## 2 Methods and Materials  
### Wideband THz Transmittance Spectroscopy  
Our THz spectrometer is the coherent, frequency-domain, frequency-scanning photomixing transceiver shown in Figure 1[16; 17; 18], consisting of a single frequency tunable transmitter; a tunable receiver mutually coherent to the transmitter; and a free space path in between \(\approx\)18 inches long. We modified the traditional all horizontal beam path of the spectroscopic instruments and introduced sections of vertical path. This allowed us to orient nanofluidic chips horizontally to alleviate gravitational effects and facilitate the filling of the nanochannels by capillary action. The nanofluidic chip samples of interest were located at the lens port of the transmit photomixer, as shown in Figure 1, just below a Si (hyperhemispherical) lens. Here, the spot diameter is small (\(\sim\)3 mm diameter), which underfills the active aperture of the chip (\(\approx\)5 \(\times\) 5 mm). Careful initial alignment of the chip was required to minimize beam steering with respect to the receiver. Moreover, the THz path was not evacuated, so water vapor lines--notorious in the THz frequency region--are expected to be present and are discussed below. Further details on our THz photomixing spectroscopy and its performance metrics are provided in Appendix A, with a photograph of the actual system in Figure A1.  
The THz signatures we searched for are those associated with absorption resonances from the nucleic acid samples of interest. Consistent with and as generally practiced by FTIR spectroscopy, the absorption resonances should correspond to \"dips\" in the transmittance T vs. frequency. Our frequency range for testing was approximately 500-1000 GHz because sharp (i.e., narrow and strong) signatures were initially found from the smaller nucleic acid samples in this range. The larger nucleic acid samples also displayed signatures, although broader and weaker (see the Results section, below). To obtain the transmittance spectrum T(v), three separate frequency scans were taken, all in 0.5 GHz steps: (1) a \"background\" spectrum of the received power vs. frequency, \(P_{B}(\
u)\); (2) a sample spectrum \(P_{S}(\
u)\) with the sample placed in the path; and (3) a noise spectrum \(P_{N}(\
u)\) with the transmitter power blocked (by a metal plate) and averaged over many successive scans. The transmittance was then computed as  
\[T(\
u)=[P_{S}(\
u)-P_{N}(\
u)]/[P_{B}(\
u)-P_{N}(\
u)]. \tag{1}\]  
Our experience with frequency-domain scanning spectroscopy is that this is an accurate technique when the signal-to-noise ratios (SNRs), \(P_{S}(\
u)/P_{N}(\
u)\) and \(P_{B}(\
u)/P_{N}(\
u)\), are at least 2.0 or greater at all frequencies in the scan [17; 18].  
One key aspect of our spectroscopic technique is frequency resolution. Because the linewidth of the DFB lasers used in the spectrometer is typically 50 MHz or less (see Appendix A), the THz resolution is just the step frequency, provided this is much greater than 50 MHz. Thus, in the present experiments, we set the step frequency to be 0.5 GHz. This is much finer than is typically used in THz spectroscopy (e.g., TDS, FTIR), allowing us to resolve fine signatures that other types of spectroscopy would broaden significantly or miss altogether. Another key aspect is common-mode cancellation, such as water vapor absorption in the open path between the transmitter and receiver. This affects T(v) through a frequency-dependent factor M(v) that multiplies both \(P_{S}(\
u)\) and \(P_{B}(\
u)\). Hence, provided \(P_{S}(\
u)\) and \(P_{B}(\
u)\) are both \(\approx P_{N}(\
u)\), M(v) cancels out in Equation (1) to the first order. The effect of standing waves in the nanofluidic chip etalon is a separate issue and discussed in Section 4.1.  
Figure 1: THz photomixing spectrometer with nanofluidic chip in the beam path. The chip dimensions are \(5\times 5\) mm and the THz beam has a 3 mm diameter, so underfills the chip. The nanochannels are not shown to scale, as there are approximately 5000 parallel nanochannels per chip.