Self‐Organized Glycoclusters Along DNA: Effect of the Spatial Arrangement of Galactoside Residues on Cooperative Lectin Recognition

Abstract

We describe herein the relationship between the spatial arrangement of self-organized galactose clusters and lectin recognition. beta-Galactose-modified deoxyuridine phosphoramidite was synthesized and applied to solid-phase synthesis to provide 18-, 20-, and 22-mers of site-specifically galactosylated oligodeoxynucleotides (Gal-ODNs). These Gal-ODNs were self-organized through hybridization with the corresponding 18-, 20-, and 22-mers of half-sliding complementary ODNs (hsc-ODNs) to give periodic galactoside clusters. The self-organization of ODNs was confirmed by size exclusion chromatography and gel electrophoresis. The binding of the Gal-clusters to the FITC-labeled RCA(120) lectin was analyzed by monitoring the change in fluorescence intensity. The assembly of 20-mer Gal-ODN with the 20-mer hsc-ODN was strongly and cooperatively recognized by the lectin. The 18-mer assembly was bound more weakly and less cooperatively, and the 22-mer assembly was minimally bound to the lectin. RCA(120) lectin recognized not only the density of galactoside residues, but also the spatial arrangement. The size of the Gal cluster was estimated from the association constant of Gal-ODN with hsc-ODN. The relationship between lectin-recognition and Gal-cluster size is also discussed.

A Cationic Dye Triplet as a Unique “Glue” That Can Connect Fully Matched Termini of DNA Duplexes

“…Note that the ZZZ triplet is a much stronger glue than a native oligonucleotide triplet (compare Figure 8 with Figure 9) and is also orthogonal to a native oligonucleotide. An increase in the number of natural nucleobases of the glue portion will certainly raise its sticking ability, [38][39][40] but glue that is too long might lead to unexpected miss-hybridization or sticking of the glue portion, which might precede construction of the components. These problems can be avoided with the use of ZZZ triplets.…”

Glycotargeting to improve cellular delivery efficiency of nucleic acids

“…This method was demonstrated by Kobayashi et al in the synthesis of galactosederivatized oligonucleotides [100][101][102]. First, suitably protected galactose derivatized with an alkyne function 13 is reacted with suitably protected 5-iododeoxyuridine 14 through a palladium-mediated coupling reaction to introduce a covalent bond between the galactose and uridine moieties.…”

Biomolecular Self-assembling Systems for Multivalent Ligand Display

“…A self-assembled β-Gal cluster along double strand DNA was constructed by hybridization of galactosylated oligo-DNA (Gal-DNA) with the half-sliding complementary DNA ( Fig. 2A) (16,17), which is defined as an n-mer DNA in which the right half sequence (gray) and the left half sequence (black) are complementary to the left half sequence (gray) and the right half sequence (black) of the target n-mer Gal-DNA, respectively. β-Gal cluster along double strand DNA, which displays β-Gal residues at 6.8-nm intervals with a small dihedral angle, was formed by hybridization of 20-mer Gal-DNA with the half-sliding complemen- bound to RCA 120 (Fig.…”