A Cationic Dye Triplet as a Unique “Glue” That Can Connect Fully Matched Termini of DNA Duplexes

Kashida, Hiromu; Hayashi, Tateki; Fujii, Tomoyuki; Asanuma, Hiroyuki

doi:10.1002/chem.201003059

Cited by 19 publications

(20 citation statements)

References 45 publications

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“…In this context,f ormation of the [a] T. Doi native duplex anda ggregation of the dye occur independently. [13] Study of these oligomers allowed us to evaluate the selectivity of hetero-pairing over homo-pairing.F inally,d uplexes formed by P and Q oligomers only were studied (Scheme 1c). Hetero-duplex formation was evaluated by comparing their spectroscopic behaviors with those of compounds with the designs shown in Scheme 1a and 1b.…”

Section: Resultsmentioning

confidence: 99%

Hetero‐Selective DNA‐Like Duplex Stabilized by Donor–Acceptor Interactions

Doi

Sakakibara

Kashida

et al. 2015

Chemistry A European J

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We report on the characterization of a novel hetero-selective DNA-like duplex of pyrene and anthraquinone pseudo base pairs. The pyrene/anthraquinone pairs showed excellent selectivity in hetero-recognition and even trimers were found to form a hetero-duplex. Pyrene and anthraquinone moieties were tethered on acyclic D-threoninol linkers and linked to adjacent residues by using standard phosphoramidite chemistry. When pyrene and anthraquinone were incorporated at pairing positions in complementary strands of natural DNA oligonucleotides, the duplex was stabilized significantly. Moreover, a pyrene hexamer and an anthraquinone hexamer formed a stable artificial hetero-duplex without the assistance of natural base pairs. The pyrene/anthraquinone pair was so stable that even trimers formed a hetero-duplex under conditions in which natural DNA strands of three residues do not.

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Section: Resultsmentioning

confidence: 99%

Hetero‐Selective DNA‐Like Duplex Stabilized by Donor–Acceptor Interactions

Doi

Sakakibara

Kashida

et al. 2015

Chemistry A European J

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“…58 The intermolecular associations are also observed with small aromatic molecules, and might be a more general feature in modified DNA; this can be explored as molecular glue to add another level of interactions. 59,60 …”

Section: Covalent Attachment Of Porphyrins To Dnamentioning

confidence: 99%

Nanoarchitectonics with Porphyrin Functionalized DNA

Stulz

2017

Acc. Chem. Res.

106

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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.

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“…28 When three Z residues were introduced at the 5¤ end of a DNA duplex, a dimer of duplexes is formed through Z-Z pairing. Interestingly, singlestranded DNA could not be connected by Z residues, indicating the Z-Z pairing at DNA termini was strongly stabilized by the stacking interaction with the adjacent natural base pairs.…”

Section: Cationic and Photocrosslinking Pairsmentioning

confidence: 99%

Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions

Kashida

Asanuma

2016

Bulletin of the Chemical Society of Japan

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. Currently his research interests are focused on the development of functional artificial oligonucleotides with acyclic scaffolds, such as, 1) photoregulation of DNA and RNA functions, 2) design of new XNAs, 3) new fluorescent probes for practical applications, 4) design of nucleic acid-based drugs, and 5) assembled functional molecules. AbstractThe authors have developed various kinds of pseudo base pairs using a D-threoninol scaffold. Although the chemical structures of the pseudo base pairs are much different from natural nucleobases, they can mimic supramolecular properties of natural base pairs. Moreover, modified DNA can possess various functions that cannot be achieved by natural nucleic acids, such as fluorescent switchability, photocrosslinking, insulating and emission color change. These pseudo base pairs can be used to prepare various functional nanomaterials. In the present account, we summarize our recent work on pseudo base pairs, focusing on molecular designs and functions.

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A Cationic Dye Triplet as a Unique “Glue” That Can Connect Fully Matched Termini of DNA Duplexes

Cited by 19 publications

References 45 publications

Hetero‐Selective DNA‐Like Duplex Stabilized by Donor–Acceptor Interactions

Hetero‐Selective DNA‐Like Duplex Stabilized by Donor–Acceptor Interactions

Nanoarchitectonics with Porphyrin Functionalized DNA

Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions

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