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
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