DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection: Sequence-Affinity Relation.
Identifieur interne : 000530 ( PubMed/Curation ); précédent : 000529; suivant : 000531DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection: Sequence-Affinity Relation.
Auteurs : Pavel Vorobjev [Russie] ; Anna Epanchintseva [Russie] ; Alexander Lomzov [Russie] ; Aleksey Tupikin [Russie] ; Marsel Kabilov [Russie] ; Inna Pyshnaya [Russie] ; Dmitrii Pyshnyi [Russie]Source :
- Langmuir : the ACS journal of surfaces and colloids [ 1520-5827 ] ; 2019.
Abstract
Native DNA strongly adsorbs to citrate-coated gold nanoparticles (AuNPs). The resulting composites (DNA/AuNPs) are valuable materials in many fields, especially in biomedicine. For this reason, the process of adsorption is a focus for intensive research. In this work, DNA adsorption to gold nanoparticles was studied using a molecular selection procedure followed by high-throughput DNA sequencing. The chemically synthesized DNA library containing a central N26 randomized fragment was sieved through four cycles of adsorption to AuNPs in a tree-like selection-amplification scheme (SELEX (Selective Evolution of Ligands by EXponential enrichment)). The frequencies of occurrence of specific oligomeric DNA motifs, k-mers ( k = 1-6), in the initial and selected pools were calculated. Distribution of secondary structures in the pools was analyzed. A large set of diverse A, T, and G enriched k-mers undergo a pronounced positive selection, and these sequences demonstrate faster and strong binding to the AuNPs. For facile binding, such structural motifs should be located in the loop regions of weak intramolecular complexes-hairpins with imperfect stem, or other portion of the structure, which is unpaired under selection conditions. Our data also show that, under the conditions employed in this study, cytosine is significantly depleted during the selection process, although guanine remains unchanged. These regularities were confirmed in a series of binding experiments with a set of synthetic DNA oligonucleotides. The detailed analysis of DNA binding to AuNPs shows that the sequence specificity of this interaction is low due to its nature, although the presence and the number of specific structural motifs in DNA affect both the rate of formation and the strength of the formed noncovalent associates with AuNPs.
DOI: 10.1021/acs.langmuir.9b00661
PubMed: 31117729
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wicri:level="1"><nlm:affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 </wicri:regionArea></affiliation></author><author><name sortKey="Lomzov, Alexander" sort="Lomzov, Alexander" uniqKey="Lomzov A" first="Alexander" last="Lomzov">Alexander Lomzov</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 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Avenue , Novosibirsk 630090 , Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 </wicri:regionArea></affiliation></author><author><name sortKey="Pyshnaya, Inna" sort="Pyshnaya, Inna" uniqKey="Pyshnaya I" first="Inna" last="Pyshnaya">Inna Pyshnaya</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 </wicri:regionArea></affiliation></author><author><name sortKey="Pyshnyi, Dmitrii" sort="Pyshnyi, Dmitrii" uniqKey="Pyshnyi D" first="Dmitrii" last="Pyshnyi">Dmitrii Pyshnyi</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</nlm:affiliation><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 </wicri:regionArea></affiliation></author></analytic><series><title level="j">Langmuir : the ACS journal of surfaces and colloids</title><idno type="eISSN">1520-5827</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Native DNA strongly adsorbs to citrate-coated gold nanoparticles (AuNPs). The resulting composites (DNA/AuNPs) are valuable materials in many fields, especially in biomedicine. For this reason, the process of adsorption is a focus for intensive research. In this work, DNA adsorption to gold nanoparticles was studied using a molecular selection procedure followed by high-throughput DNA sequencing. The chemically synthesized DNA library containing a central N<sub>26</sub> randomized fragment was sieved through four cycles of adsorption to AuNPs in a tree-like selection-amplification scheme (SELEX (Selective Evolution of Ligands by EXponential enrichment)). The frequencies of occurrence of specific oligomeric DNA motifs, k-mers ( k = 1-6), in the initial and selected pools were calculated. Distribution of secondary structures in the pools was analyzed. A large set of diverse A, T, and G enriched k-mers undergo a pronounced positive selection, and these sequences demonstrate faster and strong binding to the AuNPs. For facile binding, such structural motifs should be located in the loop regions of weak