Non‐covalent Versus Covalent Control of Self‐Assembly and Chirality of Nile Red‐modified Nucleoside and DNA

Varghese, Reji; Wagenknecht, Hans‐Achim

doi:10.1002/chem.201001136

Cited by 47 publications

(69 citation statements)

References 80 publications

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“…Thus, the Watson–Crick base pairing of the corresponding modified oligonucleotides should be maintained. Over the past few years we have synthetically attached various chromophores, such as ethynylpyrenes [44–45], BODIPY [46], ethynyl nile red [47–48] and others, to 2’-deoxyuridines for electron transfer studies and for fluorescent probes. To gain greater insight into the counterbase selectivity, we performed PEX experiments with a representative set of chromophore-modified oligonucleotides and found that the DNA-polymerase-catalyzed nucleotide incorporation opposite to attached chromophores at the 5-position of uridine follows Watson–Crick selectivity [49].…”

Section: Resultsmentioning

confidence: 99%

Diarylethene-modified nucleotides for switching optical properties in DNA

Barrois¹,

Wagenknecht²

2012

Beilstein J. Org. Chem.

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SummaryDiarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.

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Section: Resultsmentioning

confidence: 99%

Diarylethene-modified nucleotides for switching optical properties in DNA

Barrois¹,

Wagenknecht²

2012

Beilstein J. Org. Chem.

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“…For instance, the ethynyl nile red nucleoside 41 tends to aggregate in left-handed helicity, whereas DNA modified with five nucleosides of the type 41 forces the nile red chromophore to interact in a right-handed fashion. 101 …”

Section: Methodsmentioning

confidence: 97%

Organic Chemistry of DNA Functionalization; Chromophores as DNA Base Substitutes versus DNA Base/2′-Modifications

Schmucker¹,

Wagenknecht²

2012

Synlett

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Nucleic acids are suitable scaffolds for the precise arrangement of different kinds of artificial functionalities inside or along the double helix. In this account, we summarize our synthetic efforts over the last ten years to modify DNA chemically with organic chromophores, fluorescent probes, and metal-ion ligands. We used three different approaches: (i) replacement of DNA bases (substitutes/surrogates), (ii) modifications of DNA bases (mainly 2′-deoxyuridine), and (iii) sugar modifications at the 2′-position. The first two types of modifications were achieved mainly by the DNA building block approach, whereas the latter type is based on postsynthetic methodologies. The different synthetic concepts are described and the influence of representative modifications on the melting temperature is compared. IntroductionDNA plays the central biological role since it encodes the genetic information of all living organisms. Beside its biological functionality, DNA represents an increasingly important structural scaffold for the development of architectures and materials in nanosciences. Nucleic acids are suitable scaffolds for the precise arrangement of different kinds of artificial functionalities inside or along the double helix, such as chromophores, metal-ligand complexes, spin labels, and others. 1-6 The following key features make nucleic acids so attractive in this context: 7 (i) Selfassembly: Encoded by the canonical base pairing, two oligonucleotides assemble spontaneously into double helical or more complex tertiary structures. (ii) Geometry: Due to the base-to-base distance, double helical structures of the A-and B-type provide the ideal basis for photophysical interactions of functionalities inside or along the helix.(iii) Synthesis: Automated oligonucleotide chemistry makes DNA available in any desired base sequence and also in sufficient quantities. (iv) Structural and conformational modulations: Artificial backbones, such as peptide nucleic acids (PNA), 8 typically used in the antisense technology, represent tools to alter the double helical geometries. Moreover, conformation of the oligonucleotides can be modulated by, for example, locked nucleic acids (LNA 9 ) or pyrrolidinyl PNA. 10 (v) Hierarchically structured complexity: Highly complex tertiary and other folded structures can be realized purely based on DNA, such as 2D networks, 11 3D objects, 12 and DNA origami. 13The great advantage of nucleic acids from a synthetic organic chemistry point of view is that they are synthesized by building blocks. In this bottom-up approach, artificial functionalities can be introduced synthetically into nanoarchitectures by providing the corresponding artificial DNA building blocks. 14 Moreover, if building blocks are not synthetically obtainable, postsynthetic methodologies allow the modification of oligonucleotides. This is especially important for functionalities that are not compatible with the broadly applied phosphoramidite chemistry. 15,16 In the last few years, polymerase-assisted biochemical synthesis of ...

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“…Andererseits,d .h.m it zunehmender Menge an Py--dU in den Aggregatmischungen, werden die reinen Nr--dU-Stapel durch Py--dU unterbrochen, was das Absorptionsmaximum von 559 nm (typisch für Nr--dUStapel) [18] nach 622 nm (typisch für Nr--dU-Monomere) verschiebt. [7b,8] Obwohl die genaue Sequenz der beiden Nucleoside entlang des (dA) 20 -Templats nicht bestimmt werden kann, schließen diese beschriebenen Beobachtungen ausgedehnte Stapel bestehend aus auschließlich Py--dU oder auschließlich Nr--dU aus und lassen uns annehmen, dass insbesondere in den Mischungen Py--dU:Nr--dU = 16:4 bis 4:16 gut gemischte Chromphorsequenzen aufgebaut werden.…”

Section: Methodsunclassified

“…Das Nr--dU-typische CD-Signal besteht aus einem positiven Cotton-Effekt, gefolgt von einem negativen CottonEffekt und einem Nulldurchgang bei ungefähr 560 nm, was dem Absorptionsmaximum der Nr--dU-Stapel entspricht. Verglichen mit dem publizierten Spektrum eines kovalent angeknüpften und dadurch rechtsgängig helikalen Stapels von Nr--dU in DNA [18] ist die Chiralität des nicht-kovalenten Aggregats entlang von Fulleren-(dA) 20 gegensätzlich, also linksgängig.¾ hnliche CD-Effekte wurden auch für Py--dU beobachtet, hauptsächlich in Aggregaten mit hçherem Py--dU-Gehalt. Mit ansteigender Menge an Nr--dU in den Aggregaten (angefangen bei Py--dU:Nr--dU = 12:8) verändert sich das CD-Signals für Py--dU kontinuierlich vom reinen Excitonsignal zum Signal für Furchenbindung.…”

Section: Methodsunclassified