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.

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).

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...

The spccific conductivity of high-purity water has been measured at temperatures between 51 and 271°C along the saturated vapour pressure curve. Correction has been made for traces of contamination. The frequency dispersion of the impedance of the water-filled cell has been analyzed in terms of an equivalent electrical circuit. The data have been used to calculate the ionic product constant of water over this temperature range.Accurate values of the dissociation constant K, for water are required when setting up thermodynamic diagrams, and pH scales, and for kinetic studies involving hydrogen or hydroxyl ions. Clever ' and Holzapfel have reviewed the experimental determinations of K,. The measurements of Harned and Robinson provide the generally accepted values of K, from 0 to 60°C. At higher temperatures, up to 306"C, K, has been determined, along the saturated vapour pressure curve, by Noyes, et aZ.,4 A~kerrnann,~ Dobson and Thirsk and Mesmer, Baes and Sweeton.' In the single-phase water region, David and Harnann 8 9 and Hamann and Linton l o * l 1 determined IC, at pressures up to 13.3 GN m-2 (133 kbar), and temperatures up to 804"C, while Holzapfel and Franck measured the dissociation of supercritical water at 500,750 and 1000°C. Quist has reported extensive measurements between 300 and 800°C (at pressures up to 4000 bar).There is considerable technological interest in the intermediate temperature range 60 to 370"C, which requires that relevant values of K, are established. This paper presents values of K,, along the saturated vapour pressure curve, in the range 51-271"C, which were obtained from the experimental measurement of the specific conductivity of pure water. were derived from e m f . measurements using cells of the form : H2, Pt/HCI/AgCI, Ag ; H2, Pt/NaOH, NaCI/AgCl, Ag. The extension of this method to high temperatures is an attractive possibility in view of the work in acid solutions by Lietzke and Stoughton l4 ; it has been used with some success (Dobson and Perkovets and Kryukov '9. It is, however, prone to difficulties associated with the establishment of the Ag/Ag,O equilibrium in mixed hydroxide/chloride systems (Case and Bignold 16) and the tendency for hydrogen to be oxidized on the silver surface at higher temperatures.The higher temperature values of Noyes et aL4 were derived from the conductimetric determination of the hydrolysis and dissociation constants of ammonium acetate, ammonium hydroxide and acetic acid. These values are subject to correction in the light of modern theories of ionic solutions (Fisher 17) but the method is clearly capable of producing reliable data.The determination of K,, at low temperatures, by the direct measurement of the specific conductivity ofpure water (Kohlrausch and Heydweiller l'), is subject to errors