Strukturempfindlicher und selbstassoziierter helicaler Pyrenstapel auf Basis der DNA‐Architektur

Mayer-Enthart, Elke; Wagenknecht, Hans‐Achim

doi:10.1002/ange.200504210

Cited by 37 publications

(26 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In these studies, DNA or RNA were used as structural scaffolds for the helical arrangement of pyrenes. In contrast to these intrastrand helical stacks along a DNA or RNA backbone, [24,25] the present system describes the self-organization of two non-nucleosidic oligopyrene strands in an interstrand helical stack. An Amber-mimized model [26] (Figure 4) shows an overall right-handed helical arrangement of the twisted pyrene rings, which is in agreement with the experimental observations.…”

Section: Methodsmentioning

confidence: 96%

“…Comparison of these data, together with the already described values obtained at 260 nm, showed excellent agreement (Table 2), thus suggesting a high degree of cooperativity among the different sections of the hybrid. [23] The arrangement of pyrene molecules covalently linked to the sugar backbone in RNA [24] and to base residues in DNA [25] was published recently. In these studies, DNA or RNA were used as structural scaffolds for the helical arrangement of pyrenes.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

2007

View full text Add to dashboard Cite

Section: Methodsmentioning

confidence: 96%

Section: Methodsmentioning

confidence: 99%

Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

2007

View full text Add to dashboard Cite

“…[15] It has also been reported that the shift of the excimer emission band can be used as a signal to detect hybridization, as the excimer fluorescence could redshift or blue-shift upon hybridization by the interstrandstacked pyrenes. [16] Although both monomer and excimer emission of pyrene-labeled probes has been investigated in detail, the often complex response depends on the structure of the probe.…”

Section: Introductionmentioning

confidence: 99%

“…This means that for some DNA duplexes the fluorescence quenched by the flanking C/G base pair differs little from that of a single stranded probe. [12][13] To overcome this disadvantage, pyrene excimer emission instead of monomer emission has been explored for monitoring RNA and DNA hybridization, [14][15][16][17][18][19][20][21] as pyrene-excimer emission is less sensitive to quenching by nucleobases than monomer emission.…”

Section: Introductionmentioning

confidence: 99%

Detection of RNA Hybridization by Pyrene‐Labeled Probes

et al. 2009

View full text Add to dashboard Cite

Powerful pyrene probes: Two kinds of pyrene-labeled oligonucleotides (HNA- and RNA-skeleton probes) were explored. The enhanced fluorescence intensity in the monomer region and the disappearance of aggregate/excimer emission in duplexes has been successfully used to detect the hybridization of oligonucleotides. By covalently attaching pyrene chromophores with different linkers onto altritol nucleotides or ribonucleotides, and by varying the number of these pyrene modified altritol nucleotides and ribonucleotides in HNA (hexitol nucleic acid) and RNA, respectively, we have explored the general applicability of pyrene absorbance and especially fluorescence as a probe to monitor RNA hybridization. The results reveal that the backbone of the probes, the number of pyrene units attached and the nature of the tether can all substantially affect the absorbance and fluorescence properties of the probes both in single strand and double strand form. Moreover, the strength of hybridization is also affected. The disappearance of pyrene aggregate/excimer emission and simultaneous increase in monomer emission intensity of the multipyrene-labeled probes has been successfully used to monitor the hybridization of oligonucleotides, including a hairpin structure. Differences in optical response between the HNA- and RNA-skeleton probes upon hybridization indicate that the interaction of pyrene with the nucleobases in both types of duplexes is different.

show abstract

“…pyrene pseudonuleotides have been utilized as sensitive hybridization probes. [6] Studies of charge transfer in DNA have made use of pyrene-modified nucleosides.…”

Section: Introductionmentioning

confidence: 99%

Quenching of Fluorescent Nucleobases by Neighboring DNA: The “Insulator” Concept

et al. 2008

View full text Add to dashboard Cite

Fluorescent nucleosides are widely used as probes of biomolecular structure and mechanism in the context of DNA, but they often exhibit low quantum yields because of quenching by neighboring DNA bases. Here we characterize the quenching by DNA of fluorescent nucleosides that have pyrene (Y), perylene (E), benzopyrene (B), or 2-aminopurine (2AP) as nucleobase replacements, and we investigate the effect of inserting varied nucleosides as potential "insulators" between the fluorescent nucleosides and other nearby DNA bases as a strategy for increasing quantum yields. The data show that the hydrocarbons are quenched by adjacent pyrimidines, with thymine being the strongest quencher. The quantum yield of pyrene is quenched 120-fold by a single adjacent T, that of benzopyrene tenfold, and that of perylene by a factor of 2.5. Quenching of excimer and exciplex dinucleoside labels (Y-Y, Y-E, E-E, etc.) was considerably lessened, but was strongest with neighboring thymine. 2-Aminopurine (2AP) is most strongly quenched (15-fold) by neighboring G. We tested four different insulator candidates for reducing this quenching by measuring the fluorescence of short oligonucleotides containing insulators placed between a fluorescent base and a quenching base. The insulators tested were a C(3) abasic spacer (S), dihydrothymidine nucleoside (DHT), terphenyl nucleoside (TP), and adenine deoxynucleoside (dA). Results showed that the abasic spacer had little effect on quenching, while the other three had substantial effects. DHT and terphenyl enhanced fluorescence of the fluorophores by factors of 5 to 70. Adenine base reduced the quenching of pyrene 40-fold. The results underscore the importance of the nearest neighbors in DNA-quenching mechanisms, and establish simple strategies for enhancing fluorescence in labeled DNAs.

show abstract

Strukturempfindlicher und selbstassoziierter helicaler Pyrenstapel auf Basis der DNA‐Architektur

Abstract: Der helicale π‐Stapel aus fünf pyrenmodifizierten Uridineinheiten zeigt eine ausgeprägte Fluoreszenzverstärkung, die empfindlich auf Basenfehlpaarungen reagiert. Die Fluoreszenz ist deutlich sequenzabhängig, weshalb der Stapel als strukturempfindliche Sonde für DNA fungieren kann.

Cited by 37 publications

References 38 publications

Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

Detection of RNA Hybridization by Pyrene‐Labeled Probes

Quenching of Fluorescent Nucleobases by Neighboring DNA: The “Insulator” Concept

Contact Info

Product

Resources

About