TY - JOUR

T1 - DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection

T2 - Sequence-Affinity Relation

AU - Vorobjev, Pavel

AU - Epanchintseva, Anna

AU - Lomzov, Alexander

AU - Tupikin, Aleksey

AU - Kabilov, Marsel

AU - Pyshnaya, Inna

AU - Pyshnyi, Dmitrii

PY - 2019/6/18

Y1 - 2019/6/18

N2 - 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.

AB - 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.

KW - PERFORMANCE LIQUID-CHROMATOGRAPHY

KW - SURFACE SCIENCE

KW - ADSORPTION

KW - RNA

KW - NUCLEOBASES

KW - NUCLEOSIDES

KW - STABILITY

KW - APTAMERS

KW - AU(111)

UR - http://www.scopus.com/inward/record.url?scp=85067043690&partnerID=8YFLogxK

U2 - 10.1021/acs.langmuir.9b00661

DO - 10.1021/acs.langmuir.9b00661

M3 - Article

C2 - 31117729

AN - SCOPUS:85067043690

VL - 35

SP - 7916

EP - 7928

JO - Langmuir

JF - Langmuir

SN - 0743-7463

IS - 24

ER -