Nucleoside phosphate analogues of biological interest, and their synthesis via aryl nucleoside H-phosphonates as intermediates.

This review presents a brief account of the chemistry and mechanistic aspects of aryl H-phosphonates, and selected applications of this class of compounds as intermediates in the synthesis of a wide range of biologically important analogues of nucleoside phosphates, and oligonucleotides, in which the phosphate moieties are replaced by other structurally related groups. The aryl nucleoside H-phosphonates, compounds of controlled reactivity, have proven to be more versatile and superior to various mixed anhydrides as synthetic intermediates, particularly for preparation of nucleotide analogues bearing P-N or P-S bonds in various configurational arrangements at the phosphate moiety.

Fluorescent alpha-anomeric 1,N(6)etheno-deoxyadenosine in DNA duplexes. The alpha-epsilondA / dG pair.

Structural properties of the fluorescent alpha-anomeric 1,N(6)ethenodeoxyadenosine residue placed in opposition to all four canonical deoxynucleotide units within 11-mer DNA duplexes have been studied. The duplex with alpha-epsilondA / dG pairing is most thermodynamically stable while the alpha-epsilondA / dC one is the least stable. Fluorescence measurements confirm the thermodynamic data and indicate base-pair dependent stacking properties of alpha-epsilondA within duplex structures. Results of molecular dynamics (MD) simulations in aqueous solution for the most stable duplex point to the presence of different conformational states of the alpha-1,N(6)etheno-deoxyadenosine residue, including formation of a hydrogen bonded pair with the dG and possible occurrence of severe kinking in the duplex.

Metal ion-dependent hydrolysis of RNA phosphodiester bonds within hairpin loops. A comparative kinetic study on chimeric ribo/2'-O-methylribo oligonucleotides.

Several chimeric ribo/2'- O -methylribo oligonucleotides were synthesized and their hydrolytic cleavage studied in the presence of Mg2+, Zn2+, Pb2+and the 1,4,9-triaza-cyclododecane chelate of Zn2+(Zn2+[12]aneN3) to evaluate the importance of RNA secondary structure as a factor determining the reactivity of phosphodiester bonds. In all the cases studied, a phosphodiester bond within a 4-7 nt loop was hydrolytically more stable than a similar bond within a linear single strand, but markedly less stable than that in a double helix. With Zn2+and Zn2+[12]aneN3, the hydrolytic stability of a phosphodiester bond within a hairpin loop gradually decreased on increasing the distance from the stem. A similar but less systematic trend was observed with Pb2+. Zn2+- and Pb2+-promoted cleavage was observed to be considerably more sensitive to the secondary structure of the chain than that induced by Zn2+[12]aneN3. This difference in behaviour may be attributed to bidentate binding of uncomplexed aquo ions to two different phosphodiester bonds. Mg2+was observed to be catalytically virtually inactive compared with the other cleaving agents studied.

2-Aminopurine labelled RNA bulge loops. Synthesis and thermodynamics.

The chemical introduction of the blue-fluorescent 2-aminopurine riboside into oligoribonucleotides synthesized using the 2'-O-t-butyl-dimethylsilyl protection is reported. The proposed purification procedure led to the synthetic RNAs of high purity required for spectrofluorimetry studies. Thermodynamic parameters for the RNA bulge loops of type (A)n labelled with the 2-aminopurine (2AP) have been determined by optical melting. Results indicate that a bulge (B) in the RNA duplexes GUCG(B)GCUG + CAGCCGAC destabilize a regular helix structure and the destabilization increases monotonically as bulge length increases in the following order of (B) = A-2AP-A > 2AP-A; A-2AP > 2AP. The analysis of the free energy increments for bulged loops, delta G(o)37(bulge), allows to conclude that the structural properties of 2-aminopurine in RNA bulge loops are very similar to those of isomeric adenine. The fluorescent 2-aminopurine could therefore be used as non-invasive conformational probe.