2′-Bis-Pyrene Modified Oligonucleotides: Sensitive Fluorescent Probes of Nucleic Acids Structure

Новопашина, Д. С.; Stetsenko, Dmitry A.; Totskaya, O. S.; Репкова, М. Н.; Venyaminova, Alya G.

doi:10.1081/ncn-200060038

Cited by 8 publications

(5 citation statements)

References 6 publications

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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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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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“…It has been applied for the detection of point mutations using tandem hybridization of 5′- and 3′-pyrene-labeled oligonucleotides on complementary targets – . Various excimer-forming pyrene bichromophores were used to monitor hybridization – . Two or more pyrene residues attached to one ,– or several different oligonucleotides ,– were used in studies of NA hybridization, including parallel duplexes , , triplexes ,,,, , and quadruplexes .…”

Section: Introductionmentioning

confidence: 99%

“…It has been applied for the detection of point mutations using tandem hybridization of 5′-and 3′-pyrene-labeled oligonucleotides on complementary targets (4)(5)(6)(7)(8)(9). Various excimerforming pyrene bichromophores were used to monitor hybridization (10)(11)(12)(13)(14)(15)(16)(17). Two or more pyrene residues attached to one (8,(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31) or several different oligonucleotides (18,(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43) were used in studies of NA hybridization, including parallel duplexes (32,34), triplexes (30,33,40,41,…”

Section: Introductionmentioning

confidence: 99%

1-Phenylethynylpyrene (1-PEPy) as Refined Excimer Forming Alternative to Pyrene: Case of DNA Major Groove Excimer

et al. 2007

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1-Phenylethynylpyrene fluorochrome was studied as meta- and para-derivatives of arabino-uridine-2'-carbamates in ss and dsDNA. 1-PEPy showed red-shifted emission and increased fluorescence quantum yield compared to pyrene. Although 1-PEPy has very short excited lifetime (<2.5 ns), it is able to form inter- and intrastrand excimers on DNA, probably resulting from spatial preorganization of two dye molecules.

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“…Recently, we have published a preliminary communication on the preparation of the 2 -phosphorylated oligodeoxyribonucleotides and their conjugates. [3] Here we would like to 822 D. S. Novopashina et al report on the further refinement of this method and its extension to oligo(2 -O-methylribonucleotides).…”

Section: Introductionmentioning

confidence: 99%

Novel Method for the Synthesis of 2′ -Phosphorylated Oligonucleotides

Новопашина

Totskaya

Meschaninova

et al. 2007

Nucleosides, Nucleotides and Nucleic Acids

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We have developed a new method for the preparation of oligodeoxyribonucleotides and oligo(2'-O-methylribonucleotides) that contain a 2'-phosphorylated ribonucleoside residue, and optimized it to avoid 2' -3' -isomerization and chain cleavage. Structures of the 2' -phosphorylated oligonucleotides were confirmed by MALDI-TOF MS and enzymatic digestion, and the stability of their duplexes with DNA and RNA was investigated. 2'-Phosphorylated oligonucleotides may be useful intermediates for the introduction of various chemical groups for a wide range of applications.

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2′-Bis-Pyrene Modified Oligonucleotides: Sensitive Fluorescent Probes of Nucleic Acids Structure

Cited by 8 publications

References 6 publications

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

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

1-Phenylethynylpyrene (1-PEPy) as Refined Excimer Forming Alternative to Pyrene: Case of DNA Major Groove Excimer

Novel Method for the Synthesis of 2′ -Phosphorylated Oligonucleotides

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