance of the anomeric carbons approximates those of the common DNA base pairs.

Synthesis of 5-aza-7-deazaguanine nucleoside derivatives as potential anti-flavivirus agents.

Coupling suitable sugars (D- or L-ribofuranose, 2' or 3-deoxysugar, branched sugars) with 2-aminoimidazo[1,2-a]-s-triazin-4-one was carried out using the different reaction conditions: 1) condensation in the presence of sodium hydride; or 2) condensation using Vorbrüggen's methods. The 5-aza- 7-deazaguanine nucleoside analogues obtained were evaluated in cell culture experiments for the inhibition of the replication of a number of RNA viruses, including BVDV, YFV, and WNV.

Polymer-linked 6-azauridine 5'-monophosphate, a resin of high bioaffinity to orotidine-5'-phosphate decarboxylase.

Condensation of 6-azauridine with ethyl levulinate, followed by saponification or phosphorylation, leads to 2',3'-O-[1-(2-carboxyethyl)ethylidene]-6-azauridine and its 5'-monophosphate. The latter was coupled to 6-aminohexylagarose via its carboxylic group. Using the same synthetic route, agarose-linked uridine 5'-monophosphate has been prepared. Both polymers show specific binding toward orotidine-5'-monophosphate decarboxylase. The immobilized inhibitor (6-azauridine 5'-monophosphat) binds the enzyme more strongly than the immobilized uridine 5'-monophosphate. Both resins have been used to separate orotidine-5'-monophosphate decarboxylase from orotidine-5'-monophosphate pyrophosphorylase.

Isomeric N-methyl-7-deazaguanines: synthesis, structural assignment, and inhibitory activity on xanthine oxidase.

The N-methyl isomers of 2-amino-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (2a) have been synthesized regiospecifically and their structures assigned. The 3-methyl compound 3 was obtained by alkylation of the parent chromophore 2a with dimethyl sulfate, and the 1-methyl isomer 5b was obtained by condensation of ethyl 2-cyano-4,4-diethoxybutyrate with N-methylguanidine and subsequent cyclization. Methylation of 2-amino-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (7b), however, with methyl iodide in the presence of 50% NaOH, by phase-transfer techniques, followed by the replacement of halide by hydroxyl, yielded the 7-methyl compound 2b. The N-methyl isomers of 2a were all found to be inhibitors of xanthine oxidase from cow's milk. While the 3-methyl isomer 3 exhibits a Ki of 40 microM, the 7- and 1-isomers show Ki values of 4.5 and 3 microM, respectively.

Fluorescent DNA: the development of 7-deazapurine nucleoside triphosphates applicable for sequencing at the single molecule level.

7-Deaza-2'-deoxyadenosine and -guanosine phosphoramidite building blocks as well as corresponding 5'-triphosphate derivatives are described carrying in position 7 substituents such as iodo, hexyn-1-yl or 5-aminopentyn-1-yl residues. The phosphoramidites were used to synthesize a series of modified oligodeoxynucleotides. A systematic study of the thermal stabilities of these oligonucleotide duplexes demonstrated that the 7-substituents are well accommodated in the major groove of B-DNA. The 7-(aminoalkyn-1-yl)-7-deazapurine 2'-deoxynucleoside triphosphates were labeled with bulky fluorophores such as Rhodamine Green(R) or tetramethylrhodamine.

7-Deazapurine 2'-deoxyribofuranosides are noncleavable competitive inhibitors of Escherichia coli purine nucleoside phosphorylase (PNP).

A series of 7-deazapurine 2'-deoxyribofuranosides were synthesized according to already known procedures and their substrate and inhibitor properties with purified E. coli purine nucleoside phosphorylase were examined. In agreement with previous findings, substrate activity was not detected for any of the compounds tested. Most of the nucleosides showed weak inhibition in the preliminary screening, i.e. at a concentration of about 100 microM. However some combinations of 6-chloro, 6-amino or 6-methoxy substituents with bulky hydrophobic groups at position 7 of the base and/or chloro, amino, methoxy or methylthio group at position 2 markedly enhanced affinity of such modified nucleosides for the E. coli enzyme. The most potent inhibition was observed for two nucleosides: 6-chloro- and 2-amino-6-chloro-7-deazapurine 2'-deoxyribofuranosides that show inhibition constants Ki = 2.4 and 2.3 microM, respectively. Several other compounds were also found to be good inhibitors, with inhibition constants in the range 5-50 microM. In all instances the inhibition was competitive vs. the nucleoside substrate 7-methylguanosine. Inhibition constants for 7-deazapurine nucleosides are in general several-fold lower than those observed for their purine counterparts. Therefore 7-deaza modification together with substitutions at positions 2, 6 and 7 of the base is a very promising approach to obtain competitive noncleavable inhibitors of E. coli PNP that may bind to the enzyme with inhibition constants in the microM range.

