Nuclear magnetic resonance solution structure of an undecanucleotide duplex with a complementary thymidine base opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene

Eric J. Schurter, Jane M. Sayer, Toshinari Oh-hara, Herman J C Yeh, Haruhiko Yagi, Bruce A. Luxon, Donald M. Jerina, David G. Gorenstein

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    Abstract

    The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene covalently bonded through trans ring opening at C10 of the epoxide by the N6-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C1G2G3T4C5A* 6C7G8A9G10G 11)·d(C12C13T14C 15G16T17G18A19C 20C21G22) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.

    Original languageEnglish (US)
    Pages (from-to)9009-9020
    Number of pages12
    JournalBiochemistry
    Volume34
    Issue number28
    StatePublished - 1995

    Fingerprint

    7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
    Thymidine
    Magnetic Resonance Spectroscopy
    Nuclear magnetic resonance
    Hydrocarbons
    Epoxy Compounds
    Protons
    Base Pairing
    Chirality
    Chemical shift
    Molecular Dynamics Simulation
    Sugars
    Hydroxyl Radical
    Nuclear magnetic resonance spectroscopy
    Molecular dynamics
    2'-deoxyadenosine
    Nucleotides
    Oxygen
    Water

    ASJC Scopus subject areas

    • Biochemistry

    Cite this

    Nuclear magnetic resonance solution structure of an undecanucleotide duplex with a complementary thymidine base opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. / Schurter, Eric J.; Sayer, Jane M.; Oh-hara, Toshinari; Yeh, Herman J C; Yagi, Haruhiko; Luxon, Bruce A.; Jerina, Donald M.; Gorenstein, David G.

    In: Biochemistry, Vol. 34, No. 28, 1995, p. 9009-9020.

    Research output: Contribution to journalArticle

    Schurter, Eric J. ; Sayer, Jane M. ; Oh-hara, Toshinari ; Yeh, Herman J C ; Yagi, Haruhiko ; Luxon, Bruce A. ; Jerina, Donald M. ; Gorenstein, David G. / Nuclear magnetic resonance solution structure of an undecanucleotide duplex with a complementary thymidine base opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. In: Biochemistry. 1995 ; Vol. 34, No. 28. pp. 9009-9020.
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    abstract = "The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene covalently bonded through trans ring opening at C10 of the epoxide by the N6-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C1G2G3T4C5A* 6C7G8A9G10G 11)·d(C12C13T14C 15G16T17G18A19C 20C21G22) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.",
    author = "Schurter, {Eric J.} and Sayer, {Jane M.} and Toshinari Oh-hara and Yeh, {Herman J C} and Haruhiko Yagi and Luxon, {Bruce A.} and Jerina, {Donald M.} and Gorenstein, {David G.}",
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    T1 - Nuclear magnetic resonance solution structure of an undecanucleotide duplex with a complementary thymidine base opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene

    AU - Schurter, Eric J.

    AU - Sayer, Jane M.

    AU - Oh-hara, Toshinari

    AU - Yeh, Herman J C

    AU - Yagi, Haruhiko

    AU - Luxon, Bruce A.

    AU - Jerina, Donald M.

    AU - Gorenstein, David G.

    PY - 1995

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    N2 - The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene covalently bonded through trans ring opening at C10 of the epoxide by the N6-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C1G2G3T4C5A* 6C7G8A9G10G 11)·d(C12C13T14C 15G16T17G18A19C 20C21G22) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.

    AB - The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene covalently bonded through trans ring opening at C10 of the epoxide by the N6-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C1G2G3T4C5A* 6C7G8A9G10G 11)·d(C12C13T14C 15G16T17G18A19C 20C21G22) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.

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