8-vinyl-adenosine (8VA) is a new fluorescent nucleoside analogue with improved spectroscopic properties as compared to 2-aminopurine (2AP). To further understand its photophysics, we analyzed by the time-dependent density functional theory and the configuration interaction single method, the electronic properties, and transitions of 8VA in its free form and stacked with one or two flanking bases. For free 8VA, the predicted excited-state energy gaps, absorbance peak position, and oscillator strength were found to be in excellent agreement with the experimentally determined ones. Moreover, its high fluorescence quantum yield was found to be associated with the dipole-allowed S1 --> S0 transition. Stacking of 8VA with C, T, or A in dimers or trimers resulted in fluorescence quenching through mechanisms that depend on the nature and relative orientation of the flanking base(s). When 8VA is stacked with T, quenching mainly results from nonradiative relaxation to low-lying dark excited state(s) that do not exist in free 8VA. When 8VA is stacked with A, quenching results mainly from mixing of the molecular orbitals in the ground state. Both types of quenching are thought to accompany the stacking of 8VA with C. In addition, the C-8VA-C trimer was found to exhibit a low-lying S1 emissive state that may generate an increased fluorescence quantum yield and lifetime. The predicted photophysical properties of the trimers are highly consistent with the spectroscopic data of a series of 15-mer oligonucleotides differing only by the nature of the residues flanking the central 8VA.
We describe the preparation of 3'-alkynyluridine 4a and -adenosine 4b and of 3'-alkynyl-2'-deoxyuridine 16a and -adenosine 16b starting from the corresponding nucleosides. The desired stereochemistry of the C-3' tertiary alcohol was obtained by reaction of an ethynylcerium-lithium reagent on a 3'-ketonucleoside with the hydroxyl group at C-5' unprotected. The 2'-deoxygenation was performed by a Barton-McCombie reaction under appropriate conditions where the addition of tin hydride to the triple bond was suppressed. Evaluation of the anti-HIV activity of the C-3' modified nucleosides is reported.
The synthesis of 12 analogues of adenine substituted at C-8 by an omega-hydroxyalkyl, omega-hydroxyalk-1-enyl, or omega-hydroxyalk-1-ynyl chain of various length has been carried out in five or six steps starting from adenine. The analogues were obtained using a new protecting group of adenine, the tert-butyldimethylsilyloxymethyl group. 9-tert-Butyldimethylsilyloxymethyl-adenine is more soluble than adenine in organic solvents. It was prepared regiospecificaly in two steps from adenine and was amenable to C-8 iodination under basic conditions and to subsequent introduction of the various carbon chains at C-8 by palladium-catalyzed cross-coupling reactions (Stille or Sonogashira). The protecting group was removed under acidic conditions, thus demonstrating its versatility.
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