Charge-Transfer and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide as a Base-Pair Surrogate

Zeidan, Tarek A.; Carmieli, Raanan; Kelley, Richard F.; Wilson, Thea M.; Lewis, Frederick D.; Wasielewski, Michael R.

doi:10.1021/ja803765r

Cited by 96 publications

(154 citation statements)

References 104 publications

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“…[10] The synthesis of 2 s, 2 o, 3, and 4 followed that of 1. [13] Conjugates were purified by HPLC and characterized by MALDI-TOF mass spectrometry and CD (see the Supporting Information). UV/Vis spectra of reduced species were measured through 1.4 mm I.D.…”

Section: Methodsmentioning

confidence: 99%

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Electron Hopping among Cofacially Stacked Perylenediimides Assembled by Using DNA Hairpins

et al. 2010

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The self-assembly of redox-active molecules into ordered arrays capable of rapid, long-distance charge transport is important for the development of functional nanomaterials for organic electronics. In this regard, DNA shows great promise as a structural scaffold for the helical arrangement of chromophores and other (semi)conducting materials. [1][2][3] Base substitutions and modifications, sugar modifications, and noncovalent interactions have all been used for the construction of such DNA-based structures. Perylenediimides (PDIs), which have the advantages of strong absorptivity, high fluorescence quantum yields, high photochemical and thermal stability, strong hydrophobic p-p stacking interactions, and semiconducting properties, have been incorporated in a variety of structures. [4][5][6][7][8][9][10][11][12][13][14][15][16] Recently, Wagner and Wagenknecht [10] reported the preparation of a PDI derivative, P (Figure 1), which is readily incorporated into an oligonucleotide and serves as a base-pair surrogate when located opposite an abasic site in a duplex structure. The incorporation of P in opposite complementary oligonucleotides has been shown to result in the formation of stable duplexes in which the P units are located in a zipperlike fashion within the hydrophobic interior of the resulting duplex. [5,17] The stacking of P units within the duplex resulted in an excimer-like state following photoexcitation. [16] We report herein the results of our investigation of intramolecular electron hopping within a series of synthetic DNA hairpins 1-4 (Figure 1). These hairpins possess compact 3'-CCA loop regions connecting poly(T)-poly(A) stems containing a single P moiety located opposite an abasic site (1), two P moieties located opposite abasic sites and attached either to the same strand (in 2 s) or to opposite strands (in 2 o), or three or four P moieties positioned adjacent to one another but on opposite strands in a zipperlike fashion (in 3 and 4). The EPR spectra of the singly reduced duplexes were consistent with electron hopping between two sites in both dimers (the hairpins containing two P moieties) and the trimer 3, and among three sites in the tetramer 4. Herein, we discuss the origin and implications of partial electron sharing.Oligonucleotides containing P were synthesized by the method of Wagner and Wagenknecht; [10] the CCA linker in hairpins 1-4 has been employed previously in the synthesis of stable minihairpins. [13,17,18] The characterization of 1-4, including mass spectrometry and circular dichroism (CD), is described in the Supporting Information.An intensity reversal was observed in the UV/Vis absorption spectra for the 0!0 and 0!1 transitions in 2-4 with respect to those of 1 (Figure 2). This result indicates that the p-stacked P chromophores are exciton-coupled. [19][20][21] Moreover, the A 0!0 /A 0!1 ratio for the vibronic bands decreased as the number of P units increased, and there was a notable difference between dimers 2 s and 2 o, presumably as a result of the conformational changes...

