Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles
Fluorophore (FD) labeling is widely used for detection and quantification of various compounds bound to nanocarriers. The systems, composed of gold nanoparticles (GNPs) and oligonucleotides (ONs) labeled with FDs, have wide applications. Our work was aimed at a systemic study of how FD structure (in...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Nanomaterials |
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| Online Access: | https://www.mdpi.com/2079-4991/11/5/1178 |
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| author | Anna V. Epanchintseva Ekaterina A. Gorbunova Elena I. Ryabchikova Inna A. Pyshnaya Dmitrii V. Pyshnyi |
| author_facet | Anna V. Epanchintseva Ekaterina A. Gorbunova Elena I. Ryabchikova Inna A. Pyshnaya Dmitrii V. Pyshnyi |
| author_sort | Anna V. Epanchintseva |
| collection | DOAJ |
| description | Fluorophore (FD) labeling is widely used for detection and quantification of various compounds bound to nanocarriers. The systems, composed of gold nanoparticles (GNPs) and oligonucleotides (ONs) labeled with FDs, have wide applications. Our work was aimed at a systemic study of how FD structure (in composition of ON-FDs) influenced the efficiency of their non-covalent associates’ formation with GNPs (ON-FD/GNPs). We examined ONs of different length and nucleotide composition, and corresponding ON-FDs (FDs from a series of xanthene, polymethine dyes; dyes based on polycyclic aromatic hydrocarbons). Methods: fluorometry, dynamic light scattering, high performance liquid chromatography, gel electrophoresis, molecular modeling and methods of thermodynamic and statistical analysis. We observed significant, differing several times, changes in surface density and Langmuir constant values of ON-FDs vs. ONs, evidence for the critical significance of FD nature for binding of ON-FDs with GNPs. Surface density of ON-FD/GNPs; hydrophobicity and total charge of ON or ON-FD; and charge and surface area of FDs were revealed as key factors determining affinity (Langmuir constant) of ON or ON-FDs for GNPs. These factors compose a specific set, which makes possible the highly reliable prediction of efficiency of ONs and ON-FDs binding with GNPs. The principal possibility of creating an algorithm for predictive calculation of efficiency of ONs and GNPs interaction was demonstrated. We proposed a hypothetical model that described the mechanism of contact interaction between negatively charged nano-objects, such as citrate-stabilized GNPs, and ONs or ON-FDs. |
| first_indexed | 2024-03-10T11:48:58Z |
| format | Article |
| id | doaj.art-3ae559a9d1544f018ede0dac51ada5ff |
| institution | Directory Open Access Journal |
| issn | 2079-4991 |
| language | English |
| last_indexed | 2024-03-10T11:48:58Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Nanomaterials |
| spelling | doaj.art-3ae559a9d1544f018ede0dac51ada5ff2023-11-21T17:51:59ZengMDPI AGNanomaterials2079-49912021-04-01115117810.3390/nano11051178Effect of Fluorescent Labels on DNA Affinity for Gold NanoparticlesAnna V. Epanchintseva0Ekaterina A. Gorbunova1Elena I. Ryabchikova2Inna A. Pyshnaya3Dmitrii V. Pyshnyi4Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave. 8, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave. 8, 630090 Novosibirsk, RussiaFluorophore (FD) labeling is widely used for detection and quantification of various compounds bound to nanocarriers. The systems, composed of gold nanoparticles (GNPs) and oligonucleotides (ONs) labeled with FDs, have wide applications. Our work was aimed at a systemic study of how FD structure (in composition of ON-FDs) influenced the efficiency of their non-covalent associates’ formation with GNPs (ON-FD/GNPs). We examined ONs of different length and nucleotide composition, and corresponding ON-FDs (FDs from a series of xanthene, polymethine dyes; dyes based on polycyclic aromatic hydrocarbons). Methods: fluorometry, dynamic light scattering, high performance liquid chromatography, gel electrophoresis, molecular modeling and methods of thermodynamic and statistical analysis. We observed significant, differing several times, changes in surface density and Langmuir constant values of ON-FDs vs. ONs, evidence for the critical significance of FD nature for binding of ON-FDs with GNPs. Surface density of ON-FD/GNPs; hydrophobicity and total charge of ON or ON-FD; and charge and surface area of FDs were revealed as key factors determining affinity (Langmuir constant) of ON or ON-FDs for GNPs. These factors compose a specific set, which makes possible the highly reliable prediction of efficiency of ONs and ON-FDs binding with GNPs. The principal possibility of creating an algorithm for predictive calculation of efficiency of ONs and GNPs interaction was demonstrated. We proposed a hypothetical model that described the mechanism of contact interaction between negatively charged nano-objects, such as citrate-stabilized GNPs, and ONs or ON-FDs.https://www.mdpi.com/2079-4991/11/5/1178oligonucleotidesfluorescent dyegold nanoparticlesnon-covalent adsorptionmechanismsaffinity |
| spellingShingle | Anna V. Epanchintseva Ekaterina A. Gorbunova Elena I. Ryabchikova Inna A. Pyshnaya Dmitrii V. Pyshnyi Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles Nanomaterials oligonucleotides fluorescent dye gold nanoparticles non-covalent adsorption mechanisms affinity |
| title | Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles |
| title_full | Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles |
| title_fullStr | Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles |
| title_full_unstemmed | Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles |
| title_short | Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles |
| title_sort | effect of fluorescent labels on dna affinity for gold nanoparticles |
| topic | oligonucleotides fluorescent dye gold nanoparticles non-covalent adsorption mechanisms affinity |
| url | https://www.mdpi.com/2079-4991/11/5/1178 |
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