Erratum to: “Conjugates of oligonucleotides with polyaromatic fluorophores as promising DNA probes”

Balakin, Konstantin V.; Korshun, Vladimir A.; Михалев, И И; Maleev, G V; Malakhov, Andrei D.; Prokhorenko, Igor A.; Berlin, Yu. A.

doi:10.1016/s0956-5663(99)00033-0

Cited by 9 publications

(11 citation statements)

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“…1,2 To date, a variety optical, [3][4][5][6] electronic, 7 acoustic, 8 and gravimetric 9,10 techniques have been applied to this goal. Among these, the electrochemical detection of DNA hybridization appears promising due to its rapid response time, low cost, and suitability for mass production.…”

Section: Introductionmentioning

confidence: 99%

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

et al. 2007

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E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stemloop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons.

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Section: Introductionmentioning

confidence: 99%

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

et al. 2007

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“…The most common PAH in this area is pyrene (Chart ). A long lifetime of the excited state , high fluorescence quantum yield , and the possibility to form noncovalent interactions with another PAH molecule − or nucleic acids (for example, by intercalation − ) have inspired researchers to use pyrene for the design of many different detection systems. Thus, fluorescence of a single pyrene label linked to oligonucleotides was shown to be sensitive to duplex formation ,,− .…”

Section: Introductionmentioning

confidence: 99%

Perylene Attached to 2′-Amino-LNA: Synthesis, Incorporation into Oligonucleotides, and Remarkable Fluorescence Properties in Vitro and in Cell Culture

et al. 2008

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During recent years, fluorescently labeled oligonucleotides have been extensively investigated within diagnostic approaches. Among a large variety of available fluorochromes, the polyaromatic hydrocarbon perylene is an object of increasing interest due to its high fluorescence quantum yield, long-wave emission compared to widely used pyrene, and photostability. These properties make perylene an attractive label for fluorescence-based detection in vitro and in vivo. Herein, the synthesis of 2'- N-(perylen-3-yl)carbonyl-2'-amino-LNA monomer X and its incorporation into oligonucleotides is described. Modification X induces high thermal stability of DNA:DNA and DNA:RNA duplexes, high Watson-Crick mismatch selectivity, red-shifted fluorescence emission compared to pyrene, and high fluorescence quantum yields. The thermal denaturation temperatures of duplexes involving two modified strands are remarkably higher than those for double-stranded DNAs containing modification X in only one strand, suggesting interstrand communication between perylene moieties in the studied 'zipper' motifs. Fluorescence of single-stranded oligonucleotides having three monomers X is quenched compared to modified monomer (quantum yields Phi F = 0.03-0.04 and 0.67, respectively). However, hybridization to DNA/RNA complements leads to Phi F increase of up to 0.20-0.25. We explain it by orientation of the fluorochrome attached to the 2'-position of 2'-amino-LNA in the minor groove of the nucleic acid duplexes, thus protecting perylene fluorescence from quenching with nucleobases or from the environment. At the same time, the presence of a single mismatch in DNA or RNA targets results in up to 8-fold decreased fluorescence intensity of the duplex. Thus, distortion of the duplex geometry caused by even one mismatched nucleotide induces remarkable quenching of fluorescence. Additionally, a perylene-LNA probe is successfully applied for detection of mRNA in vivo providing excitation wavelength, which completely eliminates cell autofluorescence.

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“…A pyrene fluorophore attached to the 2′‐position of uracil nucleosides in DNA5i,5j,5m or 2′‐ O ‐Me RNA5k oligomers shows a considerable increase in fluorescence intensity upon binding with complementary RNA. To the best of our knowledge, excimer emission from two pyrene fluorophores bound to different complementary strands within an internal part of a DNA duplex has previously only been observed with pyrene pseudonucleosides6g or by modification with (+)‐ anti ‐benzo[ a ]pyrene diol epoxide of two guanine residues in N 2 positions within a (5′)‐CG sequence 8. In the latter case, a pyrene excimer is formed in the minor groove of the DNA double helix 8…”

Section: Introductionmentioning

confidence: 97%

Pyrenemethyl ara‐Uridine‐2′‐carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex

et al. 2003

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The synthesis of new nucleoside derivatives, ara-uridine-2'-carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA-DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a "reversed" absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence-dependent excimer formation in the major groove.

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Erratum to: “Conjugates of oligonucleotides with polyaromatic fluorophores as promising DNA probes”

Cited by 9 publications

References 0 publications

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

Perylene Attached to 2′-Amino-LNA: Synthesis, Incorporation into Oligonucleotides, and Remarkable Fluorescence Properties in Vitro and in Cell Culture

Pyrenemethyl ara‐Uridine‐2′‐carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex

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