Abstract
ConspectusDNA is well-known as bearer of the genetic code. Since its structure elucidation nearly seven decades ago by Watson, Crick, Wilkins, and Franklin, much has been learned about its detailed structure, function, and genetic coding. The development of automated solid-phase synthesis, and with it the availability of synthetic DNA with any desired sequence in lengths of up to hundreds of bases in the best case, has contributed much to the advancement of the field of DNA research. In addition, classic organic synthesis has allowed introduction of a very large number of modifications in the DNA in a sequence specific manner, which have initially been targeted at altering the biological function of DNA. However, in recent years DNA has become a very attractive scaffold in supramolecular chemistry, where DNA is taken out of its biological role and serves as both stick and glue molecule to assemble novel functional structures with nanometer precision. The attachment of functionalities to DNA has led to the creation of supramolecular systems with applications in light harvesting, energy and electron transfer, sensing, and catalysis. Functional DNA is clearly having a significant impact in the field of bioinspired nanosystems.Of particular interest is the use of porphyrins in supramolecular chemistry and bionanotechnology, because they are excellent functional groups due to their electronic properties that can be tailored through chemical modifications of the aromatic core or through insertion of almost any metal of the periodic table into the central cavity. The porphyrins can be attached either to the nucleobase, to the phosphate group, or to the ribose moiety. Additionally, noncovalent templating through Watson–Crick base pairing forms an alternative and attractive approach. With this, the combination of two seemingly simple molecules gives rise to a highly complex system with unprecedented possibilities for modulation of function, and with it applications, particularly when combined with other functional groups. Here, an overview is given on the developments of using porphyrin modified DNA for the construction of functional assemblies. Strategies for the synthesis and characterization are presented alongside selected applications where the porphyrin modification has proven to be particularly useful and superior to other modifiers but also has revealed its limitations. We also discuss implications on properties and behavior of the porphyrin–DNA, where similar issues could arise when using other hydrophobic and bulky substituents on DNA. This includes particularly problems regarding synthesis of the building blocks, DNA synthesis, yields, solubility, and intermolecular interactions.
Highlights
The construction of nanosized functional molecules by means of a bottom-up approach is best addressed using the concepts of supramolecular chemistry, which is defined as chemistry beyond the molecule
We found that the use of Sonogashira coupling between 5-iodo-deoxyuridine (5-iodo-dU) and alkyne porphyrins is most versatile to synthesize building blocks for programmed insertion into DNA: the porphyrin is attached to the nucleobase and will protrude from the DNA into the major groove, leaving the Watson−Crick base recognition untouched.[45]
We found through spectroscopic studies that there are substantial intermolecular interactions through π-stacking of porphyrins, both in ssDNA and dsDNA,[46,53,54] similar to what has been reported by other groups.[34,35]
Summary
The construction of nanosized functional molecules by means of a bottom-up approach is best addressed using the concepts of supramolecular chemistry, which is defined as chemistry beyond the molecule. Biology provides us with ideas and templates that are ideal to draw upon In this respect, DNA has shown to be an exciting construction material, owing to its distinct properties such as predictable three-dimensional structure in form of the double helix, its programmable nature, and synthetic availability. The use of covalent chemistry in the formation of porphyrin assemblies has the advantage of taking control over sequence using the very same chemistries that are applied to the synthesis of the DNA and starting from the same building blocks. Noncovalent approaches where modified porphyrin units self-assemble on a ssDNA template through hydrogen bonding provide an alternative route,[23,24] but this Account will focus on the formation, analysis, and application of covalently modified DNA strands
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