Probing the Impact of Nucleobase Modifications on DNA Dehybridization with Temperature-Jump Infrared Spectroscopy

DNA duplex hybridization is central to biology and nanotechnology and has been the subject of numerous studies over the past decades. Recent findings from experiment and simulation demonstrate that even small oligonucleotides (<20 bp) may undergo complex structural dynamics during hybridization. DNA hybridization is complicated by many fast structural motions, such as fraying and sliding, and therefore its investigation requires the ability to probe DNA structure across both fast (ns-µs) and slow (ms-s) timescales. Along these lines we have developed temperature-jump IR and two-dimensional IR methods that can monitor DNA interactions from nanoseconds to many seconds. We are investigating how DNA dehybridization is modulated by nucleobase sequence, chemical modifications, and nucleobase protonation. Recently, we have found that the modified nucleobases 5formyl and 5carboxylcytosine can alter DNA dehybridization 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.