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Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.

Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP - Nucleic Acids Res. (2013)

Bottom Line: The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G(4) has been replaced by O(6)-Bn-dG and cytosine C(9) has been replaced with dPer to form the modified O(6)-Bn-dG:dPer (DDD-XY) duplex [5'-d(C(1)G(2)C(3)X(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 (X = O(6)-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond.This provides a binding pocket that allows the benzyl group of O(6)-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair.In contrast, the structure of the modified DDD in which cytosine at position C(9) is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA.

ABSTRACT
The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O(6)-benzyl-2'-deoxyguanosine nucleoside (O(6)-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O(6)-Bn-dG and dG in DNA. The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G(4) has been replaced by O(6)-Bn-dG and cytosine C(9) has been replaced with dPer to form the modified O(6)-Bn-dG:dPer (DDD-XY) duplex [5'-d(C(1)G(2)C(3)X(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 (X = O(6)-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O(6)-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O(6)-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C(9) is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.

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The NOESY spectrum for the DDD-GY duplex. (a) Interstrand NOEs between complementary bases. The cross-peaks are assigned as a, A5 H2→T8 N3H; b, A6 H2→T8 N3H; c, A6 H1′→T7 N3H; d, A6N6H2→T7 N3H; e, A5 H2→T7 N3H; f, A6 H2→T7 N3H; g, C3N2H1→G10 N1H; h, C3N2H2→G10 N1H; i, C11N2H1→G2 N1H; j, C11N2H2→G2 N1H; k, G4 H1′→Y9 HN; l, Y9 H1′→Y9 HN; m, G4 H1′→G4 N1H; n, Y9 H1′→G4 N1H. (b) NOE connectivity for the imino protons for the base pairs G2:C11, C3:G10, G4:Y9, A5:T8, A5:T7. The cross-peaks are assigned as T8 N3H→T7 N3H, T8 N3H→Y9 HN (p), T8 N3H→G4 N1H (o), Y9 HN→G10 N1H (s), G4 N1H→G10 N1H (r), G2 N1H→G10 N1H and Y9 HN→G4 N1H (u). Cross-peak (t) could not be assigned. The same cross-peak was observed for the DDD-XY duplex (peak k, Supplementary Figure S7). A NOESY experiment at a shorter mixing time of 70 ms showed no change in intensity and suggested that this may be an exchange cross-peak of unknown origin. The experiment was carried out at 5°C and with a mixing time of 250 ms at 600 MHz.
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gkt488-F5: The NOESY spectrum for the DDD-GY duplex. (a) Interstrand NOEs between complementary bases. The cross-peaks are assigned as a, A5 H2→T8 N3H; b, A6 H2→T8 N3H; c, A6 H1′→T7 N3H; d, A6N6H2→T7 N3H; e, A5 H2→T7 N3H; f, A6 H2→T7 N3H; g, C3N2H1→G10 N1H; h, C3N2H2→G10 N1H; i, C11N2H1→G2 N1H; j, C11N2H2→G2 N1H; k, G4 H1′→Y9 HN; l, Y9 H1′→Y9 HN; m, G4 H1′→G4 N1H; n, Y9 H1′→G4 N1H. (b) NOE connectivity for the imino protons for the base pairs G2:C11, C3:G10, G4:Y9, A5:T8, A5:T7. The cross-peaks are assigned as T8 N3H→T7 N3H, T8 N3H→Y9 HN (p), T8 N3H→G4 N1H (o), Y9 HN→G10 N1H (s), G4 N1H→G10 N1H (r), G2 N1H→G10 N1H and Y9 HN→G4 N1H (u). Cross-peak (t) could not be assigned. The same cross-peak was observed for the DDD-XY duplex (peak k, Supplementary Figure S7). A NOESY experiment at a shorter mixing time of 70 ms showed no change in intensity and suggested that this may be an exchange cross-peak of unknown origin. The experiment was carried out at 5°C and with a mixing time of 250 ms at 600 MHz.

Mentions: The sequential NOEs between the base imino protons showed a strong cross-peak between the G4 N1H imino proton and the Y9 dPer imino proton (u, Figure 5b). The sequential connectivity of the base imino protons was thus obtained from base pairs G2:C11→C3:G10→G4:Y9→A5:T8→A6:T7 (Figure 5b). The region of the spectrum showing NOEs between the base imino and amino protons and adenine H2 protons showed cross-peaks for base pairs A5:T8, A6:T7, G2:C11, G10:C3, and it showed that G4 and Y9 formed a base pair (k, l, m, n, Figure 5a). The G10 cross-peak had a similar chemical shift as compared with G2. The G4 N1H and Y9 HN resonances were shifted upfield to 10.2 and 10.7 ppm.Figure 5.


Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.

Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP - Nucleic Acids Res. (2013)

The NOESY spectrum for the DDD-GY duplex. (a) Interstrand NOEs between complementary bases. The cross-peaks are assigned as a, A5 H2→T8 N3H; b, A6 H2→T8 N3H; c, A6 H1′→T7 N3H; d, A6N6H2→T7 N3H; e, A5 H2→T7 N3H; f, A6 H2→T7 N3H; g, C3N2H1→G10 N1H; h, C3N2H2→G10 N1H; i, C11N2H1→G2 N1H; j, C11N2H2→G2 N1H; k, G4 H1′→Y9 HN; l, Y9 H1′→Y9 HN; m, G4 H1′→G4 N1H; n, Y9 H1′→G4 N1H. (b) NOE connectivity for the imino protons for the base pairs G2:C11, C3:G10, G4:Y9, A5:T8, A5:T7. The cross-peaks are assigned as T8 N3H→T7 N3H, T8 N3H→Y9 HN (p), T8 N3H→G4 N1H (o), Y9 HN→G10 N1H (s), G4 N1H→G10 N1H (r), G2 N1H→G10 N1H and Y9 HN→G4 N1H (u). Cross-peak (t) could not be assigned. The same cross-peak was observed for the DDD-XY duplex (peak k, Supplementary Figure S7). A NOESY experiment at a shorter mixing time of 70 ms showed no change in intensity and suggested that this may be an exchange cross-peak of unknown origin. The experiment was carried out at 5°C and with a mixing time of 250 ms at 600 MHz.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3753623&req=5

gkt488-F5: The NOESY spectrum for the DDD-GY duplex. (a) Interstrand NOEs between complementary bases. The cross-peaks are assigned as a, A5 H2→T8 N3H; b, A6 H2→T8 N3H; c, A6 H1′→T7 N3H; d, A6N6H2→T7 N3H; e, A5 H2→T7 N3H; f, A6 H2→T7 N3H; g, C3N2H1→G10 N1H; h, C3N2H2→G10 N1H; i, C11N2H1→G2 N1H; j, C11N2H2→G2 N1H; k, G4 H1′→Y9 HN; l, Y9 H1′→Y9 HN; m, G4 H1′→G4 N1H; n, Y9 H1′→G4 N1H. (b) NOE connectivity for the imino protons for the base pairs G2:C11, C3:G10, G4:Y9, A5:T8, A5:T7. The cross-peaks are assigned as T8 N3H→T7 N3H, T8 N3H→Y9 HN (p), T8 N3H→G4 N1H (o), Y9 HN→G10 N1H (s), G4 N1H→G10 N1H (r), G2 N1H→G10 N1H and Y9 HN→G4 N1H (u). Cross-peak (t) could not be assigned. The same cross-peak was observed for the DDD-XY duplex (peak k, Supplementary Figure S7). A NOESY experiment at a shorter mixing time of 70 ms showed no change in intensity and suggested that this may be an exchange cross-peak of unknown origin. The experiment was carried out at 5°C and with a mixing time of 250 ms at 600 MHz.
Mentions: The sequential NOEs between the base imino protons showed a strong cross-peak between the G4 N1H imino proton and the Y9 dPer imino proton (u, Figure 5b). The sequential connectivity of the base imino protons was thus obtained from base pairs G2:C11→C3:G10→G4:Y9→A5:T8→A6:T7 (Figure 5b). The region of the spectrum showing NOEs between the base imino and amino protons and adenine H2 protons showed cross-peaks for base pairs A5:T8, A6:T7, G2:C11, G10:C3, and it showed that G4 and Y9 formed a base pair (k, l, m, n, Figure 5a). The G10 cross-peak had a similar chemical shift as compared with G2. The G4 N1H and Y9 HN resonances were shifted upfield to 10.2 and 10.7 ppm.Figure 5.

Bottom Line: The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G(4) has been replaced by O(6)-Bn-dG and cytosine C(9) has been replaced with dPer to form the modified O(6)-Bn-dG:dPer (DDD-XY) duplex [5'-d(C(1)G(2)C(3)X(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 (X = O(6)-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond.This provides a binding pocket that allows the benzyl group of O(6)-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair.In contrast, the structure of the modified DDD in which cytosine at position C(9) is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA.

ABSTRACT
The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O(6)-benzyl-2'-deoxyguanosine nucleoside (O(6)-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O(6)-Bn-dG and dG in DNA. The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G(4) has been replaced by O(6)-Bn-dG and cytosine C(9) has been replaced with dPer to form the modified O(6)-Bn-dG:dPer (DDD-XY) duplex [5'-d(C(1)G(2)C(3)X(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 (X = O(6)-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O(6)-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O(6)-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C(9) is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.

Show MeSH
Related in: MedlinePlus