Probing The Contributions To Dna Hybridization Dynamics With Time-Resolved Infrared Spectroscopy

DNA can undergo a diverse set of folding and hybridization transitions of which the energetics and dynamics are highly sensitive to the local solution environment as well as nucleobase chemical modifications. Such sensitivity is used to perform various biological functions and can fuel many nanotechnology applications. However, the physical properties of folding and hybridization reactions that underly these applications often remain poorly understood. DNA folding and hybridization is complicated by many fast structural motions, such as fraying and sliding, and therefore investigation of DNA folding and hybridization requires the ability to probe DNA structure across both fast (ns-µs) and slow (ms-s) timescales. infrared (IR) spectroscopy offers the capability to probe dynamics from ultrafast timescales to seconds with nucleobase-specific information. Along these lines our group has developed temperature-jump (T-jump) IR and two-dimensional IR (2D IR) methods that can monitor DNA interactions from nanoseconds to many seconds. We are investigating DNA unfolding and duplex dehybridization and how they are modulated by nucleobase sequence, chemical modifications, and nucleobase protonation using T-jump IR spectroscopy. Recently, we have found that the modified nucleobases 5-formyl- and 5-carboxylcytosine can alter DNA base pairing and hybridization with great sensitivity to solution pH. Our results provide insight into a complex interplay between sequence, chemical modification, and sequence that may tune DNA hybridization dynamics.