Freezing‐directed Stretching and Alignment of DNA Oligonucleotides

Abstract

Most single-stranded DNAo ligonucleotides are random coils with ap ersistence length of below1nm. So far, no good methods are available to stretcho ligonucleotides. Herein, it is shown that freezing can stretchDNA,asconfirmed using fluorescence resonance energy transfer,t hiazole-orange staining,a nd surface-enhanced Raman spectroscopy. Lateral inter-strand interactions are critical, and the stretched DNA oligonucleotides are aligned. This work also provides as et of methods for studying frozen oligonucleotides.U pon freezing, DNAo ligonucleotides are readily adsorbed onto various nanomaterials,i ncluding gold nanoparticles,g raphene oxide, iron oxide,a nd WS 2 via the most thermodynamically stable conformation, leading to more stable conjugates. Cy3-30-Cy5 mixed with 200 mm sDNA in 5mm HEPES, pH 7.6 with 50 mm NaCl before and after freezing. Schemes for two possible reasons of enhanced FRET by freezing (c), and inhibited intermolecular FRET by adding excess non-labeled sDNA (f).

Modulation of DNAzyme Activity via Butanol Dehydration

“…They described the precipitates generated by butanol as a dehydrated “solid solution” for accommodating chemical reactions, in which an extremely crowded, size‐reduced and charge suppressed environment was formed to overcome steric hinderance as well as electrostatic repulsion within the DNA and AuNP mixture. The freezing‐created environment is also greatly dehydrated and similar, as the water molecules turn to ice crystals, concentrating the chemicals left in the gaps between the ice crystals [46–48] …”

Oriented Assembly of Gold Nanoparticles with Freezing‐Driven Surface DNA Manipulation and Its Application in SERS‐Based MicroRNA Assay

“…[17,18] It further demonstrated that freezing can stretch DNA on the surface of AuNPs in comparison to the typical salt-aging method and facilitate oriented assemblies. [19] In this case, due to the high local DNA concentration repelled by the crystallization of water molecules, DNAs attach tightly to the AuNP surface and Exceptional amplification of electronic, magnetic, and optical signals can be achieved by assembling inorganic nanoparticles with well-defined structures in certain orientations. DNA-programmed assembly of gold nanoparticles (AuNPs) has been employed to construct highly ordered nanostructures for surface-enhanced Raman scattering (SERS)-based biosensing.…”

“…Recently, an extremely simple yet effective freezing method was reported to achieve DNA modification on the surface of AuNPs, where a single step was used without the need for any additional reagents, and it demonstrated promising application potentials in biosensing . It further demonstrated that freezing can stretch DNA on the surface of AuNPs in comparison to the typical salt‐aging method and facilitate oriented assemblies . In this case, due to the high local DNA concentration repelled by the crystallization of water molecules, DNAs attach tightly to the AuNP surface and enhance DNA attachment kinetics .…”

DNA Origami-Enabled Plasmonic Sensing

“…An alternative to this approach is the freeze–thaw method reported by Liu and Liu. , The authors showed that freezing a solution containing AuNPs, DNA, and salt could help to speed up the conjugation process dramatically. The freezing results in ice crystals composed of pure water, pushing the nonwater components into gaps between the crystals, where they reach saturated concentrations, allowing the DNA to efficiently bind to gold via its thiolated end.…”