Slow Rotational Dynamics of Cytosine NH2Groups in Double-Stranded DNA

Xi Wang; Binhan Yu; Junji Iwahara

doi:10.1021/acs.biochem.2c00299

Slow Rotational Dynamics of Cytosine NH₂Groups in Double-Stranded DNA

Xi Wang, Binhan Yu, Junji Iwahara

Biochemistry & Molecular Biology

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Aromatic NH₂groups are essential as hydrogen-bond donors in secondary structures of DNA and RNA. Although rapid rotations of NH₂groups of adenine and guanine bases were previously characterized, there has been a lack of quantitative information about slow rotations of cytosine NH₂groups in Watson-Crick base pairs. In this study, using an NMR method we had recently developed, we determined the kinetic rate constants and energy barriers for cytosine NH₂rotations in a 15-base-pair DNA duplex. Our data show that the rotational dynamics of cytosine NH₂groups depend on local environments. Qualitative correlation between the ranges of ¹⁵N chemical shifts and rotational time scales for various NH₂groups of nucleic acids and proteins illuminates a relationship between the partial double-bond character of the C-N bond and the time scale for NH₂rotations.

Original language	English (US)
Pages (from-to)	1415-1418
Number of pages	4
Journal	Biochemistry
Volume	61
Issue number	14
DOIs	https://doi.org/10.1021/acs.biochem.2c00299
State	Published - Jul 19 2022

ASJC Scopus subject areas

Biochemistry

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10.1021/acs.biochem.2c00299

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title = "Slow Rotational Dynamics of Cytosine NH2Groups in Double-Stranded DNA",

abstract = "Aromatic NH2groups are essential as hydrogen-bond donors in secondary structures of DNA and RNA. Although rapid rotations of NH2groups of adenine and guanine bases were previously characterized, there has been a lack of quantitative information about slow rotations of cytosine NH2groups in Watson-Crick base pairs. In this study, using an NMR method we had recently developed, we determined the kinetic rate constants and energy barriers for cytosine NH2rotations in a 15-base-pair DNA duplex. Our data show that the rotational dynamics of cytosine NH2groups depend on local environments. Qualitative correlation between the ranges of 15N chemical shifts and rotational time scales for various NH2groups of nucleic acids and proteins illuminates a relationship between the partial double-bond character of the C-N bond and the time scale for NH2rotations.",

author = "Xi Wang and Binhan Yu and Junji Iwahara",

note = "Funding Information: This work was supported by Grant R35-GM130326 from the National Institutes of Health and Grant H-2104-20220331 from the Welch Foundation. We thank Karina Bien for language editing. Publisher Copyright: {\textcopyright} 2022 American Chemical Society. All rights reserved.",

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T1 - Slow Rotational Dynamics of Cytosine NH2Groups in Double-Stranded DNA

AU - Wang, Xi

AU - Yu, Binhan

AU - Iwahara, Junji

N1 - Funding Information: This work was supported by Grant R35-GM130326 from the National Institutes of Health and Grant H-2104-20220331 from the Welch Foundation. We thank Karina Bien for language editing. Publisher Copyright: © 2022 American Chemical Society. All rights reserved.

PY - 2022/7/19

Y1 - 2022/7/19

N2 - Aromatic NH2groups are essential as hydrogen-bond donors in secondary structures of DNA and RNA. Although rapid rotations of NH2groups of adenine and guanine bases were previously characterized, there has been a lack of quantitative information about slow rotations of cytosine NH2groups in Watson-Crick base pairs. In this study, using an NMR method we had recently developed, we determined the kinetic rate constants and energy barriers for cytosine NH2rotations in a 15-base-pair DNA duplex. Our data show that the rotational dynamics of cytosine NH2groups depend on local environments. Qualitative correlation between the ranges of 15N chemical shifts and rotational time scales for various NH2groups of nucleic acids and proteins illuminates a relationship between the partial double-bond character of the C-N bond and the time scale for NH2rotations.

AB - Aromatic NH2groups are essential as hydrogen-bond donors in secondary structures of DNA and RNA. Although rapid rotations of NH2groups of adenine and guanine bases were previously characterized, there has been a lack of quantitative information about slow rotations of cytosine NH2groups in Watson-Crick base pairs. In this study, using an NMR method we had recently developed, we determined the kinetic rate constants and energy barriers for cytosine NH2rotations in a 15-base-pair DNA duplex. Our data show that the rotational dynamics of cytosine NH2groups depend on local environments. Qualitative correlation between the ranges of 15N chemical shifts and rotational time scales for various NH2groups of nucleic acids and proteins illuminates a relationship between the partial double-bond character of the C-N bond and the time scale for NH2rotations.

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Slow Rotational Dynamics of Cytosine NH₂Groups in Double-Stranded DNA

Abstract

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