Synthesis of N-(2-deoxy-β-d-ribosyl) 4-thiomethylindole: A purine surrogate for incorporation into oligonucleotides

Synthesis and photophysical characterization of fluorescent indole nucleoside analogues

Fluorescent nucleosides are useful chemical tools for biochemical research and are frequently incorporated into nucleic acids for a variety of applications. The most widely utilized fluorescent nucleoside is 2-aminopurine-2'-deoxyribonucleoside (2APN). However, 2APN is limited by a moderate Stokes shift, molar extinction coefficient, and quantum yield. We recently reported 4-cyanoindole-2'-deoxyribonucleoside (4CIN), which offers superior photophysical characteristics in comparison to 2APN. To further improve upon 4CIN, a focused library of additional analogues combining the structural features of 2APN and 4CIN were synthesized and their photophysical properties were quantified. Nucleosides 2-6 were found to possess diverse photophysical properties with some features superior to 4CIN. In addition, the structure-function relationship data gained from 1-6 can inform the design of next-generation fluorescent indole nucleosides.

Synthesis of spirocyclic C-arylglycosides and -ribosides by ruthenium-catalyzed cycloaddition

Spirocyclic C-arylglycosides were synthesized from the appropriately protected delta-gluconolactones. Addition of lithium acetylide followed by glycosylation with 3-(trimethylsilyl)propargyl alcohol converted the delta-gluconolactones into silylated diynes. After desilylation, subsequent ruthenium-catalyzed cycloaddition of the resultant diynes with alkynes or chloroacetonitrile gave spirocyclic C-arylglycosides in good yields and selectivity. This strategy was also extended to the synthesis of spirocyclic C-arylribosides from the known gamma-ribonolactone derivative. Moreover, silver-catalyzed iodination of the sugar diynes followed by ruthenium-catalyzed cycloaddition with acetylene delivered spirocyclic C-iodophenylglycosides and -ribosides, which were subjected to palladium-catalyzed C-C bond-forming reactions and copper-catalyzed coupling with nitrogen heterocycles to lead to various derivatives.

Electrospray mass spectrometry of phosphoramidites, a group of acid-labile compounds

In contemporary solid-phase synthesis of oligonucleotides, phosphoramidites containing O-beta-cyanoethyl and N,N -diisopropyl groups are the most widespread monomer units. The N,N -diisopropyl phosphoramidite group can be activated by mild acidic treatment and then it easily reacts with nucleophiles (alcohols, water, etc.) to furnish the required phosphodiester linkage efficiently and cleanly. Owing to these properties, these compounds cannot be investigated using classical electrospray ionization. Their mass spectometric analysis is further hampered by the fact that they are often transiently protected with acid-sensitive groups (4, 4'-dimethoxytrityl, 4-monomethoxytrityl or trityl), which give intense signals in the spectra. Nanoelectrospray measurements from non-aqueous solvents (e.g. acetonitrile, methanol, tetrahydrofuran) were carried out in order to eliminate the nucleophilic water. Different types of alkali metal salts were used to form adduct ions. Among these salts, lithium chloride was found to be the most suitable for the analysis of amidites. Fairly abundant [M+Li](+) and [M+Cl](-) ions are formed in the positive and negative ion mode, respectively. These ions represent the base peaks in most cases whereas the intensities of the peaks corresponding to the protecting group are reduced by approximately 20%. This method is a powerful tool for the mass spectrometric identification of phosphoramidites. Copyright 1999 John Wiley & Sons, Ltd.

Structure and Base Pairing Properties of a Replicable Nonpolar Isostere for Deoxyadenosine

We report the synthesis, structure, and pairing properties in DNA of an isostere for deoxyadenosine which lacks all hydrogen-bonding functionality on the Watson-Crick pairing edge. A deoxyribo-nucleoside derivative of 4-methylbenzimidazole (1), which was recently shown to be inserted into DNA by Klenow DNA polymerase (Morales, J. C.; Kool, E. T. Nature Struct. Biol.1998, 5, 950), is prepared from 1-chloro-2-deoxy-3,5-bis-O-p-toluoyl-α-D-erythro-pentofuranose. The X-ray crystal structure of the nucleoside confirms that the compound is a close steric match for deoxyadenosine (2), although the methylbenzimidazole base is in the syn glycosidic orientation in the crystal. In D(2)O solution, 1H NMR studies show that 1 and 2 have similar (60% vs 70% S) sugar conformations and anti glycosidic orientations. Compound 1 is incorporated into a 12mer oligodeoxynucleotide and its base pairing properties in duplexes assessed by thermal denaturation. The results show that 1 has low affinity for the four natural bases but displays a stronger preference for being situated opposite a nonpolar difluorotoluene nucleoside analogue of thymine (3). The structural similarities of 1 and 2, combined with recent polymerase studies, add support to the hypothesis that steric complementarity plays an important role in base pair replication by polymerase enzymes and that Watson-Crick hydrogen bonds are not absolute requirements. Compound 1 should have significant utility as a probe of the importance of electrostatic effects in protein-DNA and protein-nucleotide binding as well as in DNA replication.