Studies of the structure and ultrafast dynamics of DNA using 2D-IR spectroscopy

In this thesis, two-dimensional infrared spectroscopy (2D-IR) spectroscopy is used to study changes in structure and dynamics in deoxyribonucleic acid (DNA) containing only Adenine-Thymine (AT) base pairs. The aims of the studies in this thesis are to demonstrate the ability of 2D-IR spectroscopy to extract unique dynamic information, not accessible via established experimental methods from nucleic acid systems, as it has for protein- and peptide-based systems. The underlying theory of both linear and nonlinear 2D-IR spectroscopies is described in the initial Chapter, following this the details of the types of information already obtained using these methods from DNA in the current literature is presented.;Chapter (2) describes the experimental setups and methodologies used to acquire the data in this thesis. A description of FTIR spectroscopy as well as the two laser systems used to acquire 2D-IR data (ULTRA and LIFEtime) are presented. In Chapter (3), the thermal denaturation of an AT DNA sequence 15 base pairs in length is studied with 2D-IR in the spectral region where vibrational modes of the DNA bases are observed. Changes in the unique features observed in these spectra that are sensitive to DNA conformation are described along with the suitability of 2D-IR for accurately following the transition from double- to single stranded DNA compared to established methods. Changes in solvation dynamics experienced by functional groups of the DNA bases are also discussed.;Chapter (4) demonstrates the ability of 2D-IR to explore multiple spectral regions simultaneously using a two-colour 2D-IR method. This allowed examination of communication between the vibrational modes of the DNA bases and those of the DNA backbone in the same DNA sequence used in the previous Chapter. Dynamics extracted from the features linking these two spectral regions present evidence for an energy transfer pathway through DNA that could be responsible for allowing dissipation of excess energy absorbed by DNA, preventing photo-damage of sequences. Chapter (5) expands on the studies in the previous Chapter by employing the same experimental methodology to AT DNA sequences of lengths varying from 15 bases pairs to a single base mononucleotide. The changes in observed features that link the base and backbone regions for the different sequences is presented along with the effects varying the sequence length has on the timescales of the energy transfer mechanism described in the previous Chapter.In Chapter (6) the conclusions presented in the Chapters prior to this point are drawn together to highlight progress made in gaining new insights into structure and dynamics of DNA and also presents possible future directions for studying nucleic acid systems with 2D-IR.In this thesis, two-dimensional infrared spectroscopy (2D-IR) spectroscopy is used to study changes in structure and dynamics in deoxyribonucleic acid (DNA) containing only Adenine-Thymine (AT) base pairs. The aims of the studies in this thesis are to demonstrate the ability of 2D-IR spectroscopy to extract unique dynamic information, not accessible via established experimental methods from nucleic acid systems, as it has for protein- and peptide-based systems. The underlying theory of both linear and nonlinear 2D-IR spectroscopies is described in the initial Chapter, following this the details of the types of information already obtained using these methods from DNA in the current literature is presented.;Chapter (2) describes the experimental setups and methodologies used to acquire the data in this thesis. A description of FTIR spectroscopy as well as the two laser systems used to acquire 2D-IR data (ULTRA and LIFEtime) are presented. In Chapter (3), the thermal denaturation of an AT DNA sequence 15 base pairs in length is studied with 2D-IR in the spectral region where vibrational modes of the DNA bases are observed. Changes in the unique features observed in these spectra that are sensitive to DNA conformation are described along with the suitability of 2D-IR for accurately following the transition from double- to single stranded DNA compared to established methods. Changes in solvation dynamics experienced by functional groups of the DNA bases are also discussed.;Chapter (4) demonstrates the ability of 2D-IR to explore multiple spectral regions simultaneously using a two-colour 2D-IR method. This allowed examination of communication between the vibrational modes of the DNA bases and those of the DNA backbone in the same DNA sequence used in the previous Chapter. Dynamics extracted from the features linking these two spectral regions present evidence for an energy transfer pathway through DNA that could be responsible for allowing dissipation of excess energy absorbed by DNA, preventing photo-damage of sequences. Chapter (5) expands on the studies in the previous Chapter by employing the same experimental methodology to AT DNA sequences of lengths varying from 15 bases pairs to a single base mononucleotide. The changes in observed features that link the base and backbone regions for the different sequences is presented along with the effects varying the sequence length has on the timescales of the energy transfer mechanism described in the previous Chapter.In Chapter (6) the conclusions presented in the Chapters prior to this point are drawn together to highlight progress made in gaining new insights into structure and dynamics of DNA and also presents possible future directions for studying nucleic acid systems with 2D-IR