Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes
Sulfonated indocyanines 3 and 5 (sCy3, sCy5) are widely used to label biomolecules. Their high molar absorption coefficients and lack of spectral overlap with biopolymers make them ideal as linker components for rapid assessment of bioconjugate stoichiometry. We recently found that the determination...
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2024-12-01
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| author | Evgeny L. Gulyak Vladimir A. Brylev Mikhail Y. Zhitlov Olga A. Komarova Alexey V. Ustinov Ksenia A. Sapozhnikova Vera A. Alferova Vladimir A. Korshun Daniil A. Gvozdev |
| author_facet | Evgeny L. Gulyak Vladimir A. Brylev Mikhail Y. Zhitlov Olga A. Komarova Alexey V. Ustinov Ksenia A. Sapozhnikova Vera A. Alferova Vladimir A. Korshun Daniil A. Gvozdev |
| author_sort | Evgeny L. Gulyak |
| collection | DOAJ |
| description | Sulfonated indocyanines 3 and 5 (sCy3, sCy5) are widely used to label biomolecules. Their high molar absorption coefficients and lack of spectral overlap with biopolymers make them ideal as linker components for rapid assessment of bioconjugate stoichiometry. We recently found that the determination of the sCy3:sCy5 molar ratio in a conjugate from its optical absorption spectrum is not straightforward, as the sCy3:sCy5 absorbance ratio at the maxima tends to be larger than expected. In this work, we have investigated this phenomenon in detail by studying the spectral properties of a series of sCy3-sCy5 conjugates in which the dyes are separated by linkers of various lengths, including DNA duplexes. It was found that when sCy3 and sCy5 are located in close proximity, they consistently exhibit an “abnormal” absorbance ratio. However, when the two dyes are separated by long rigid DNA-based spacers, the absorbance ratio becomes consistent with their individual molar absorption coefficients. This phenomenon should be taken into account when assessing the molar ratio of the dyes by UV-Vis spectroscopy. |
| format | Article |
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| institution | Kabale University |
| issn | 1420-3049 |
| language | English |
| publishDate | 2024-12-01 |
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| series | Molecules |
| spelling | doaj-art-324eb2eca0124a459e5bb61c40210d242025-01-10T13:18:44ZengMDPI AGMolecules1420-30492024-12-013015710.3390/molecules30010057Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA DuplexesEvgeny L. Gulyak0Vladimir A. Brylev1Mikhail Y. Zhitlov2Olga A. Komarova3Alexey V. Ustinov4Ksenia A. Sapozhnikova5Vera A. Alferova6Vladimir A. Korshun7Daniil A. Gvozdev8Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, RussiaDepartment of Biology, Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, RussiaSulfonated indocyanines 3 and 5 (sCy3, sCy5) are widely used to label biomolecules. Their high molar absorption coefficients and lack of spectral overlap with biopolymers make them ideal as linker components for rapid assessment of bioconjugate stoichiometry. We recently found that the determination of the sCy3:sCy5 molar ratio in a conjugate from its optical absorption spectrum is not straightforward, as the sCy3:sCy5 absorbance ratio at the maxima tends to be larger than expected. In this work, we have investigated this phenomenon in detail by studying the spectral properties of a series of sCy3-sCy5 conjugates in which the dyes are separated by linkers of various lengths, including DNA duplexes. It was found that when sCy3 and sCy5 are located in close proximity, they consistently exhibit an “abnormal” absorbance ratio. However, when the two dyes are separated by long rigid DNA-based spacers, the absorbance ratio becomes consistent with their individual molar absorption coefficients. This phenomenon should be taken into account when assessing the molar ratio of the dyes by UV-Vis spectroscopy.https://www.mdpi.com/1420-3049/30/1/57sulfocyanine dyesabsorption spectradyes interactionenergy transferoligonucleotide duplex |
| spellingShingle | Evgeny L. Gulyak Vladimir A. Brylev Mikhail Y. Zhitlov Olga A. Komarova Alexey V. Ustinov Ksenia A. Sapozhnikova Vera A. Alferova Vladimir A. Korshun Daniil A. Gvozdev Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes Molecules sulfocyanine dyes absorption spectra dyes interaction energy transfer oligonucleotide duplex |
| title | Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes |
| title_full | Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes |
| title_fullStr | Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes |
| title_full_unstemmed | Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes |
| title_short | Indocarbocyanine–Indodicarbocyanine (sCy3–sCy5) Absorptive Interactions in Conjugates and DNA Duplexes |
| title_sort | indocarbocyanine indodicarbocyanine scy3 scy5 absorptive interactions in conjugates and dna duplexes |
| topic | sulfocyanine dyes absorption spectra dyes interaction energy transfer oligonucleotide duplex |
| url | https://www.mdpi.com/1420-3049/30/1/57 |
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