Current Organic Chemistry, 2008, 12, 263-290 263 1385-2728/08 $55.00+.00 © 2008 Bentham Science Publishers Ltd. Chemical Strategies for Oligonucleotide-Conjugates Synthesis Y. Singh 1, 2 , N. Spinelli 1 and E. Defrancq 1* 1 Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France; 2 Current Affiliation: Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State Uni- versity of New Jersey, Piscataway, NJ 08854-8022, USA Abstract: Oligonucleotide conjugates have found numerous applications in the field of diagnostics and therapeutics. Structurally diverse oligonucleotide conjugates have been prepared and evaluated for various applications. Research ef- forts have focused on the development of synthetic procedures to accomplish efficient oligonucleotide conjugation with different target molecules. Both on-support and solution-phase coupling procedures have been used to conjugate oligonu- cleotides. This review gives an account of major synthetic approaches available to prepare covalent oligonucleotide con- jugates with diverse target molecules. 1. INTRODUCTION Synthetic oligonucleotides and their analogues have been investigated to accomplish specific inhibition of gene ex- pression, preparation of micro-arrays and design of DNA- based nanostructures. Oligonucleotides can achieve inhibi- tion of gene expression by targeting the mRNA by either antisense [1] or RNAi mechanism [2], double stranded DNA by triplex (antigene) mechanism [3], or proteins by aptamer selection [4] “(Fig. 1)”. The antisense oligonucleotides in particular have gener- ated significant interest on account of their potential use as therapeutic agents and tools to investigate gene function [5]. Zamecnik and Stephenson showed the potential of oligode * Address correspondence to this author at the Département de Chimie Molé- culaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Greno- ble Cedex 9, France. Email: Eric.Defrancq@ujf-grenoble.fr. oxynucleotides to act as antisense agents by using them to inhibit viral replication in cell cultures [6]. These antisense oligonucleotides are usually 15-20 nucleotides long and complementary to the mRNA target sequence. These un- dergo hybridisation with the target mRNA and inhibit trans- lation of mRNA into protein by either physical prevention of the splicing/translation machinery or RNase H dependent cleavage of mRNA after the binding to the target. RNase H is a ubiquitous enzyme that hydrolyses the RNA strand of an RNA-DNA hetero-duplex [7]. These antisense molecules have shown in vitro and in vivo anti-tumour activity in pre- clinical models. Currently, several antisense agents are being evaluated in clinical trials for the treatment of viral diseases [8]. Food and Drug Administration has approved one an- tisense agent (vitravene, formivirsen-sodium) for the treat- ment of cytomegalovirus-induced retinitis in patients suffer- ing from AIDS. Fig. (1). Inhibition of gene expression by targeting the mRNA (antisense mechanism), double stranded DNA (triplex/antigene mechanism) and proteins (aptamer selection). Antisense Nucleus messenger RNA Translation Protein Cytoplasm Transcription DNA STOP STOP Cell Aptamer STOP STOP