intramolecular complexes-hairpins with imperfect stem, or other portion of the structure, which is unpaired under selection conditions. Our data also show that, under the conditions employed in this study, cytosine is significantly depleted during the selection process, although guanine remains unchanged. These regularities were confirmed in a series of binding experiments with a set of synthetic DNA oligonucleotides. The detailed analysis of DNA binding to AuNPs shows that the sequence specificity of this interaction is low due to its nature, although the presence and the number of specific structural motifs in DNA affect both the rate of formation and the strength of the formed noncovalent associates with AuNPs.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">31117729</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1520-5827</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>24</Issue><PubDate><Year>2019</Year><Month>Jun</Month><Day>18</Day></PubDate></JournalIssue><Title>Langmuir : the ACS journal of surfaces and colloids</Title><ISOAbbreviation>Langmuir</ISOAbbreviation></Journal><ArticleTitle>DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection: Sequence-Affinity Relation.</ArticleTitle><Pagination><MedlinePgn>7916-7928</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/acs.langmuir.9b00661</ELocationID><Abstract><AbstractText>Native DNA strongly adsorbs to citrate-coated gold nanoparticles (AuNPs). The resulting composites (DNA/AuNPs) are valuable materials in many fields, especially in biomedicine. For this reason, the process of adsorption is a focus for intensive research. In this work, DNA adsorption to gold nanoparticles was studied using a molecular selection procedure followed by high-throughput DNA sequencing. The chemically synthesized DNA library containing a central N<sub>26</sub> randomized fragment was sieved through four cycles of adsorption to AuNPs in a tree-like selection-amplification scheme (SELEX (Selective Evolution of Ligands by EXponential enrichment)). The frequencies of occurrence of specific oligomeric DNA motifs, k-mers ( k = 1-6), in the initial and selected pools were calculated. Distribution of secondary structures in the pools was analyzed. A large set of diverse A, T, and G enriched k-mers undergo a pronounced positive selection, and these sequences demonstrate faster and strong binding to the AuNPs. For facile binding, such structural motifs should be located in the loop regions of weak intramolecular complexes-hairpins with imperfect stem, or other portion of the structure, which is unpaired under selection conditions. Our data also show that, under the conditions employed in this study, cytosine is significantly depleted during the selection process, although guanine remains unchanged. These regularities were confirmed in a series of binding experiments with a set of synthetic DNA oligonucleotides. The detailed analysis of DNA binding to AuNPs shows that the sequence specificity of this interaction is low due to its nature, although the presence and the number of specific structural motifs in DNA affect both the rate of formation and the strength of the formed noncovalent associates with AuNPs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vorobjev</LastName><ForeName>Pavel</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Novosibirsk State University , 2, Pirogova Street , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Epanchintseva</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lomzov</LastName><ForeName>Alexander</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Novosibirsk State University , 2, Pirogova Street , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tupikin</LastName><ForeName>Aleksey</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kabilov</LastName><ForeName>Marsel</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-2777-0833</Identifier><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pyshnaya</LastName><ForeName>Inna</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pyshnyi</LastName><ForeName>Dmitrii</ForeName><Initials>D</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2587-3719</Identifier><AffiliationInfo><Affiliation>Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Novosibirsk State University , 2, Pirogova Street , Novosibirsk 630090 , Russia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>06</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Langmuir</MedlineTA><NlmUniqueID>9882736</NlmUniqueID><ISSNLinking>0743-7463</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31117729</ArticleId><ArticleId IdType="doi">10.1021/acs.langmuir.9b00661</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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