Before applying the T 13 C2 edited signal as a sub-molecular thermometer, it is important to first account for the amount each atom in the thymine molecular structure is displaced during the vibration observed at 1720 cm -1 (Figure ) when the C2=O bond is in a weak, canonical Watson-Crick base pair (Figure ). Assigning atomic contributions to the molecular response at 1720 cm -1 ideally requires isotopic substitution at each position in thymine's molecular structure to determine the extent to which each atom is displaced when an atomic standing wave is driven at a particular frequency. A small thermometer would be a heat-sensitive normal mode with only 2 or 3 atoms displaced during the mode. In contrast, modes in which the displacements are distributed across all the atoms in the structure cover more of the base's total area and are less sensitive to interactions at specific parts of the duplexed structure. While prior work on the thymine monomer found that the high frequency signal was indeed mostly arising from C2=O stretching, the number of atoms and the degree to which each is displaced at this frequency may change upon entry of the monomer into the polymeric, base-paired DNA duplex environment. This physical effect is important to account for, as it would change the dimensions of our potential thermometer. To determine if this change occurs, we site-specifically incorporated isotopes (T 13 C4=O and T 15 N3-H) into a DNA duplex and acquired the light and heavy spectra for the sequences. We then performed subtractions to assign which atoms contribute to resonance at 1720 cm -1 , which is quite intense when the isotope is incorporated at the TC2 position of the base (Table ).