DNA as Supramolecular Scaffold for Porphyrin Arrays on the Nanometer Scale

Abstract

Tetraphenyl porphyrin substituted deoxyuridine was used as a building block to create discrete multiporphyrin arrays via site specific incorporation into DNA. The successful covalent attachment of up to 11 tetraphenyl porphyrins in a row onto DNA shows that there is virtually no limitation in the amount of substituents, and the porphyrin arrays thus obtained reach the nanometer scale (approximately 10 nm). The porphyrin substituents are located in the major groove of the dsDNA and destabilize the duplex by deltaT(m) 5-7 degrees C per porphyrin modification. Force-field structure minimization shows that the porphyrins are either in-line with the groove in isolated modifications or aligned parallel to the nucleobases in adjacent modifications. The CD signals of the porphyrins are dominated by a negative peak arising from the intrinsic properties of the building block. In the single strands, the porphyrins induce stabilization of a secondary helical structure which is confined to the porphyrin modified part. This arrangement can be reproduced by force-field minimization and reveals an elongated helical arrangement compared to the double helix of the porphyrin-DNA. This secondary structure is disrupted above approximately 55 degrees C (T(p)) which is shown by various melting experiments. Both absorption and emission spectroscopy disclose electronic interactions between the porphyrin units upon stacking along the outer rim of the DNA leading to a broadening of the absorbance and a quenching of the emission. The single-stranded and double-stranded form show different spectroscopic properties due to the different arrangement of the porphyrins. Above T(p) the electronic properties (absorption and emission) of the porphyrins change compared to room temperature measurements due to the disruption of the porphyrin stacking at high temperature. The covalent attachment of porphyrins to DNA is therefore a suitable way of creating helical stacks of porphyrins on the nanometer scale.

Significantly Enhanced DNA Thermal Stability Resulting from Porphyrin H‐Aggregate Formation in the Minor Groove of the Duplex

“…Recently, the synthesis of a DNA containing eleven meso-functionalized porphyrins attached to 5-ethynyl-2'-deoxyuridines was carried out from the corresponding phosphoramidites; however, this showed a significant thermal destabilization of the resulting duplex. [6] A stabilizing effect of +0.5 8C per modification was observed when the porphyrins were placed adjacent in complementary strands. [7] Molecular modelling showed that the porphyrins were arranged in a zigzag fashion and stacked in pairs.…”

“…[4] Covalent attachment of porphyrin moieties to DNA has been achieved by using a variety of methodologies, including: the modification of nucleobases, [5][6][7][8] ribofuranose residues, [9][10][11][12][13] phosphate backbone [14][15][16] and by using acyclic linkers. [17,18] This provides structures that have porphyrin residues as 3'-or 5'-molecular caps, [12,[18][19][20] thus introducing them instead of a nucleobase in the middle of the helix [17] or as a label in the minor [10,16] and major [6][7][8] grooves.…”

“…[17,18] This provides structures that have porphyrin residues as 3'-or 5'-molecular caps, [12,[18][19][20] thus introducing them instead of a nucleobase in the middle of the helix [17] or as a label in the minor [10,16] and major [6][7][8] grooves. Recently, the synthesis of a DNA containing eleven meso-functionalized porphyrins attached to 5-ethynyl-2'-deoxyuridines was carried out from the corresponding phosphoramidites; however, this showed a significant thermal destabilization of the resulting duplex.…”

Duplex Stabilization and Energy Transfer in Zipper Porphyrin–DNA

“…Since our initial proposal to use DNA as a scaffold for porphyrin arrays [4] as compared to noncovalent assemblies, [5] we have studied both tetraphenylporphyrin (TPP) and diphenylporphyrin (DPP)-substituted DNA [6] and found significant differences in the thermal stability and the electronic properties of the multiporphyrin systems. [7,8] The attachment of substituents on one strand has an especially profound impact on the stability of the DNA duplex. In contrast to this one-strand modification, individual porphyrins, [9,10] metal-chelating ligands, [11] and pyrene-perylene systems [12] have been attached to both complementary strands, which leads to new supramolecular systems after hybridization.…”

“…[17] As we know from previously synthesized strands, the attachment of TPP in 2 onto one DNA strand leads to a decrease in the T m of DT m = À13.5 8C for three porphyrins, or DT m = À34.1 8C for eleven porphyrins compared to the corresponding natural DNA strand in a 21 base-pair (bp) sequence. [8] The zipper array 4 b·5 b, incorporating three stacked TPP moieties after hybridization, displays DT m = À4.1 8C, that is, an effective DT m of + 9.4 8C for the zipper in comparison with the one-strand porphyrin-DNA. The effect is even more remarkable in the duplex 6 b·7 b.…”