Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection

The attachment manner matters

Kira Astakhova, Andrey V. Golovin, Igor A. Prokhorenko, Alexey V. Ustinov, Irina A. Stepanova, Timofei S. Zatsepin, Vladimir A. Korshun

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

1-Phenylethynylpyrene fluorophore (1-PEPy) has long-wavelength shifted emission and higher photo stability compared to pyrene, retaining, however, pyrene's ability to form excimers. Here we report the synthesis of 2'-O-[3(and 4)-(pyren-1-ylethynyl)benzyl]-uridines and their tandem incorporation into deoxyribo- and 2'-O-Me-ribo-oligonucleotide probes. Excimer forming probes of type NN center dot center dot center dot NNXXNN center dot center dot center dot NN (X = 2'-O-[meta(or para)-(pyren-1-ylethyny1)-benzyl]uridine) containing two adjacent fluorescent nucleosides within an oligonucleotide are available in four types (meta-meta; para-meta; meta-para; para-para). Both DNA (N = deoxyribonucleotides) and 2'-O-Me-RNA (N = 2'-O-Me-ribo-nucleotides) probes were synthesized and their hybridization with complementary and singly mismatched DNA and RNA was studied. Several probes show a dramatic response of their excimer-to-monomer intensity ratio upon hybridization. Remarkably, most spectacular fluorescence changes were demonstrated for probes with para-meta and meta-para combination within 2'-O-Me-ribo-oligonucleotides. Using excimer forming probes, three natural SNP in Helicobacter pylori 23S RNA gene (A2144G, A2143G, A2143C) and the wild type gene can be distinguished. (C) 2017 Elsevier Ltd. All rights reserved.
OriginalsprogEngelsk
TidsskriftTetrahedron
Vol/bind73
Udgave nummer23
Sider (fra-til)3220-3230
ISSN0040-4020
DOI
StatusUdgivet - 8. jun. 2017

Fingeraftryk

RNA Probes
Single Nucleotide Polymorphism
RNA
DNA
Uridine
Oligonucleotide Probes
Oligonucleotides
Helicobacter pylori
Genes
Deoxyribonucleotides
Fluorescence
Fluorophores
Pyrene
Nucleosides
Nucleotides
Monomers
Wavelength

Citer dette

Astakhova, K., Golovin, A. V., Prokhorenko, I. A., Ustinov, A. V., Stepanova, I. A., Zatsepin, T. S., & Korshun, V. A. (2017). Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron, 73(23), 3220-3230. https://doi.org/10.1016/j.tet.2017.04.045
Astakhova, Kira ; Golovin, Andrey V. ; Prokhorenko, Igor A. ; Ustinov, Alexey V. ; Stepanova, Irina A. ; Zatsepin, Timofei S. ; Korshun, Vladimir A. / Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection : The attachment manner matters. I: Tetrahedron. 2017 ; Bind 73, Nr. 23. s. 3220-3230.
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title = "Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters",
abstract = "1-Phenylethynylpyrene fluorophore (1-PEPy) has long-wavelength shifted emission and higher photo stability compared to pyrene, retaining, however, pyrene's ability to form excimers. Here we report the synthesis of 2'-O-[3(and 4)-(pyren-1-ylethynyl)benzyl]-uridines and their tandem incorporation into deoxyribo- and 2'-O-Me-ribo-oligonucleotide probes. Excimer forming probes of type NN center dot center dot center dot NNXXNN center dot center dot center dot NN (X = 2'-O-[meta(or para)-(pyren-1-ylethyny1)-benzyl]uridine) containing two adjacent fluorescent nucleosides within an oligonucleotide are available in four types (meta-meta; para-meta; meta-para; para-para). Both DNA (N = deoxyribonucleotides) and 2'-O-Me-RNA (N = 2'-O-Me-ribo-nucleotides) probes were synthesized and their hybridization with complementary and singly mismatched DNA and RNA was studied. Several probes show a dramatic response of their excimer-to-monomer intensity ratio upon hybridization. Remarkably, most spectacular fluorescence changes were demonstrated for probes with para-meta and meta-para combination within 2'-O-Me-ribo-oligonucleotides. Using excimer forming probes, three natural SNP in Helicobacter pylori 23S RNA gene (A2144G, A2143G, A2143C) and the wild type gene can be distinguished. (C) 2017 Elsevier Ltd. All rights reserved.",
keywords = "Oligonucleotide, Single nucleotide polymorphism, Phenylethynylpyrene, Hybridization, Fluorescence",
author = "Kira Astakhova and Golovin, {Andrey V.} and Prokhorenko, {Igor A.} and Ustinov, {Alexey V.} and Stepanova, {Irina A.} and Zatsepin, {Timofei S.} and Korshun, {Vladimir A.}",
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month = "6",
day = "8",
doi = "10.1016/j.tet.2017.04.045",
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Astakhova, K, Golovin, AV, Prokhorenko, IA, Ustinov, AV, Stepanova, IA, Zatsepin, TS & Korshun, VA 2017, 'Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters', Tetrahedron, bind 73, nr. 23, s. 3220-3230. https://doi.org/10.1016/j.tet.2017.04.045

Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection : The attachment manner matters. / Astakhova, Kira; Golovin, Andrey V.; Prokhorenko, Igor A.; Ustinov, Alexey V.; Stepanova, Irina A.; Zatsepin, Timofei S.; Korshun, Vladimir A.

I: Tetrahedron, Bind 73, Nr. 23, 08.06.2017, s. 3220-3230.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection

T2 - The attachment manner matters

AU - Astakhova, Kira

AU - Golovin, Andrey V.

AU - Prokhorenko, Igor A.

AU - Ustinov, Alexey V.

AU - Stepanova, Irina A.

AU - Zatsepin, Timofei S.

AU - Korshun, Vladimir A.

PY - 2017/6/8

Y1 - 2017/6/8

N2 - 1-Phenylethynylpyrene fluorophore (1-PEPy) has long-wavelength shifted emission and higher photo stability compared to pyrene, retaining, however, pyrene's ability to form excimers. Here we report the synthesis of 2'-O-[3(and 4)-(pyren-1-ylethynyl)benzyl]-uridines and their tandem incorporation into deoxyribo- and 2'-O-Me-ribo-oligonucleotide probes. Excimer forming probes of type NN center dot center dot center dot NNXXNN center dot center dot center dot NN (X = 2'-O-[meta(or para)-(pyren-1-ylethyny1)-benzyl]uridine) containing two adjacent fluorescent nucleosides within an oligonucleotide are available in four types (meta-meta; para-meta; meta-para; para-para). Both DNA (N = deoxyribonucleotides) and 2'-O-Me-RNA (N = 2'-O-Me-ribo-nucleotides) probes were synthesized and their hybridization with complementary and singly mismatched DNA and RNA was studied. Several probes show a dramatic response of their excimer-to-monomer intensity ratio upon hybridization. Remarkably, most spectacular fluorescence changes were demonstrated for probes with para-meta and meta-para combination within 2'-O-Me-ribo-oligonucleotides. Using excimer forming probes, three natural SNP in Helicobacter pylori 23S RNA gene (A2144G, A2143G, A2143C) and the wild type gene can be distinguished. (C) 2017 Elsevier Ltd. All rights reserved.

AB - 1-Phenylethynylpyrene fluorophore (1-PEPy) has long-wavelength shifted emission and higher photo stability compared to pyrene, retaining, however, pyrene's ability to form excimers. Here we report the synthesis of 2'-O-[3(and 4)-(pyren-1-ylethynyl)benzyl]-uridines and their tandem incorporation into deoxyribo- and 2'-O-Me-ribo-oligonucleotide probes. Excimer forming probes of type NN center dot center dot center dot NNXXNN center dot center dot center dot NN (X = 2'-O-[meta(or para)-(pyren-1-ylethyny1)-benzyl]uridine) containing two adjacent fluorescent nucleosides within an oligonucleotide are available in four types (meta-meta; para-meta; meta-para; para-para). Both DNA (N = deoxyribonucleotides) and 2'-O-Me-RNA (N = 2'-O-Me-ribo-nucleotides) probes were synthesized and their hybridization with complementary and singly mismatched DNA and RNA was studied. Several probes show a dramatic response of their excimer-to-monomer intensity ratio upon hybridization. Remarkably, most spectacular fluorescence changes were demonstrated for probes with para-meta and meta-para combination within 2'-O-Me-ribo-oligonucleotides. Using excimer forming probes, three natural SNP in Helicobacter pylori 23S RNA gene (A2144G, A2143G, A2143C) and the wild type gene can be distinguished. (C) 2017 Elsevier Ltd. All rights reserved.

KW - Oligonucleotide

KW - Single nucleotide polymorphism

KW - Phenylethynylpyrene

KW - Hybridization

KW - Fluorescence

U2 - 10.1016/j.tet.2017.04.045

DO - 10.1016/j.tet.2017.04.045

M3 - Journal article

VL - 73

SP - 3220

EP - 3230

JO - Tetrahedron

JF - Tetrahedron

SN - 0040-4020

IS - 23

ER -

Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS et al. Design of 2 `-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron. 2017 jun 8;73(23):3220-3230. https://doi.org/10.1016/j.tet.2017.04.045