Effect of oligomer length on vibrational coupling and energy relaxation in double-stranded DNA

Gordon Hithell, Paul M. Donaldson, Gregory M. Greetham, Michael Towrie, Anthony W. Parker, Glenn Burley, Neil T. Hunt

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The effect of oligomer length on the vibrational mode coupling and energy relaxation mechanisms of AT-rich DNA oligomers in double- and single-stranded conformations has been investigated using two-dimensional infrared spectroscopy. Vibrational coupling of modes of the DNA bases to the symmetric stretching vibration of the backb one phosphate group was observed for oligomers long enough to form duplex-DNA structures. The coupling was lost upon melting of the duplex. No significant effect of oligomer length or DNA secondary structure was found on either the timescale for vibrational relaxation of the base modes or the mechanism, which was consistent with a cascade process from base modes to intermediate modes, some of which are located on the deoxyribose group, and subsequently to the phosphate backbone. The study shows that vibrational coupling between base and backbone requires formation of the double-helix structure while vibrational energy management is an inherent property of the nucleotide.
LanguageEnglish
Number of pages24
JournalChemical Physics
Early online date19 Dec 2017
DOIs
Publication statusE-pub ahead of print - 19 Dec 2017

Fingerprint

oligomers
Oligomers
deoxyribonucleic acid
DNA
phosphates
Phosphates
Deoxyribose
energy
nucleotides
Energy management
molecular relaxation
helices
coupled modes
Stretching
Conformations
Infrared spectroscopy
vibration mode
cascades
Melting
Nucleotides

Keywords

  • ultrafast spectoscopy
  • infrared
  • DNA
  • vibrational relaxation
  • vibrational coupling

Cite this

Hithell, Gordon ; Donaldson, Paul M. ; Greetham, Gregory M. ; Towrie, Michael ; Parker, Anthony W. ; Burley, Glenn ; Hunt, Neil T. / Effect of oligomer length on vibrational coupling and energy relaxation in double-stranded DNA. In: Chemical Physics. 2017.
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abstract = "The effect of oligomer length on the vibrational mode coupling and energy relaxation mechanisms of AT-rich DNA oligomers in double- and single-stranded conformations has been investigated using two-dimensional infrared spectroscopy. Vibrational coupling of modes of the DNA bases to the symmetric stretching vibration of the backb one phosphate group was observed for oligomers long enough to form duplex-DNA structures. The coupling was lost upon melting of the duplex. No significant effect of oligomer length or DNA secondary structure was found on either the timescale for vibrational relaxation of the base modes or the mechanism, which was consistent with a cascade process from base modes to intermediate modes, some of which are located on the deoxyribose group, and subsequently to the phosphate backbone. The study shows that vibrational coupling between base and backbone requires formation of the double-helix structure while vibrational energy management is an inherent property of the nucleotide.",
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author = "Gordon Hithell and Donaldson, {Paul M.} and Greetham, {Gregory M.} and Michael Towrie and Parker, {Anthony W.} and Glenn Burley and Hunt, {Neil T.}",
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Effect of oligomer length on vibrational coupling and energy relaxation in double-stranded DNA. / Hithell, Gordon; Donaldson, Paul M.; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Burley, Glenn; Hunt, Neil T.

In: Chemical Physics, 19.12.2017.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Effect of oligomer length on vibrational coupling and energy relaxation in double-stranded DNA

AU - Hithell, Gordon

AU - Donaldson, Paul M.

AU - Greetham, Gregory M.

AU - Towrie, Michael

AU - Parker, Anthony W.

AU - Burley, Glenn

AU - Hunt, Neil T.

PY - 2017/12/19

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N2 - The effect of oligomer length on the vibrational mode coupling and energy relaxation mechanisms of AT-rich DNA oligomers in double- and single-stranded conformations has been investigated using two-dimensional infrared spectroscopy. Vibrational coupling of modes of the DNA bases to the symmetric stretching vibration of the backb one phosphate group was observed for oligomers long enough to form duplex-DNA structures. The coupling was lost upon melting of the duplex. No significant effect of oligomer length or DNA secondary structure was found on either the timescale for vibrational relaxation of the base modes or the mechanism, which was consistent with a cascade process from base modes to intermediate modes, some of which are located on the deoxyribose group, and subsequently to the phosphate backbone. The study shows that vibrational coupling between base and backbone requires formation of the double-helix structure while vibrational energy management is an inherent property of the nucleotide.

AB - The effect of oligomer length on the vibrational mode coupling and energy relaxation mechanisms of AT-rich DNA oligomers in double- and single-stranded conformations has been investigated using two-dimensional infrared spectroscopy. Vibrational coupling of modes of the DNA bases to the symmetric stretching vibration of the backb one phosphate group was observed for oligomers long enough to form duplex-DNA structures. The coupling was lost upon melting of the duplex. No significant effect of oligomer length or DNA secondary structure was found on either the timescale for vibrational relaxation of the base modes or the mechanism, which was consistent with a cascade process from base modes to intermediate modes, some of which are located on the deoxyribose group, and subsequently to the phosphate backbone. The study shows that vibrational coupling between base and backbone requires formation of the double-helix structure while vibrational energy management is an inherent property of the nucleotide.

KW - ultrafast spectoscopy

KW - infrared

KW - DNA

KW - vibrational relaxation

KW - vibrational coupling

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SN - 0301-0104

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