7-aminobutynyl-8-aza-7-deazahypoxanthine as a quasi-universal nucleobase.

Several 7-(hydroxy, amino, methylureido, and guanidino)alkynyl-substituted 8-aza-7-deaza- hypoxanthine analogues were investigated as potential universal nucleobases. 7-Aminobutynyl-8-aza-7-deazahypoxanthine was found to be the most promising quasi-universal nucleobase with improved hybridization and polymerase chain reaction (PCR) enhancing properties as compared to commonly used hypoxanthine (the nucleobase of inosine). It demonstrated improved ambiguity for pairing with A, T, and C bases and its base pairing properties can be summarized as follows: X:C∼X:A∼X:T > X:G.

Chemistry of minor groove binder-oligonucleotide conjugates.

Various types of minor groove binders have been attached to synthetic oligodeoxynucleotides, and the interactions of these conjugates (MB-ODNs) with DNA are reviewed here. MB-ODNs have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short MB-ODNs hybridize with ssDNA to give more stable DNA duplexes than unmodified ODNs with similar lengths.

Mild synthesis of asymmetric 2'-carboxyethyl-substituted fluoresceins.

Asymmetric fluoresceins bearing a carboxyethyl group in the chromophoric portion of the dyes were prepared by a reaction of substituted phthalic anhydride with a carboxyethyl substituted resorcinol analogue followed by a condensation with a second resorcinol analogue. In order to avoid an accumulation of symmetric side products, the second step was performed in two substeps: acid-catalyzed formation of a triphenylmethyl intermediate followed by base-catalyzed cyclization which furnished the desired dyes.

Novel DNA probes with low background and high hybridization-triggered fluorescence.

Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5'-end and a non-fluorescent quencher at the 3'-end of the DNA sequence. This configuration provides surprisingly low background and high hybridization-triggered fluorescence.

A novel endonuclease IV post-PCR genotyping system.

Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base gap. The oligonucleotide probe contains a non-fluorescent quencher at the 5' end and fluorophore attached to the 3' end through a special rigid linker.