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Fick RJ, Liu AY, Nussbaumer F, Kreutz C, Rangadurai A, Xu Y, Sommer RD, Shi H, Scheiner S, Stelling AL. Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy. J Phys Chem B 2021; 125:7613-7627. [PMID: 34236202 PMCID: PMC8311644 DOI: 10.1021/acs.jpcb.1c01351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
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Measuring the strength
of the hydrogen bonds between DNA base pairs
is of vital importance for understanding how our genetic code is physically
accessed and recognized in cells, particularly during replication
and transcription. Therefore, it is important to develop probes for
these key hydrogen bonds (H-bonds) that dictate events critical to
cellular function, such as the localized melting of DNA. The vibrations
of carbonyl bonds are well-known probes of their H-bonding environment,
and their signals can be observed with infrared (IR) spectroscopy.
Yet, pinpointing a single bond of interest in the complex IR spectrum
of DNA is challenging due to the large number of carbonyl signals
that overlap with each other. Here, we develop a method using isotope
editing and infrared (IR) spectroscopy to isolate IR signals from
the thymine (T) C2=O carbonyl. We use solvatochromatic studies
to show that the TC2=O signal’s position in the IR spectrum
is sensitive to the H-bonding capacity of the solvent. Our results
indicate that C2=O of a single T base within DNA duplexes experiences
weak H-bonding interactions. This finding is consistent with the existence
of a third, noncanonical CH···O H-bond between adenine
and thymine in both Watson–Crick and Hoogsteen base pairs in
DNA.
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Affiliation(s)
- Robert J Fick
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Amy Y Liu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Atul Rangadurai
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Roger D Sommer
- Molecular Education, Technology, and Research Innovation Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States.,Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
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