Duplex Stabilization and Energy Transfer in Zipper Porphyrin–DNA

Abstract

The use of functionalized DNA in the construction of new materials for potential nanotechnological applications is becoming more and more widespread. [1] In particular, the site-specific incorporation of fluorophores or metal complexes into DNA has led to the creation of supramolecular arrays with promising properties in optoelectronics. Both the interior [2] and exterior [3] of the DNA or RNA duplex are being used for attachment of modifications, and DNA proves to be a versatile supramolecular scaffold to create helical arrays of functional entities. 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. The design of longer zipper arrays based on an RNA or DNA scaffold, which have been reported by the groups of Wengel, [13] Leumann, [14] Häner, [15] and Wagenknecht, [16] is also very intriguing. Herein, we report that mixed porphyrin arrays can be created through a zipper-like arrangement by modifying both complementary strands, which can lead to a stabilization of the DNA duplex and resonance energy transfer between the chromophores after hybridization.The two porphyrin-modified deoxyuridines, in which a diphenylporphyrin (dU 2HDPP , 1) or a tetraphenylporphyrin (dU 2HTPP , 2) are attached to the 5-position of the nucleobase, can be incorporated into DNA using standard solid-phase synthesis (Scheme 1). The destabilization of the DNA duplex in the one-strand-modified DNA is highly dependent on the nature, the number and the sequence of the porphyrin modification. In all cases we found a leveling of the destabilization effect at higher numbers (> 4 modifications) of porphyrin groups in the DNA. TPP destabilized the DNA duplex by about À3 8C per porphyrin, and DPP by about À7 8C per porphyrin.To test whether attachment of the porphyrins on complementary strands would alter the duplex stability, we synthesized the palindromic sequence 3 b, incorporating two modified groups 1 in the center, which will form a four-porphyrin array upon hybridization. The melting temperature of the unmodified self-complementary strand 3 a·3 a is T m = 72 8C, whereas for the porphyrin-substituted strand 3 b·3 b it is T m = 61 8C (Table 1). The DT m of À10.4 8C corresponds to a destabilization per porphyrin of only DT m,P = À2.6 8C. The interlocking stacking of the porphyrins thus has a substantial effect on the stability of the duplex. The melting profile showed a rather large hysteresis with...

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

“…[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.…”

“…To the best of our knowledge this is the first report showing such a significant thermal duplex stabilization as a result of interaction between porphyrin moieties in comparison with previously studied DNA-porphyrin constructs, in which porphyrins were linked to DNA through the substitution at one of the meso phenyl rings. [6][7][8]16] The adverse interactions between these phenyl rings led to notably slower duplex association and significantly lower thermal stabilities. [6][7][8]16] On the basis of molecular modelling and CD spectroscopy studies, we proposed that porphyrins might not necessarily follow the sequence of nucleotides in duplexes due to the flexible tether.…”

“…[6][7][8]16] The adverse interactions between these phenyl rings led to notably slower duplex association and significantly lower thermal stabilities. [6][7][8]16] On the basis of molecular modelling and CD spectroscopy studies, we proposed that porphyrins might not necessarily follow the sequence of nucleotides in duplexes due to the flexible tether. However, duplex 13, in which porphyrins actually followed the sequence of nucleotides, should be considered as a model for the DNA-based chromophoric assemblies possessing flexible linkers.…”

“…[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. Finally, an effective energy transfer between a zinc porphyrin and a free-base porphyrin in the major groove of the DNA duplex was observed.…”

“…Finally, an effective energy transfer between a zinc porphyrin and a free-base porphyrin in the major groove of the DNA duplex was observed. [7] Due to their chemical nature, the stability of porphyrin phosphoramidites as DNA building blocks is usually limited [10,11] and depends on the structure of the molecule. H-phosphonate porphyrin analogues were also employed in DNA synthesis; [10,19] however, coupling yields are usually not satisfactory for their multiple incorporation.…”