Porphyrin-DNA: A Supramolecular Scaffold for Functional Molecules on the Nanometre Scale

Abstract

We are pursuing the aim to use DNA as a supramolecular scaffold for the creation of electronically functional molecules on the nanometre scale. Here, we give a review on our results on porphyrin modified nucleotides used for this purpose. A general synthetic route to porphyrin-nucleotides has been devised, and the building blocks can be incorporated into oligonucleotides using standard solid phase synthesis methods. Up to 11 porphyrins were incorporated into DNA, reaching a length of approximately 4 nm in the array. The spectroscopic data are consistent with a porphyrin induced secondary structure stabilisation in the single strands.

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

“…[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.…”

Synthesis of β‐Pyrrolic‐Modified Porphyrins and Their Incorporation into DNA

“…The azide 26 was synthesised in 61 % yield by the reaction of the iodo precursor 12 with NaN 3 , sodium ascorbate, N,N-DMEA and Cu- 4 PF 6 in dry DMSO. Alternative reaction conditions using CuI as catalyst or toluene as solvent resulted in the isolation of the starting material 12.…”

“…The model triazoles 21-23 were synthesised from the corresponding azides 24-26 and 2'-deoxy-5'-O-DMT-5-ethynyluridine (16) with 2 equiv of Cu-A C H T U N G T R E N N U N G (ACN) 4 PF 6 in THF. This copper catalyst, which is soluble in organic solvents, was used as it had previously shown improved results in comparison with CuSO 4 ·5H 2 O or CuI in CuAAC reactions.…”

“…Several tethers have been used for the covalent attachment of porphyrins including maleimidothiols, [8,17] amides, [11][12][13]15] phosphates [16] and alkynes. [4][5][6][7]9] The incorporation of the porphyrins as 5 and 3 caps has been shown to improve base-pair fidelity and duplex stability [10] as well as showing the ability for the porphyrins to electronically communicate with each other (exciton coupling). This feature enables porphyrins to be used as detectors of DNA secondary structures in circular dichroism (CD) spectroscopy.…”

“…Porphyrins are useful labels and have been widely studied in a variety of applications including in light-harvesting devices [2] and the production of reactive oxygen species. [3] The site-specific covalent attachment of porphyrin moieties to DNA has been achieved by using a variety of methodologies including the modification of nucleobases, [4][5][6][7][8][9] ribofuranose residues, [10][11][12][13][14][15] the phosphate backbone [16,17] and acyclic linkers. [18,19] Porphyrin moieties have been introduced as 3'-or 5'-molecular caps, [13,[19][20][21] as a nucleobase substituent in the middle of the helix [18] or as a label in the minor [11,17,22] and major [5][6][7][8][9] grooves.…”