Synthesis and application of novel nucleoside phosphonates and phosphoramidites modified at the base moiety.

The H-phosphonates and phosphoramidites of 2'-deoxyisoguanosine, 2'-deoxyisoinosine, 5-aza-7-deaza-2'-deoxyguanosine, and N1-methyl-2'-deoxyformycin A were prepared. The diphenylcarbamoyl group was chosen for the 2-O-protection of 2'-deoxyisoinosine and 2'-deoxyisoguanosine, and dimethylaminoalkylidene groups were used to block the amino function of the various monomers. The synthesis of isoguanine oligonucleotides was found to be much more efficient using the 2-O-protected building blocks compared to those without oxygen protection. Oligodeoxynucleotides containing 2'-deoxyisoguanosine and 2'-deoxycytidine form parallel duplex structures. The self-complementary duplex containing 5-aza-7-deaza-2'-deoxyguanosine and 2'-deoxycytidine forms a stable duplex in acidic solution (pH = 5.0) while it is destabilized under neutral conditions.

Substrate- and product-affinity resins for adenosine deaminase obtained by immobilisation of adenosine and inosine via 2',3'-cyclic acetal derivatives.

Immobilised inosine (6a) and adenosine (6c) and their 5'-phosphates have been synthesized. Reaction of the nucleosides with ethyl levulinate, followed by saponification or phosphorylation and then saponification, gave the 2',3'-O-[1-(2-carboxyethyl)ethylidene] derivatives 3 and 4 and the corresponding 5'-phosphates 2b and 2d. 6-Aminohexylagarose (5) was severally coupled to 2b, 2d, 3, and 4 through the carboxyl groups to give the polymers 6a-d. Adenosine deaminase converts 3 into 4, and 6c into 6a. The polymers can be used as affinity resins for adenosine deaminase, which is bound more strongly to 6c than to 6a. The operational capacity of 6a for adenosine deaminase is constant at 15--25 degrees, but decreases by approximately 16% from 25 degrees to 35 degrees. The resin 6a has been used to separate adenosine deaminase from mixtures containing other enzymes, for example, guanase or alcohol dehydrogenase.

Agarose-linked xanthosine: a biospecific resin for guanine aminohydrolase.

Polymer-bound xanthosine (4) has been prepared. Condensation of xanthosine with ethyl 4-oxovalerate and saponification of the product gave 2',3'-O-[1-(2-carboxyethyl)ethylidene] xanthosine. The latter was coupled to 6-aminohexylagarose through its carboxylic group, to yield the polymer 4. The content of bound ligand was 8 mumol/g of moist gel, a value that agrees with the number of free amino groups determined by the trinitrobenzenesulfonic acid assay before coupling. Immobilised xanthosine was used as a biospecific resin (inhibitor resin) for guanine aminohydrolase (EC 3.5.4.3), to separate the enzyme from a mixture containing adenosine deaminase (EC 3.5.4.4).

8-aza-7-deazaadenine and 7-deazaguanine: synthesis and properties of nucleosides and oligonucleotides with nucleobases linked at position-8.

The 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin-4-amine) N8-(2'-deoxyribonucleoside) (2) and the 7-deazaguanine (pyrrolo[3,4-d]pyrimidine-2-amin-(3H)-4-one) C8-(2'-deoxyribonucleoside) (4) were synthesized and incorporated in oligonucleotides employing phosphoramidite chemistry. Oligonucleotides carrying compound 2 are able to form base pairs with the four canonical DNA constituents without significant structural discrimination. The nucleoside 4 was obtained from the corresponding ribonucleoside by deoxygenation. Oligonucleotides containing compound 4 showed similar base pairing properties as those with 2'-deoxyisoguanosine.

Fluorescence properties and base pair stability of oligonucleotides containing 8-aza-7-deaza-2'-deoxyisoinosine or 2'-deoxyisoinosine.

The fluorescence and the base pairing properties of 8-aza-7-deaza-2'-deoxyisoinosine (1) are described and compared with those of 2'-deoxyisoinosine (2). The corresponding phosphoramidites (11, 12) are synthesized using the diphenylcarbamoyl (DPC) residue for the 2-oxo group protection. The nucleosides 1 and 2 base pair with 2'-deoxy-5-methylisocytidine in DNA duplexes with antiparallel chain orientation and with 2'-deoxycytidine in a parallel DNA. These base pairs are less stable than the canonical dA-dT pair and that of 2'-deoxyinosine (4) with 2'-deoxycytidine. The fluorescence of the nucleosides 1 and 2 is quenched (approximately 95%) in duplex DNA. The residual fluorescence is used to determine the Tm-values, which are found to be the same as determined UV-spectrophotometrically.

Synthesis and base pairing properties of 9-deazapurine N7-nucleosides in oligonucleotide duplexes and triplexes.

