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In this study, the acid-base properties of the adenine cation radical are investigated by means of experiment and theory. Adenine cation radical (A?+) is produced by one-electron oxidation of dAdo and of the stacked DNA-oligomer (dA)6 by Cl2?- in aqueous glass (7.5 M LiCl in H2O and in D2O) and investigated by ESR spectroscopy. Theoretical calculations and deuterium substitution at C8-H and N6-H in dAdo aid in our assignments of structure. We find the pKa value of A?+ in this system to be ca. 8 at 150 K in seeming contradiction to the accepted value of ≤1 at ambient temperature. However, upon thermal annealing to ≥160 K, complete deprotonation of A?+ occurs in dAdo in these glassy systems even at pH ca. 3. A?+ found in (dA)6 at 150 K also deprotonates on thermal annealing. The stability of A?+ at 150 K in these systems is attributed to charge derealization between stacked bases. Theoretical calculations at various levels (DFT B3LYP/6-31G*, MPWB95, and HF-MP2) predict binding energies for the adenine stacked dimer cation radical of 12 to 16 kcal/mol. Further DFT B3LYP/6-31G* calculations predict that, in aqueous solution, monomeric A?+ should deprotonate spontaneously (a predicted pKa of ca. -0.3 for A?+). However, the charge resonance stabilized dimer AA?+ is predicted to result in a significant barrier to deprotonation and a calculated pK a of ca. 7 for the AA?+ dimer which is 7 pH units higher than the monomer. These theoretical and experimental results suggest that A?+ isolated in solution and A?+ in adenine stacks have highly differing acid-base properties resulting from the stabilization induced by hole derealization within adenine stacks.

(Chemical Equation Presented) A variant of the semipinacol rearrangement that was observed in our laboratory has been applied to the synthesis of several furanose and pyranose derivatives. The process consists of an "orchestrated" [1,2]-hydride shift with

Positively charged DNG oligonucleotide mixed sequences containing A/T bases were prepared by solid-phase synthesis. Synthesis proceeds in 3′→5′ direction and involves coupling of 3′-Fmoc protected thiourea in the presence of HgCl2/TEA with the corresponding 5′-amine of the growing oligo chain. DNG binding characteristics with complementary DNA and with itself have been evaluated.

A mild, efficient and inexpensive detritylation method is reported that uses trifluoroacetic acid on a silica gel column to obtain pure, detritylated compounds in one-step. This method is applicable to acid stable as well as acid sensitive compounds with only slight alterations in the procedure. Nineteen examples are given.

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Alternative syntheses of 9-(3-deoxy-β-D-threo-pentofuranosyl)adenine (4), the core nucleoside of agrocin 84 [and its 2'-deoxy threo isomer 5] were devised: (1) direct conversion of 9-(β-D-arabinofuranosyl)adenine into 9- (2,3-anhydro-β-D-lyxofuranosyl)adenine and regioselective opening of its oxirane ring with sodium borohydride to give 4 and 5 (~7.5:1); (2) treatment of adenosine with sodium hydride and 2,4,6-triisopropylbenzenesulfonyl chloride, and subjection of the resulting 2'(3')-sulfonates to the reductive [1,2]-hydride shift rearrangement with lithium triethylborohydride to give 4 and 5 (~2:1); and (3) subjection of the phenoxythiocarbonyl esters of 9- [2(3),5-bis-O-(tert-butyldimethylsilyl)-β-D-arabinofuranosyl]adenine to Barton deoxygenation, and deprotection to give 4 and 2'-deoxyadenosine (~5:1). Methods (2) and (3) gave lower yields. Syntheses of simplified 6-N- and 5'-O-adenosine phosphoramidate model compounds were explored to examine potential access to such features in the structure proposed for agrocin 84.

The effect of 20-ns pulses of 193-nm laser light on aqueous solutions of purine bases, (2′-deoxy)nucleosides, and (2′-deoxy)nucleotides was investigated, and monophotonic ionization was observed. Although (deoxy)ribose and (deoxy)ribose phosphates are also ionized by 193-nm light, the photoionization of the (deoxy)nucleosides and -tides takes place predominantly (90%) at the purine moiety, due to the much higher extinction coefficients at 193 nm of the bases as compared to the (deoxy)ribose phosphates. The quantum yields of photoionization (φPl) of the purines are in the range 0.01 to 0.08, based on φ(Cl-) at 193 nm of 0.46. As shown by comparison with data obtained from pulse radiolysis, the ionized purines, i.e., the radical cations, deprotonate in neutral solution, yielding neutral radicals. The radical cation of 1-methylguanosine, produced by photoionization in oxygen-saturated aqueous solution, deprotonates with the rate constant 3.5 × 105 s-1. In the absence of oxygen, the hydrated electrons resulting from the photoionization react with the untransformed purine derivatives to yield the corresponding radical anions. As these are rapidly protonated by water (as concluded from pulse radiolysis), the photoionization in deaerated neutral solution results in two different neutral radicals: a deprotonated radical cation and a protonated radical anion.

Treatment of selectively 3',5'-protected β-D-xylofuranosyl nucleosides (4) with phenyl chlorothionocarbonate and DMAP followed by hydrogenolysis of the resulting (2'-O-phenoxythiocarbonyl) phenyl thionocarbonate esters (6) with tributylstannane/AIBN, and

A new procedure is described for the synthesis of the title compounds by lithium aluminium hydride or deuteride reduction of appropriately protected 2',3'-anhydro-lyxo-adenosine.

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