## 2 Methods and Materials
### Nanofluidic Chips  
To investigate the absorption signatures in nucleic acid solutions, we utilized a nanoporous silica-on-fused quartz substrate nanochannel technology, as described in Appendix B. An SEM cross-sectional photograph of a representative structure is shown in Figure 11. The substrates were 2 \(\times\) 2 cm wide by 1 mm thick, but the nanochannel region occupied only the central 5 \(\times\) 5 mm square. These dimensions were designed to easily accommodate the \(\sim\)3 mm diameter (1/e\({}^{2}\) intensity points) focused THz beam in our spectrometer, so no significant \"spill-over\" was expected. Because the wavelengths investigated were \(\sim\)0.5 mm or less, the diffractive effects (from the substrate edges) should be negligible, too. For our particular chips, the nanochannel dimensions were typically 500 nm wide by 600 nm deep, with a period of \(\approx\)1.0 \(\upmu\)m. For nanochannel dimensions much smaller than this, the capillary flow was usually slow and sporadic, especially for the larger molecule samples tested. This caused a time variation of the THz transmittance that would appear as false signatures when the spectrometer frequency was scanned.  
The nanofluidic chips also provided the ability to reduce the effect of substrate standing wave interference and observe the absorption effects primarily of the nucleic acids in solution. This entailed a \"pre-wet\" step in the sample preparation, whereby the \"background\" spectrum was the THz transmittance through the nanofluidic chip with its channels filled by a buffer solution of tri-phosphate ethylene-diaminetetraacetic acid (TPE), a common buffer for nucleic acids and compatible with the Tris-HCL ethylenediaminetetraacetic-acid (EDTA) that the samples are delivered in. After measuring the background spectrum \(\mathrm{P_{B}(v)}\) with the channels full of buffer, the nucleic acid solution of choice was added to the reservoirs and allowed to flow into the channels for a time of \(\sim\)20 min before measuring the sample spectrum \(\mathrm{P_{S}(v)}\), and subsequently calculating T(v) via Equation (1).  
For this research, we originally used silica nanochannels fabricated on 0.5 mm-thick, high-resistivity silicon chips because of their ease of fabrication and the widespread availability of Si substrates [15]. However, the fluidic flow in the channels could not be observed by simple visible inspection because of the opacity of the Si. Furthermore, there was evidence of standing wave effects in the THz spectrum through the periodic behavior of T(v), even after nanochannel \"pre-wet\". Standing waves occur from multi-pass interference, as occurs in optical etalons, of which the nanofluidic substrate is an example. According to plane-wave propagation theory, they create an oscillating transmittance, having a peak-to-peak separation of \(\Delta\)f \(\approx\) c/(2 nd), where n is the refractive index and d is the etalon thickness (substrate + nanochannel layer). The etalon transmittance has a peak-to-trough ratio that increases rapidly with n. High-resistivity Si has a relatively large refractive index n \(\approx\) 3.42 in the sub-THz region, but a very low absorption coefficient (\(\alpha\) < 1.0 cm\({}^{-1}\)) [19]. By contrast, fused quartz has a lower refractive index n \(\approx\) 1.95, but a more significant absorption (\(\alpha\)\(\approx\) 2.5-3.0 cm\({}^{-1}\)) [20]. These lead to an etalon peak separation of \(\Delta\)f \(\approx\) 88 GHz for the Si, and \(\approx\)77 GHz for the quartz. As discussed in the Results section below, the strongest absorption signatures measured with our quartz substrate nanofluidic chip are _spectrally confined_, meaning that they appear in a limited range of frequencies, but either weaken or disappear entirely outside of this range. This is categorically different from the wideband quasi-sinusoidal behavior expected for plane-wave propagation through a low-loss etalon.