The 9-deazaguanine N7-2'-deoxyribofuranoside (3) as well as the bromo and iodo derivatives 4a,b were synthesized and incorporated in oligonucleotide duplexes and triplexes. Their base pairing properties were investigated and compared with those of the parent purine N7-2'-deoxyribofuanosides.

Parallel DNA containing pyrazolo[3,4-D]pyrimidine analogues of isoguanine.

The phosphoramidites of 8-aza-7-deaza-2'-deoxyisoguanosine (1a) and its bromo derivative 1b as well as of 6-aza-2'-deoxyisocytidine and its 5-methyl derivative (3a,b) were synthesized. Parallel-stranded duplexes containing the nucleosides 1a,b show a significantly enhanced duplex stability compared to those containing 2'-deoxyisoguanosine.

Synthesis and properties of halogenated 7-deaza-2'-deoxyxanthosine and protected derivatives for oligonucleotide synthesis.

The 7-bromo- (4a) and 7-iodo- (4b) derivatives of 7-deaza-2'-deoxyxanthosine (5) are prepared. Furthermore, the building blocks 6-8 of 7-deaza-2'-deoxyxanthosine (5) are synthesized and tested for their usage in oligonucleotide synthesis.

Oligonucleotides incorporating N7-(2'-deoxy-beta-D-erythro-pentofuranosyl)isoguanine.

The H-phosphonate and the phosphoramidite of N7-2'-deoxyisoguanosine (2) were prepared and incorporated into oligonucleotide duplexes. Their base pairing properties were investigated and compared with those of the parent purine nucleosides.

Pyrrolo[2,3-d]pyrimidine nucleosides: synthesis and antitumor activity of 7-substituted 7-deaza-2'-deoxyadenosines.

A one step synthesis, using the nucleoside 7-iodo-2'-deoxytubercidin (2b) in a Pd(0)/Cu(I)-catalyzed cross coupling reaction furnished a series of 7-alkynyl-2'-deoxytubercidin derivatives. The 7-iodo-, 7-chloro- or 7-bromo 2'-deoxytubercidins 2b-d as well as certain 7-alkynyl derivatives show significant activity against several tumor cell lines, with 7-iodo-2'-deoxytubercidin (2b) as the most effective compound.

Pyrazolo[3,4-d]pyrimidine nucleic acids: adjustment of the dA-dT to the dG-dC base pair stability.

The pyrazolo[3,4-d]pyrimidine-4,6-diamine nucleosides 2b-d stabilize the dA-dT base pair significantly when the dA-residue is replaced. Oligonucleotide duplexes incorporating 2b-d show a 4-6 degrees C Tm increase per modification. The 7-bromo compound 2b harmonizes the stability of the dA-dT vs. the dG-dC pair. According to this the stability of such duplexes depends no longer on the base pair composition of a DNA molecule.

Oligonucleotides incorporating 7-(aminoalkyn-1-yl)-7-deaza-2'-deoxyguanosines: duplex stability and phosphodiester hydrolysis by exonucleases.

Self-complementary [[5'-d(G-C)4]2] and non-selfcomplementary oligonucleotides [5'-d(TAG GTC AAT ACT) x 3'-d(ATC CAG TTA TGA)] containing 7-(omega-aminoalkyn-1-yl)-7-deaza-2'-deoxyguanosines (1a-c) (1) and 7-deaza-2'-deoxyguanosine instead of dG were studied regarding their thermal stability as well as their phosphodiester hydrolysis by either 3' --> 5'- or 5' --> 3'-phosphodiesterase studied by MALDI-TOF MS.

Pyrophosphoryl derivatives of 1-(2-deoxy-3-O-phosphono-methyl-beta- and -alpha-D-erythro-pentofuranosyl)thymine: synthesis and substrate properties towards some DNA polymerases.

The synthesis of 1-(2-deoxy-3-O-phosphonomethyl-beta-D-erythropentofuranosyl)thymine (17) and its alpha-anomer 18 is described. Attempts to prepare 1-[2-deoxy-3-O-(pyrophosphoryl)phosphonomethyl-beta-D-erythro-pentofuranosyl]thymine (19) by an activation of the respective phosphonate 17 with 1,1'-carbonyldiimidazole (Im2CO) resulted in the quantitative formation of the corresponding pyrophosphonate derivative 21 (Scheme 2). Activation of inorganic pyrophosphate with Im2CO followed by the condensation with the phosphonates 17 and 18 afforded the desired analogues of nucleoside triphosphate 19 (35%) and its alpha-anomer 20 (27%) along with the respective pyrophosphonate derivatives 21 (37%) and 24 (38%) (Scheme 3). It was found that compounds 19 and 20 display (i) no substrate properties toward calf thymus terminal deoxynucleotidyl transferase (TDT) and AMV reverse transcriptase, and (ii) moderate substrate activity with E. coli DNA polymerase I (Klenow fragment).