Graham Beaton

Chemical synthesis of deoxyoligonucleotides and deoxyoligonucleotide analogs.

Publisher Summary This chapter discusses advances in chemical methodologies, which include the development of new protecting group strategies and procedures for the attachment of reporter groups to DNA. Because of these achievements, the time required to synthesize DNA has been reduced, and an even larger repertoire of applications for synthetic deoxyoligonucleotides has been achieved. An attempt is made to review some of these many excellent contributions, but only one detailed protocol for labeling DNA is included. This is a relatively recent, unpublished procedure for attaching reporter groups to a new DNA analog called “dithioate DNA.” Deoxyoligonucleotides having a deoxynucleoside–OPS 2 O–deoxynucleoside linkage, dithioate DNA, are excellent mimics of natural DNA. At least partially, this is because they are isosteric and isoelectronic with normal DNA. They are, however, completely resistant to snake venom, calf spleen, P 1 exonucleases, all the nucleases found in HeLa nuclear and cytoplasmic extracts, and even the very potent exonucleolytic activity of T 4 DNA polymerase. These attractive features combined with the ability of dithioate DNA to form stable DNA duplexes have led to several potential applications.

Application of the Pictet-Spengler reaction in combinatorial chemistry

Abstract Reaction of polymer bound tryptophan with a variety of aldehydes and ketones under Pictet-Spengler like conditions was found to produce 1,2,3,4-tetrahydro-β-carbolines in excellent yield. The straightforward, easily automated chemistry and the availability of numerous commercial aldehydes and ketones makes this approach ideal for combinatorial chemistry application.

Synthesis of oligonucleotide phosphorodithioates

Abstract The synthesis of DNA containing sulfur at the two nonbonding internucleotide valencies is reported. Several different routes using either tervalent or pentavalent mononucleotide synthons are described.

Chemical and Biochemical Studies with Dithioate DNA

Abstract Dithioate DNA was synthesized and used for various biochemical studies. Results from these studies indicate that dithioate DNA is a potent inhibitor of HIV Reverse Transcriptase, activates endogenous RNase H in Hela cell nuclear extracts, and is a useful probe for studying protein-DNA interactions.

Synthesis of phosphorodithioate DNA by the H-phosphonothioate method

Abstract A novel method for the efficientsynthesis phosphorodithioate DNA using H-phosphonothioate synthons is described. The 5′-DMT-nucleoside H-phosphonothioate monomers were prepared in two high yielding steps from commercially available phosphoramidites. This strategy for the synthesis of H-phosphonothioate monomers proved versatile and allowed for the synthesis of cholesterol H-phosphonothioate synthons. Synthetic protocols for the assembly of phosphorodithioate DNA using an automated synthesizer were developed. The H-phosphonothioate solid-phase synthesis method facilitates the preparation of oligonucleotide conjugates, as demonstrated by the example of attachment of 5′-cholesterol oligonucleotides.

Oligonucleotide Phosphonates—Solid Phase Synthesis and Biochemical Characterization

Abstract A novel method for the automated synthesis of oligonucleotide-3′-phosphonates is described. Oligonucleotide analogs synthesized by this method exhibited appreciable stability to exonuclease digestion.

Solid phase synthesis of peptidomimetics

The characteristic peptide properties of low bioavailability and short half life present significant problems in their development as therapeutic agents. One approach to overcoming these problems has been the identification of non-peptide structures whose topological features enable them to mimic binding of the native peptide at the receptor level. These compounds are collectively known as peptidomimetics and have been the subject of several extensive reviews [1, 2, 3]. Recent advances in solid phase organic synthesis have the potential to accelerate the discovery and lead optimization phases of medicinal chemistry, including the area of peptidomimetic research. While much peptidomimetic chemistry has traditionally been performed by solution phase methods, the application of solid phase methodology can offer many of the same inherent advantages with respect to speed and ease of automation which have been realized in solid phase peptide synthesis. Our initial efforts have centered around the development of solid phase methods for two well established peptidomimetic scaffolds shown in Fig.l, the l,4-benzodiazepine-2,5-diones 1 [4], and the 4-(3H)-quinazolinones 2 [5].