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Synlett 2007(1): 0001-0018  
DOI: 10.1055/s-2006-958449
ACCOUNT
© Georg Thieme Verlag Stuttgart · New York

Synthesis and Properties of Oligonucleotides with Acylamido Substituents

Clemens Richert*, Peter Grünefeld
Institute of Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
Fax: +49(721)6084825; e-Mail: cr@rrg.uka.de;
Further Information

Publication History

Received 25 May 2006
Publication Date:
20 December 2006 (online)

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Abstract

This account recounts how a project, initially designed to generate folded peptidyl-DNA motifs for cellular delivery, led to the discovery of acylamido substituents that increase affinity for target strands and improve mismatch discrimination of hybridization probes. Our syntheses of oligonucleotides with acylamido groups involve phosphoramidites of aminodideoxynucleosides as inter­mediates and amide-forming reactions on solid support, performed after assembly of the DNA chain. The richly functionalized intermediates invite a host of side reactions. Strategies to suppress these side reactions are discussed. In our quest for oligonucleotides with improved biophysical and biological properties we used late, on-support combinatorial couplings to generate small chemical libraries subjected to mass-spectrometrically monitored selection experiments. The combinatorial approach was used to identify acylamido substituents at the termini that act as caps for DNA duplexes. Though truly bioavailable DNA derivatives were not found, oligonucleotides with a short dendrimer at the 5′-terminus and a blocked 3′-terminus were shown to possess improved enzymatic stability, while retaining high affinity for target strands. The on-support ­synthesis of acylamido DNA gives access to structurally diverse molecules with potential in biomedical applications, including the use in high-fidelity DNA microarrays.

  • 1 Introduction

  • 2 Synthesis of Acylamido-DNA and the Stability of Its ­Duplexes

  • 2.1 Design and General Synthetic Aspects

  • 2.2 Common Side Reactions

  • 2.3 Combinatorial Syntheses

  • 2.4 Oligodeoxynucleotide-Peptide Hybrids

  • 2.5 Dendrimer-DNA Hybrids with Increased Nuclease ­Resistance

  • 3 Oligonucleotides with Improved Duplex-Forming ­Properties

  • 3.1 General Considerations

  • 3.2 Oligodeoxynucleotides with Directly Linked Acylamido Substituents

  • 3.3 Acylamido Caps with Linkers that Can Be Introduced as Phosphoramidites

  • 3.4 Acylamido Substituents in the Interior of DNA Strands

  • 4 Outlook

Abbreviations: Alloc, allyloxycarbonyl; cpg, controlled pore glass; dA, 2′-deoxyadenosine residue; dbf, di-N-butylformamidine; dC, 2′-deoxy­cytidine residue; dG, 2′-deoxyguanosine residue; DIEA, diisopropylethylamine; dT, thymidine residue; DMT, dimethoxytrityl; HBTU, 2-(1H-benzotriazole-1-yl)-1,1,3,3-tetra­methyluronium hexafluorophosphate; HOBT, hydroxybenzo­triazole; MMT, monomethoxy trityl; SMOSE, spectrometrically monitored selection experiment.

Key words

DNA - nucleosides - nucleobases - acylations - amides - peptides

31

Printz M., Richert C. J. Comb. Chem., accepted.

51

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Rojas Stütz, J. A.; Kervio, E.; Deck, C.; Richert, C.; manuscript submitted.