Characterizing the Incorporation of DNA into Single NIPAm Hydrogel Nanoparticles with Surface Plasmon Resonance Imaging Measurements

Abstract

N-Isopropylacrylamide-based hydrogel nanoparticles (HNPs) that incorporate 30 mer single-stranded DNA (ssDNA) oligonucleotides were synthesized and characterized with single-nanoparticle surface plasmon resonance imaging (SPRI) microscopy, dynamic light scattering, transmission electron microscopy, and fluorescence measurements. The synthesized HNPs had an averaged diameter of 230 nm and exhibited a large (5−10×) increase in the average single-nanoparticle SPRI refractive index (Δ% R NP ), as compared with HNPs without DNA. A combination of SPRI and fluorescence measurements was used to measure the uptake of approximately 20 000 complementary ssDNA into each HNP, resulting in a Langmuir isotherm adsorption coefficient of 4.89 × 10 8 M −1 . Single-nanoparticle SPRI measurements also showed that approximately 35% of the incorporated ssDNA was accessible for both hybridization uptake and enzymatic hydrolysis using exonuclease I. We attribute the presence of an inactive ssDNA population in the nanoparticle to a combination of acrylamide Michael addition reactions with adenine, cytosine, and guanine nucleotides, as well as the possible formation of self-complementary secondary structures in the polymerized ssDNA.

Adsorption of DNA Oligonucleotides by Boronic Acid-Functionalized Hydrogel Nanoparticles

“…To study DNA adsorption, we used a T 15 DNA (15 consecutive thymines) bearing a carboxyfluorescein (FAM) label. Unlike many inorganic nanomaterials such as graphene oxide, − gold nanoparticles, − and metal oxides, the hydrogel nanoparticles are not good fluorescence quenchers . Therefore, we cannot use fluorescence quenching to study DNA adsorption.…”

“…Unlike many inorganic nanomaterials such as graphene oxide, 42−44 gold nanoparticles, 45−47 and metal oxides, 48 the hydrogel nanoparticles are not good fluorescence quenchers. 49 Therefore, we cannot use fluorescence quenching to study DNA adsorption. Instead, we incubated the gel nanoparticles with the DNA for 1 h and then centrifuged the samples.…”

Smart Nucleic Acid Hydrogels with High Stimuli-Responsiveness in Biomedical Fields

“…Since then, the era of co-synthesis of NAHs by polymers and FNAs has been entered. In recent years, polymers and nanomaterials have started to be used to prepare NAHs with nucleic acids, including, but not limited to, graphene oxide graphene oxide (GO) [15][16][17], carbon dots (CD) [18][19][20], carbon nanotubes [21], quantum dots [22], magnetic beads [23], polyacrylamide (PAM) [24][25][26][27][28][29][30], poly-N-isopropylacrylamide (p-NIPAM) [31,32], polyethylene glycol (PEG) [33][34][35][36], and poly-L-lysine (PLL) [37]. The use of these materials helps to improve the performance of hydrogels, reduce nucleic acid use, and speed up the synthesis of hydrogels.…”

Smart and Functionalized Development of Nucleic Acid‐Based Hydrogels: Assembly Strategies, Recent Advances, and Challenges

“…Currently, the synthetic polymers used for constructing DNA‐polymer hybrid hydrogels mainly include polyacrylamide (PAM), [ 57 , 58 , 59 , 60 , 61 ] poly‐ N ‐isopropylacrylamide (pNIPAM), [ 62 , 63 , 64 ] polyethyleneimine (PEI), [ 65 ] and polyethylene glycol (PEG). [ 66 , 67 , 68 ] In addition, poly‐L‐lysine (PLL), [ 69 , 70 ] carboxymethyl cellulose (CMC), [ 71 , 72 ] and other high‐molecular polymers obtained via polymerization or by modifying natural raw materials can also work as the backbone or cross‐linkers in the hybrid DNA hydrogels.…”