Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

Zip it up: Attachment of porphyrins onto complementary DNA strands leads to zipper-porphyrin arrays and, in the presence of eleven modifications, an increase in the melting temperature of the duplex. Mixed zinc and free-base porphyrin arrays undergo energy transfer from the zinc porphyrin to the free-base porphyrin in the annealed duplex but not in the denatured form (see scheme), giving access to reversible formation of potential photonic wires.

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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...

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