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Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules.

Nakano S, Uotani Y, Sato Y, Oka H, Fujii M, Sugimoto N - Nucleic Acids Res. (2013)

Bottom Line: Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases.We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds.The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.

View Article: PubMed Central - PubMed

Affiliation: Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1, Okamoto, Higashinada-ku, Kobe, 658-8501, Japan, Molecular Engineering Institute (MEI), Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan and Department of Environmental and Biological Chemistry, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan.

ABSTRACT
DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2'-deoxyadenosine and 2'-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2'-deoxycytidine lesions form the base pair with guanine while the 2'-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.

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(A) Rate constants for the KMnO4 oxidation of thymines opposite dAphe or dAnaph in AXA or TXT in the absence (−) and presence of netropsin (net) or distamycin (dst). (B) Chemical structure of a synthetic polyamide, Abu-Py-Py-Py. (C) PAGE for the KMnO4 oxidation of thymines opposite dAphe in AXA or TXT in the absence (−) or presence (+) of Abu-Py-Py-Py. (D) A pictorial representation of the base pairing between the 2′-deoxyadenosine lesions (R represents a phenylcarbamoyl or naphthylcarbamoyl group) and thymine in a DNA duplex, stabilized by interactions with a minor grove binding molecule.
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gkt608-F7: (A) Rate constants for the KMnO4 oxidation of thymines opposite dAphe or dAnaph in AXA or TXT in the absence (−) and presence of netropsin (net) or distamycin (dst). (B) Chemical structure of a synthetic polyamide, Abu-Py-Py-Py. (C) PAGE for the KMnO4 oxidation of thymines opposite dAphe in AXA or TXT in the absence (−) or presence (+) of Abu-Py-Py-Py. (D) A pictorial representation of the base pairing between the 2′-deoxyadenosine lesions (R represents a phenylcarbamoyl or naphthylcarbamoyl group) and thymine in a DNA duplex, stabilized by interactions with a minor grove binding molecule.

Mentions: The DNA duplexes, AXA and TXT, offer the binding sites for netropsin and distamycin if the 2′-deoxyadenosine lesions form the base pair with thymine. The binding to the duplexes was confirmed by the DNase I footprinting experiments, and the melting temperature increased by ∼10°C after the addition of netropsin or distamycin at 10 µM. We found that these compounds reduced the efficiency of the KMnO4 oxidation of thymines opposite dAphe and dAnaph in AXA and TXT, whereas the reduction was not observed with GXG and CXC that did not have consecutive dA/dT base pairs (Supplementary Figure S6). The experiments using CMCT also gave the same results (data not shown). Figure 7A shows that netropsin more effectively reduced the oxidation efficiency than distamycin, consistent with its higher binding capacity to a target DNA (37). Moreover, a synthetic polyamide, Abu-Py-Py-Py, comprising three pyrrole rings with a positive charge presented in Figure 7B, which was designed to bind to consecutive dA/dT base pair sites (38,39), also reduced the oxidation efficiency of AXA and TXT (Figure 7C). It can be concluded that the conformation of thymine opposite the 2′-deoxyadenosine lesions changes owing to the interactions with the minor groove-binding molecules (Figure 7D).Figure 7.


Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules.

Nakano S, Uotani Y, Sato Y, Oka H, Fujii M, Sugimoto N - Nucleic Acids Res. (2013)

(A) Rate constants for the KMnO4 oxidation of thymines opposite dAphe or dAnaph in AXA or TXT in the absence (−) and presence of netropsin (net) or distamycin (dst). (B) Chemical structure of a synthetic polyamide, Abu-Py-Py-Py. (C) PAGE for the KMnO4 oxidation of thymines opposite dAphe in AXA or TXT in the absence (−) or presence (+) of Abu-Py-Py-Py. (D) A pictorial representation of the base pairing between the 2′-deoxyadenosine lesions (R represents a phenylcarbamoyl or naphthylcarbamoyl group) and thymine in a DNA duplex, stabilized by interactions with a minor grove binding molecule.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3794578&req=5

gkt608-F7: (A) Rate constants for the KMnO4 oxidation of thymines opposite dAphe or dAnaph in AXA or TXT in the absence (−) and presence of netropsin (net) or distamycin (dst). (B) Chemical structure of a synthetic polyamide, Abu-Py-Py-Py. (C) PAGE for the KMnO4 oxidation of thymines opposite dAphe in AXA or TXT in the absence (−) or presence (+) of Abu-Py-Py-Py. (D) A pictorial representation of the base pairing between the 2′-deoxyadenosine lesions (R represents a phenylcarbamoyl or naphthylcarbamoyl group) and thymine in a DNA duplex, stabilized by interactions with a minor grove binding molecule.
Mentions: The DNA duplexes, AXA and TXT, offer the binding sites for netropsin and distamycin if the 2′-deoxyadenosine lesions form the base pair with thymine. The binding to the duplexes was confirmed by the DNase I footprinting experiments, and the melting temperature increased by ∼10°C after the addition of netropsin or distamycin at 10 µM. We found that these compounds reduced the efficiency of the KMnO4 oxidation of thymines opposite dAphe and dAnaph in AXA and TXT, whereas the reduction was not observed with GXG and CXC that did not have consecutive dA/dT base pairs (Supplementary Figure S6). The experiments using CMCT also gave the same results (data not shown). Figure 7A shows that netropsin more effectively reduced the oxidation efficiency than distamycin, consistent with its higher binding capacity to a target DNA (37). Moreover, a synthetic polyamide, Abu-Py-Py-Py, comprising three pyrrole rings with a positive charge presented in Figure 7B, which was designed to bind to consecutive dA/dT base pair sites (38,39), also reduced the oxidation efficiency of AXA and TXT (Figure 7C). It can be concluded that the conformation of thymine opposite the 2′-deoxyadenosine lesions changes owing to the interactions with the minor groove-binding molecules (Figure 7D).Figure 7.

Bottom Line: Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases.We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds.The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.

View Article: PubMed Central - PubMed

Affiliation: Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1, Okamoto, Higashinada-ku, Kobe, 658-8501, Japan, Molecular Engineering Institute (MEI), Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan and Department of Environmental and Biological Chemistry, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan.

ABSTRACT
DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2'-deoxyadenosine and 2'-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2'-deoxycytidine lesions form the base pair with guanine while the 2'-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.

Show MeSH
Related in: MedlinePlus