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Section: Methodsmentioning

confidence: 99%

“…[13,17,18] The characterization of 1-4, including mass spectrometry and circular dichroism (CD), is described in the Supporting Information.…”

mentioning

confidence: 99%

Electron Hopping among Cofacially Stacked Perylenediimides Assembled by Using DNA Hairpins

et al. 2010

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“…[6,9] More detailed studies by time-resolved methods using perylene bisimide as an internal DNA base substitution in hairpins [14] revealed that the photoexcited chromophore is able to inject electron holes into adjacent purine, but not pyrimidine bases. Electron holes that were injected primarily into adenine tracts are trapped efficiently on guanines.…”

Section: Synthesis Of the Apbi Dna Building Blockmentioning

confidence: 99%

“…[9] Additionally, two special perylene bisimide building blocks based on active esters were developed for the DNA-directed assembly of this dye in thermophilic foldamers and for single molecule measurements. [10,11] Especially, two of the mentioned perylene bisimide phosphoramidites were extensively applied to construct exceptionally stable DNA triplexes, [12,13] for electron-transfer studies, [14] for fluorescence quenching in highly sensitive molecular beacons, [15] and for forced base-flipping. [16] We showed that perylene bisimide stacks as a chiral oligochromophore inside the double helical framework.…”

Section: Introductionmentioning

confidence: 99%

Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions

Menacher

Wagenknecht

2011

Eur J Org Chem

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Perylene‐3,4:9,10‐tetracarboxylic acid bisimide represents a particularly attractive building block for DNA‐based multichromophores and nanoassemblies due to its unique combination of optical and electronic properties. Despite the broad applicability of the perylene bisimide dye for DNA‐based assemblies, significant fluorescence quenching by photoinduced charge‐transfer processes to guanines in DNA represents a major disadvantage. In order to develop a redox actively and optically tuned perylene bisimide derivative with fluorescence that does not photooxidize guanines in DNA, we chose to attach two N‐pyrrolidinyl substituents as strongly electron‐donating substituents at the 1‐ and 7‐positions of the bay area (“APBI”). The corresponding phosphoramidite 1 was synthesized and incorporated synthetically into oligonucleotides by using the automated DNA building block chemistry. The 2′‐deoxyribofuranoside of natural nucleosides was replaced by (S)‐1‐aminopropane‐2,3‐diol as an acyclic linker between the phosphodiester bridges that is tethered to one of the imide nitrogen atoms of the APBI dye. Electrochemical and optical characterization of the isolated APBI dye shows that photoinduced charge transfer with guanines is indeed very unlikely. Single APBI DNA base substitutions show an exciplex‐type emission with pH sensitivity. The interstrand APBI dimer in DNA could be regarded as a hydrophobically interacting base pair that stabilizes the thermal stability of the double strand. The APBI dimer behaves like an H aggregate, and the fluorescence is quenched quantitatively.

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“…This extremely low emission is attributable to the almost complete quenching of PDI by electron transfer from nucleobases to PDI. [17] However, when two H-H pairs were inserted between PDI and its neighboring nucleobases (H2AD/H2B), distinct emission at 550 nm was observed from PDI. As summarized in Table 1, the quantum yield (F) of H2AD/ H2B was 0.020 whereas that of D1/N was less than 0.001.…”

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confidence: 99%

Insulator Base Pairs for Lighting‐up Perylenediimide in a DNA Duplex

Kashida

Sekiguchi

Asanuma

2010

Chemistry A European J

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Quenched: Perylenediimide (PDI) is highly quenched by nucleobases, which greatly restricts its application as a fluorescent probe. Here, we propose "insulator base pairs" tethering cyclohexane ring through D-threoninol. When "insulator base pairs" were inserted between PDI and nucleobases, the quantum yield of PDI drastically increased several thousand-fold. The "insulator base pairs" reported here also have the potential to increase the quantum yields of other fluorophores.

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Charge-Transfer and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide as a Base-Pair Surrogate

Cited by 96 publications

References 104 publications

Electron Hopping among Cofacially Stacked Perylenediimides Assembled by Using DNA Hairpins

Electron Hopping among Cofacially Stacked Perylenediimides Assembled by Using DNA Hairpins

Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions

Insulator Base Pairs for Lighting‐up Perylenediimide in a DNA Duplex

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