Targeting Base Residues of Specific Sequences

The reactions or photoreactions of metal complexes with DNA described previously usually occur randomly at guanine sites of nucleic acids. Recently, different authors studied the possibility of directing the photoreaction of Ru11 complexes to a specific gene. Oligonucleotides can indeed be used to target specifically a sequence of mRNA (called anti-sense strategy) or double-stranded DNA (called anti-gene strategy) with triple-helix formation.72 75 The derivatiza-tion of an oligonucleotide by a metallic complex should allow the combination of the specific recognition of the sequence by the oligonucleotide with the (photo)-reactivity of a ruthenium complex. Such a system would allow the targeting of a specific gene (the complementary sequence of the derivatized oligonucleotide) and the induction of the (photo)reaction on a specific base unit of this gene.

This approach was used by Ossipov and co-workers who studied oligonucleotides derivatized by the photoreactive and intercalating [Run(terpy) (dppz)(CH3CN)]2+ complex (dppz = dipyrido [3,2-a:2',3'-c] phenazine, Figure 19.11).76 In this case, the photoreaction is not initiated by a photoelectron transfer. Instead, the visible illumination of this compound induces the loss of the CH3CN ligand, giving rise to the corresponding aqua complex [RuII(terpy)(dppz)(H2O)]2+ which forms an adduct on DNA similar to the Pt aqua complexes. The [RuII(terpy)(dppz)(CH3CN)]2+ complex has thus been anchored to different synthetic oligonucleotides. After hybridization with the complementary sequence, the illumination of the corresponding derivatized duplexes results in the photo-addition of the aqua complex on a guanine residue of the complementary strand. This sequence-specific photoreaction inducing the cross-linking of the duplex strands could be interesting in the development of anti-cancer agents or tools for DNA diagnostic studies.

In order to combine the photo-redox properties of a Ru TAP complex described previously, with the sequence specificity of an oligonucleotide, Kirsch-De Mesmaeker and co-workers chose a system comprising a

Figure 19.11 The photoreactive [RuII(terpy)(dppz)(CH3CN)]2+ complex anchored via the dppz ligand onto an oligonucleotide
Figure 19.12 The [RuII(TAP)2dip']2+ complex anchored onto a synthetic oligonucleo-tide at the level of the 5-position of a thymine (see Plate 2)

[RuII(TAP)2dip0]2+ (dip' = dip-(CH2)4COOH) complex anchored to different synthetic 17 mer oligonucleotides (Figure 19.12).77 79 [RuII(TAP)2dip']2+ contains two p-deficient TAP ligands in order to make the complex photo-oxidizing and a dip' ligand for the derivatization. The derivatized probe strands are free of guanine residues (to prevent intramolecular reactions) and were hybridized to their complementary sequences containing various numbers of guanine units located in different positions. It was demonstrated that an electron transfer occurs from the guanine moieties of the complementary strand to the excited complex anchored to the probe strand. The recombination of the radicals generated by this primary photoprocess as described above leads to the formation of a photoadduct of the tethered complex on a guanine of the complementary strand. As evidenced by denaturing gel electrophoresis and by ESMS, this adduct is responsible for the photocross-linking of the two oligonucleotide strands (Figure 19.12).80,81 Interestingly, this photocross-linking

Primer

Ru-labeled ''oligonucleotide

-GAGGTAGTATAGG TTTTTTTCTTAAATTTA-3'

-CTCCATCATATCCAATCTACTATAAAAAAAGAATTTAAAT-5'

Matrix7

Photocross-linking and inhibition of the enzymes at this site

Figure 19.13 Representation of the system studied by Kirsch-De Mesmaeker and co-workers, comprising a 13mer DNA primer and a 17mer Run labeled oligonucleotide, both hybridized to a 40 mer matrix is able to block in vitro the action of different enzymes such as a digestion enzyme (exonuclease III) and different DNA-polymerases, with 100% efficiency.81 Thus, a 17 mer RuII-labeled oligonucleotide was hybridized to its complementary sequence located on the 5' extremity of a 40 mer matrix. After illumination, the elongation of the 13 mer DNA primer hybridized to the 3' extremity of the same matrix was completely blocked at the position corresponding to the formation of the photocross-linking (Figure 19.13).

In conclusion, these data obtained with Ru-labeled oligonucleotides indicate quite interestingly that the cross-linking of the two strands induced under illumination could be developed for future applications, either in the frame of the anti-sense or anti-gene strategy, or for DNA diagnostic studies.

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