Dinucleoside

Chirahty at the phosphoms is an unavoidable problem in all phosphorothioate syntheses. The phosphoramidite method produces a mixture of both the and the diastereomers having a small excess of the isomer (53). Although some progress has been made in the chiral synthesis of dinucleoside phosphorothioates, low yields have limited the utility of these approaches. The chiral center may be eliminated by replacing the other, nonbridging oxygen with sulfur. Avoidance of the chirahty problem is one reason for the interest in phosphorodithioates. 

Scheme 40 Triplet-sensitized photorearrangement of allylphosphites applied to the preparation of dinucleosides...

A method for the direct spectrophotometric determination of dinucleoside monophosphates has been developed which relies on changes in u.v. absorbance after enzymic hydrolysis. - Hydrolytic fission of the dinucleoside monophosphate with a phosphodiesterase causes a change in the u.v. absorbance of the solution allowing the 5 -nucleoside to be estimated. Addition of a phosphomonoesterase to the hydrolysate causes a further change in u.v. absorbance, allowing the 3-nucleoside to be estimated. 

Several groups have used dinucleoside-3 phosphoramidites as... 

Analogues of Dinucleoside Di(Tri)phosphates and Oligonucleotides with a Di(Tri)phosphate Bridge... 

The following diphosphates and triphosphates can be prepared by reaction of nucleotide azolides with nucleotides, sugar phosphates, phosphopeptides, or aminohexyl phosphates, a) NAD-analogues and P1, / -dinucleoside-S -diphosphates 801... 

In ref. [123], 1-triisopropylbenzenesulfonyl- or mesitylenesulfonyl-5-(pyridine-2-yl)-tetrazole (VIII) was successfully used as a coupling agent for the synthesis of protected di- and trinucleotides. In comparison with the sulfonic acid tetrazolides these are able to achieve a stereoselective synthesis of dinucleoside monophosphate aryl esters. 311 1241... 

Ref. [152] discusses the transformation of a dinucleoside pyrophosphate into a reactive azolide with an azole (e.g., 3-nitro-1,2,4-triazole or tetrazole). With quinoline-8-sulfonyl chloride the concomitantly formed phosphordiester can be converted back to the dinucleoside pyrophosphate (see scheme on the next page). 

Recently a very mild method was discovered for the synthesis of dinucleoside fluorophosphates in the conversion of a dinucleoside phosphite with iV V -oxalyldiimi-dazole into the corresponding phosphoric imidazolide, which is then treated with acyl fluoride [204] <202]... 

Utilizing method B, mixed anhydrides of a dinucleoside phosphate and methylsul-fonic or trifluoroacetic acid could be prepared 2043... 

Interestingly, it was recently shown that the one-electron oxidation reaction promoted by photoexcited menadione (MQ) gives rise to A -formylade-nine (52) and A -acetyladenine (53) residues (Scheme 5) in several dinucleoside monophosphates including d(ApA), d(CpA) and d(ApC) [92]. 

The HPLC-MS/MS assay was also successfully applied to the measurement of UV-induced dimeric pyrimidine photoproducts [123, 124]. The latter lesions were released from DNA as modified dinucleoside monophosphates due to resistance of the intra-dimer phosphodiester group to the exonuclease activity during the hydrolysis step [125, 126]. The hydrolyzed photoproducts exhibit mass spectrometry and chromatographic features that allow simultaneous quantification of the three main classes of photolesions, namely cyclobutane dimers, (6-4) photoproducts, and Dewar valence isomers, for each of the four possible bipyrimidine sequences. It may be added that these analyses are coupled to UV detection of normal nucleosides in order to correct for the amount of DNA in the sample and obtain a precise ratio of oxidized bases or dimeric photoproducts to normal nucleosides. 

The hydroxy groups of the pyrimido[l,6-c][l,3]oxazine 316 (R1 = R2 = H) were mono-tritylated with 4,4 -(MeO)2-trityl chloride in pyridine/NEt3. The mixture of the two products 316 (R1 =4,4 -(MeO)2-trityl R2 = H) and 316 (R1 = H R2 = 4,4 -(MeO)2-trityl) was coupled with nucleoside phosphoramidites, oxidized to protected dinucleosides and the isomers were separated <1999NN2031>. 

Table 11.1 Biophysical and biochemical properties of dinucleoside tri-, tetra-, and pentaphosphate cap analogs... 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

Figure 30. Schematic diagrams of overlap of ring systems in (a) the alkylated nucleoside described here, (b) daunomycin intercalated in a hexanucleotide (143), (c) proflavine intercalated in a dinucleoside phosphate (70), Td) a model of a diol epoxide of DMBA semi-intercalated in a manner analogous to that in (a) so that N2 of guanine may be alkylated, (e) a model of a diol epoxide of DMBA semi-intercalated in a manner analogous to that in (c) so that 06 of guanine may be alkylated.

Using phosphotriester methods, dinucleoside (3 - 50-monophosphates containing 6-methyl-2,-deoxyuridine at the 3 - or 5 -end have been prepared.44 N.m.r. spectroscopy indicates that this nucleoside possesses the syn conformation in these compounds, and, on treatment with snake venom phosphodiesterase, d(m6UpT) is degraded, while d(Apm6U) is not, indicating that this enzyme, a 3 -exonuclease, requires the anti conformation to be present in the substrate. Two modified nucleo-side-5 -monophosphates, (20) and (21), which are resistant to 5 -nucleotidase, have been isolated from tRNA snake venom hydrolysates.45 A synthesis of (20) has been reported.46... 

Diester methods have been used to synthesize analogues of the initiator codon ApUpG in which the adenine residue has a fixed torsion angle, as for instance in (78),132 and triester methods have been used to prepare dinucleoside phosphates and codon analogues133 134 containing the hydroxyalkyl nucleosides 9-(4 -hydroxybutyl)-adenine (80), 9-(3 -hydroxypropyl)adenine (81), and 1 -(3 -hydroxypropyl)uracil (82), with a view to determining the effect of the achiral residues on the c.d. spectra. 

Electron attachment to dinucleoside phosphates leads to the formation of radical ions in which the electron has added to the more easily reduced heterocyclic base.35... 

The e.s.r. spectra of y-irradiated diethyl phosphate and its salts have been studied111 and the structures of the phosphonates(89)112 and some nucleoside phosphates113 have been studied from the e.s.r. spectra of the nitroxide spin-labelled compounds. An e.s.r. study of electron transfer in dinucleoside phosphate anions indicates preferen-... 

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