Circular Dichroism of Neutral Zinc Porphyrin–Oligonucleotide Conjugates Modified with Flexible Linker

Abstract

Neutral zinc porphyrin containing flexible alkyl linker, 5-[4-(5-hydroxypentyloxy)phenyl]-10,15,20-tri-p-tolylporphyrinatozinc, was attached to the 5′ ends of 20- and 30-bp oligodeoxynucleotides (ODN) by solid-phase synthesis. Zinc porphyrin-modified double-stranded DNA (dsDNAs), which included dsDNAs with porphyrin moieties on one end and on both ends (ZnPor–ds20, ds20–ZnPor, ZnPor–ds20–ZnPor, ZnPor–ds30, ds30–ZnPor, and ZnPor–ds30–ZnPor), were successfully prepared and were analyzed by variable-temperature UV–vis spectroscopy and CD measurements to elucidate the interaction behavior of the porphyrin ring. Detailed investigation revealed that the zinc porphyrin–DNA conjugates exhibited intra-duplex porphyrin–ODN interaction in a low-salt condition and inter-duplex porphyrin–porphyrin interaction in a high-salt condition.

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

“…Introduction of a third porphyrin moiety into the duplex did not result in further increase of the thermal stability (Table 1, duplexes [17][18][19][20][21][22]. It was observed that T m values in the porphyrin region for duplexes 17 and 18 (73.0 and 73.2 8C, respectively) were higher than that for duplex 20 (68.5 8C), in which flipping of porphyrin substituents is unlikely to occur (see the discussion above for duplex 13).…”

“…[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.…”

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

“…In the case of ON14 and ON15, in which the porphyrin is incorporated as a bulged insertion into the triplex strands, the porphyrin may either penetrate through the DNA duplex (Figure 3 C) or intercalate between bases in the duplex such that the meso-phenyl rings are located in the grooves of the triplex (Figure 3 D). These two orientations are possible as a result of the long linker between the porphyrin and the phosphate backbone (19 ). Intercalation, similar to that shown in twisted intercalating nucleic acids (TINA) configurations, [44] was found to be of higher energy (À20 034 kJ mol This difference in energy is most likely a result of the destabilising bulge in the phosphate backbone of the TFO strand, which is required for porphyrin intercalation between the bases of the duplex strands.…”

“…Recently, intermolecular, end-to-end porphyrinporphyrin stacking between DNA duplexes and, consequently, distinctive multi-signate CD signals in the porphyrin Soret band region were observed for duplexes possessing a porphyrin at the 5'-end at high ionic strength (150 mm NaCl for copper-porphyrin, 450 mm for zinc-porphyrin). [19,21] Clearly, porphyrin-porphyrin intermolecular interactions in the DNA structures are strongly dependent upon the ON sequence, the length, the porphyrin insertion and the ionic strength. For instance, in the course of our study of purinepyrimidine 18-mer DNA possessing modification 4 in the middle of the sequence, [22] we did not observe aggregate formation for single-stranded ONs probably due to increased electrostatic repulsion between negatively charged phosphates.…”

“…[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. Several tethers have been used for the covalent attachment of porphyrins including maleimidothiols, [8,17] amides, [11][12][13]15] phosphates [16] and alkynes.…”