Manipulating the Salt and Thermal Stability of DNA Multilayer Films via Oligonucleotide Length

Abstract

DNA films are promising materials for diverse applications, including sensing, diagnostics, and drug/gene delivery. However, the ability to tune the stability of DNA films remains a crucial aspect for such applications. Herein, we examine the role of oligonucleotide length on the formation, and salt and thermal stability, of DNA multilayer films using oligonucleotides of homopolymeric diblocks (polyAG and polyTC), with each block (A, G, T, or C) ranging from 5 to 30 bases (10-, 20-, 30-, 40-, and 60-mer). Using a combination of quartz crystal microgravimetry, dual polarization interferometry, and flow cytometry, we demonstrate that at least 10 bases per hybridizing block in the DNA diblocks (that is, 20-mer) are required for successful hybridization and, hence, DNA multilayer film formation. Films assembled using longer oligonucleotide blocks were more stable in low salt conditions, with the DNA multilayer films assembled from the 60-mer oligonucleotides remaining intact in solutions of about 25 mM NaCl. A systematic increase in film melting temperature ( T m) was observed for the DNA multilayer films (assembled on colloids) with increasing oligonucleotide length, ranging from 38.5 degrees C for the 20-mer films to 53 degrees C for the 60-mer films. Further, an alternating trend in T m of the DNA multilayer films was observed with layer number (AG or TC); DNA multilayer films terminated with an AG layer exhibited a higher T m (44-49 degrees C) than films with an outermost TC layer (ca. 38 degrees C), suggesting a rearrangement of the film structure upon hybridization of the outermost layer. This work shows that the stability of DNA multilayer films can be tuned by varying the length of the oligonucleotide building blocks, thus providing a versatile means to tailor the salt and thermal stability of DNA films, which is necessary for the application of such films.

DNA multilayer film for loading and release of DNA oligomer

“…The solutions were injected in the recorder equipped with the oscillator at a flow rate of 1.26 μL/min and the temperature was kept at 25 o C during the assembly. Because the large dissipation changes were observed during the DNA LbL assembly [8,10], the Sauerbrey equation [18] does not hold. Therefore, the layer growth and degradation are qualitatively shown as a frequency change (Δf).…”

Direct and label-free monitoring oligonucleotide immobilization, non-specific binding and DNA biorecognition

“…The ability for recognition 26 complementary DNA strands discriminating non-complementary ones was applied for species 27 identification in mixtures. 28 The studies and uses of nucleic acids have been growing up for decades, and the trend 3 is to keep on in first line. Thus, basic research on nucleic acids provides fundamental knowledge 4 for in vivo and in vitro applications.…”

“…similar or higher than the best achieved with ICPTS, except when using BSA 27 for blocking (30%). 28 According to data shown in Table 4, and target B contour length (~8 nm), a theoretical 29 thickness increment of 0.280 nm can be estimated. The experimental net value was 0.190 nm, 30 which indicates that hybridization takes place in a partially flattened oligonucleotide 1 conformation.…”

“…Finally, a DPI calibration procedure was carried out, consisting of three stages [26,28]: 12 linearisation, performed by injecting an 80% v/v ethanol/water mixture over the chip followed 13 by stabilization back to the buffer baseline; chip calibration, by registering absolute signal of 14 the ethanol/water mixture; and bulk calibration, performed by recording signals when flushing 15 pure water. 16 17 1 2 In order to employ the same chip for more than one experiment, a cleaning-regeneration 3 procedure was performed.…”

Peptide Nucleic Acid Films and Capsules: Assembly and Enzymatic Degradation

“…[7][8][9] When the DNA films are assembled on particles, subsequent dissolution of the templates [10,11] results in the formation of free-standing structures known as hollow DNA capsules. [6,[12][13][14] For LbL assembly using DNA, two complementary strands are alternately hybridized to the film. The selection of DNA sequences is crucial to successful LbL growth.…”