HPLC electrospray mass spectrometric characterization of trimeric building blocks for oligonucleotide synthesis

Screening combinatorial libraries of cyclic peptides using the yeast two-hybrid assay

Peptides are useful reagents for reverse analysis of protein function in a variety of organisms, as they have a dominant mode of action that can inhibit protein interactions or activities. Further, peptides are important tools for validating proteins as therapeutic targets, for determining structure/activity relationships, and for designing small molecules. Genetic selection strategies have been developed for screening combinatorial peptide libraries to rapidly isolate peptides that interact with a given target. In genetic selections and biological assays, linear peptides are not very stable and are rapidly degraded. In contrast, cyclic peptides are more stable and bind with higher affinity. Genetic selections of cyclic peptides are difficult as they are not compatible with most selection technologies. Thus, there has been limited number of applications that use cyclic peptides for the reverse analysis of protein function.Here, we describe a protocol to isolate cyclic peptides that bind proteins in the yeast two-hybrid assay. Cyclic peptides used in the yeast two-hybrid assay are referred to as "lariat" peptides. Lariat peptides are made by blocking the intein-producing cyclic peptide reaction at an intermediate step. They consist of a lactone cyclic peptide or "noose" region connected by an amide bond to a transcription activation domain. Combinatorial libraries of >10(7) lariat peptides can be screened using the yeast two-hybrid assay to isolate lariat peptides for studying the function or validating the therapeutic potential of protein targets.

Improved synthesis of trinucleotide phosphoramidites and generation of randomized oligonucleotide libraries

A new method to produce a set of 20 high quality trinucleotide phosphoramidites on a 5-10 g scale each was developed. The procedure starts with condensation reactions of P-components with N-acyl nucleosides, bearing the 3 '-hydroxyl function protected with 2-azidomethylbenzoyl, to give fully protected dinucleoside phosphates 13. Upon cleavage of dimethoxytrityl group from 13, dinucleoside phosphates 16 are initially transformed into trinucleoside diphosphates 19 and then the 2-azidomethylbenzoyl is selectively removed under neutral conditions to generate trinucleoside diphosphates 5 in excellent yield. Subsequent 3 '-phosphitylation affords target trinucleotide phosphoramidites 7. When mutagenic oligonucleotides are synthesized employing mixtures of building blocks 7 as well as following the new synthetic protocol, representative oligonucleotide libraries are generated in good yields.