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Review
. 2017 Apr 18;50(4):823-831.
doi: 10.1021/acs.accounts.6b00583. Epub 2017 Mar 8.

Nanoarchitectonics With Porphyrin Functionalized DNA

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Free PMC article
Review

Nanoarchitectonics With Porphyrin Functionalized DNA

Eugen Stulz. Acc Chem Res. .
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Abstract

DNA 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.

Conflict of interest statement

The author declares no competing financial interest.

Figures

Figure 1
Figure 1
(a) Depiction of the DNA double helix (B-form), which is most commonly found in nature, with example of a complementary sequence for selective duplex formation via Watson–Crick base pairing of A=T and G≡C. (b) DNA as rigid stick and flexible glue molecule for the construction of DNA nanoarchitectures. (c) Concept of programmed self-assembly of DNA nanostructures: complementary ssDNA sequences (orange and red, light and dark blue) will hybridize to form predefined rigid constructs.
Figure 2
Figure 2
(a) First examples of end-of-DNA modification with porphyrinoids to create artificial sequence specific nucleases., (b) Structure (left) and schematic (middle) of porphyrins acting as caps (red and blue bars) for the blunt end of DNA; modeled DNA structure and induced Soret-band CD spectra of the porphyrins (right), showing DNA structure dependent exciton coupling. Reproduced from ref (28) with permission from the Royal Society of Chemistry.
Figure 3
Figure 3
(a) Structures of base replacement and nucleoside surrogates, for porphyrins embedded within the base stacking region of DNA. (b) DNA interior porphyrin stack creating stable H-aggregates through interlocked formation of the assembly from complementary porphyrin modified DNA strands. Reprinted with permission from ref (39). Copyright 2014 American Chemical Society.
Figure 4
Figure 4
(a) Attachment of the porphyrin to the 2′-position of the ribose through tethers (left) or direct amidation (right) will position the substituents in the minor groove of the DNA. (b) Conjugation to the phosphate backbone leads to external placement, and face-to-face stacked dimers can lead to a stabilizing effect in the duplex, which is dependent on the central metal and its potential additional axial ligands. Reprinted with permission from ref (42). Copyright 2008 American Chemical Society.
Figure 5
Figure 5
(a) Postsynthetic modification of DNA with porphyrins through click chemistry or Diels–Alder reaction; the flexibility of the linker allows the porphyrin to intercalate into the DNA. (b) Attachment of the porphyrins through the β-pyrrolic position reduces steric hindrances, leading to stable H-aggregates of the porphyrins in the minor groove. Reprinted by permission of John Wiley & Sons, Inc. from ref (44).
Figure 6
Figure 6
(a) First generation of porphyrin arrays with putative structure of the dsDNA array and induced helical stack in the ssDNA. Reprinted with permission from ref (49). Copyright 2007 American Chemical Society. (b) Second generation zipper-porphyrin array, where the porphyrins are attached to both complementary DNA strands; different metalation leads to a photonic wire showing efficient energy transfer from ZnTPP to 2HTPP.,, Reproduced from ref (46) with permission from the Royal Society of Chemistry.
Figure 7
Figure 7
(a) Schematic of an electrochemical genosensor based on cobalt porphyrin with an efficient “signal-off” detection of the target sequence in the femtomolar range. (b) DNA bundle consisting of six DNA helices with two porphyrins as lipophilic anchors to create artificial nanopores with a 2 nm inner pore diameter, Reprinted by permission of John Wiley & Sons, Inc. from ref (63). (c) A minimal porphyrin–DNA pore where the current is induced through a flow of ions along the DNA backbone (left). This is compared to a two-porphyrin-DNA with longer linkers and elongated distance between the porphyrin attachment sites (right), embedding the porphyrins in the membrane while keeping the underlying DNA scaffold in the aqueous environment. Reproduced from ref (66) with permission from the Royal Society of Chemistry.

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References

    1. Wilkins M. H. F.; Stokes A. R.; Wilson H. R. Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids. Nature 1953, 171, 738–740. 10.1038/171738a0. - DOI - PubMed
    1. Watson J. D.; Crick F. H. C. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature 1953, 171, 737–738. 10.1038/171737a0. - DOI - PubMed
    1. Franklin R. E.; Gosling R. G. Molecular Configuration in Sodium Thymonucleate. Nature 1953, 171, 740–741. 10.1038/171740a0. - DOI - PubMed
    1. Stulz E. DNA Architectonics: towards the Next Generation of Bio-inspired Materials. Chem. - Eur. J. 2012, 18, 4456–4469. 10.1002/chem.201102908. - DOI - PubMed
    1. Bandy T. J.; Brewer A.; Burns J. R.; Marth G.; Nguyen T.; Stulz E. DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology. Chem. Soc. Rev. 2011, 40, 138–148. 10.1039/B820255A. - DOI - PubMed

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