Porphyrin–DNA conjugates: porphyrin induced adenine–guanine homoduplex stabilization and interduplex assemblies

Abstract

DNA has found widespread uses as a nanosized scaffold for assembly of patterned multichomophoric nanostructures. Herein we report the synthesis, self-assembly, stability, and spectroscopic studies of short alternating non-self-complementary DNA sequences 5'-(dGdA)(4) and 5'-(dAdG)(4) with non-charged tetraarylporphyrins covalently linked to the 5' position of deoxyadenosine or deoxyguanosine via a phosphate or amide linker. The linker, the metal in the porphyrin coordination center, and the neighboring nucleobase have very distinct effects on the duplex formation of porphyrin-deoxyguanosine-deoxyadenosine oligodeoxynucleotides. At ionic strength between 5 mM and 40 mM, free base trispyridylphenylporphyrin appended to the 5' termini of 5'-(dAdG)(4) oligonucleotide via short non-polar amide linker served as a hydrophobic molecular cap inducing deoxyadenosine-deoxyguanosine antiparallel homoduplex. At ionic strength of ≥60 mM, the free base porphyrin functioned as a molecular 'glue' and induced the formation of porphyrin-DNA inter-homoduplex assemblies with characteristic tetrasignate CD Cotton effects in the porphyrin Soret band region. When the porphyrin cap was covalently attached to 5' position of deoxyguanosine or deoxyadenosine via charged phosphate linker, no significant deoxyadenosine-deoxyguanosine hybridization was observed even at elevated ionic strengths.

Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease

“…End-to-end stacking of alkynyl substituted PAHs is observed in crystal lattices and seems to play a major role in cases where interhelical stacking is possible. Such oligo- or polymerization has been observed previously for phosphodiester-linked oligomers, not only for pyrene (71) or phenanthrene (62), but also for DNA containing other chromophores, such as perylenediimide (72) or porphyrins (73). In all the three structures described here, the non-natural building blocks are involved in head-to-head or head-to-tail contacts between the protein–DNA complexes in the crystal lattice.…”

Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling

“…Similar multiple CD bands due to porphyrin–porphyrin stacking in inter-duplex aggregates have been described by Berova et al 53 The phenomenon of intermolecular interactions can also be seen with pyrenes, 71 , 72 perylenes 73 , 74 or other porphyrin constructs. 35 , 75 …”

Transition metal induced switch of fluorescence and absorption response of a Zn(ii)porphyrin–DNA conjugate to cysteine derivatives

“…53,54 The uorescence and absorption titration experiments were performed as follows: aliquots of amino acids (0.8 mL, concentration of the stock solutions ¼ 1 mM) were added into a 800 mL solution of the The concentration of ZnPorT8 stock solution was determined by UV-vis absorption spectroscopy using the extinction coefficient 3 ZnPorT8 ¼ 2.9 Â 10 5 M À1 cm À1 at 425 nm.…”