title: Evidence for coupling between nitrile groups using DNA templates: a promising new method for monitoring structures with infrared spectroscopy.
abstract: Infrared spectroscopy is a common method for monitoring biomolecular structures but suffers from spectral congestion. Non-natural vibrational probes provide a way to regain structural specificity because they provide a unique vibrational signature and can be incorporated into proteins or other biomolecules at specific locations. A popular probe is the nitrile group because its frequency is sensitive to the electrostatics of its environment. In this work, we show that pairs of nitrile groups can be used to directly probe distances and angles in dual labeled molecules. By labeling model DNA oligomers with pairs of nitrile tags, we demonstrate that the vibrational coupling between two nitrile groups is strong enough that Fourier transform infrared (FTIR) spectra can be used to probe relative nitrile distances >4.5 A. Our approach is similar in spirit to monitoring structures with fluorescence resonance energy transfer (FRET) using a pair of fluorescent labels or a pair of spin labels in electron spin resonance spectroscopy. The small sizes of nitrile groups make especially valuable probes of sterically confined regions like the inner cores of large biomolecules where other spectroscopic probes do not fit.
authors.affiliation: University of Wisconsin-Madison, Department of Chemistry, 1101 University Avenue, Madison, Wisconsin 53703, USA.
authors.forename: Amber T
authors.initials: AT
authors.lastname: Krummel
authors.forename: Martin T
authors.initials: MT
authors.lastname: Zanni
mesh_terms: D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer; D009570:Nitriles / Q000737:chemistry*; D012997:Solvents; D013055:Spectrophotometry, Infrared / Q000379:methods*; D017550:Spectroscopy, Fourier Transform Infrared; D013113:Spin Labels
chemical_list: D004277:DNA, Single-Stranded; D009570:Nitriles; D012997:Solvents; D013113:Spin Labels; D004247:DNA