Silicon dioxide (SiO2) is ubiquitous in biomedical diagnostics and other applications as a capture medium for nucleic acids and proteins. Diagnostic devices have seen rapid miniaturisation in recent years, due to the increased demand for portable point-of-care diagnostics. However, there are increasing challenges with incorporating SiO2 nanostructures into diagnostic devices, due to the complexity of nanostructured SiO2 synthesis, often involving etching and chemical vapour deposition under high vacuum conditions. We report a novel and straightforward method for deposition of high-quality, nanoscale SiO2 films and 3D SiO2 structures using thermal decomposition of polydimethylsiloxane (PDMS), in a furnace at atmospheric pressure at 500 °C. This method allows individual nanometre controllability of conformal pinhole-free layers on a variety of materials and morphologies. The temperature ramp rate is a key factor in determining the SiO2 deposit morphology, with slower ramp rates leading to highly conformal 2D films and faster ones yielding 3D nanodentrite structures. For the 2D films, the film thickness, as determined by spectroscopic ellipsometry and confirmed by SEM data, is shown to correlate excellently with initial PDMS source material mass in the thickness range 0.8–18 nm. Fits to ellipsometry models confirm that the refractive index of the deposited film matches the expected value for SiO2, while electrical breakdown measurements confirm that the breakdown strength of the films is comparable to that of high-quality thermal oxides. Depositions on high aspect ratio ZnO nanostructures are shown to be highly conformal, leading to core-shell ZnO-SiO2 nanostructures whose shell thickness is in excellent agreement with the expected values from deposition on planar substrates. At faster ramp rates an abrupt morphological transition is seen to a deposit which displays a 3D nanodentrite morphology. The possibilities for applications of both morphologies (and core-shell combinations with other nanostructured materials) in biosensing and related areas are briefly discussed, and the DNA capture capabilities of each nanostructure are measured. The high aspect ratio nanodendrite structures allow for significant DNA capture within microfluidic devices in the presence of low DNA concentrations, with a maximum average capture efficiency of 43.4 % achieved in the presence of 10 ng/mL of DNA, which is an improvement by a factor of ∼ 3 over planar Si surfaces. Improvements by factors of >10 over planar surfaces were achieved at higher DNA concentrations of 100 and 1000 ng/mL.