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Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors.

Mukherjee S, Guainazzi A, Schärer OD - Nucleic Acids Res. (2014)

Bottom Line: Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs.We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation.Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.

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Models of structures of nitrogen mustard ICLs. A. C1/C2/HY ICL isosteric to a native nitrogen mustard ICL with a bridge length of 7.2 Å inducing a 20° bend in the DNA as predicted by molecular modeling studies (22); B. C2/C3/NH3 ICL with a bridge length of 8.4 Å, inducing a distortion in the DNA. C. C3/C3/NH3 ICL with a bridge length of 9.6 Å without DNA distortion. The structure in (A) was calculated using molecular dynamic simulations (22), (B) and (C) were manually generated using VMD 1.9 (42).
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Figure 6: Models of structures of nitrogen mustard ICLs. A. C1/C2/HY ICL isosteric to a native nitrogen mustard ICL with a bridge length of 7.2 Å inducing a 20° bend in the DNA as predicted by molecular modeling studies (22); B. C2/C3/NH3 ICL with a bridge length of 8.4 Å, inducing a distortion in the DNA. C. C3/C3/NH3 ICL with a bridge length of 9.6 Å without DNA distortion. The structure in (A) was calculated using molecular dynamic simulations (22), (B) and (C) were manually generated using VMD 1.9 (42).

Mentions: We used oligonucleotides with 7-deazaguanine residues having alkyl aldehyde chains of different lengths (C1, C2, C3) at the 7 position and studied ICL formation with ammonia, hydrazine and DMEDA using a reductive amination reaction. The efficiency of ICL formation was found to be correlated with the length of the ICL and the reactivity of the amine (summarized in Figure 5). We were able to form ICLs with bridge lengths ranging from 7.2 Å, for which our molecular modeling studies predict a bend of about 20° in the DNA duplex (22), to those of 10.8 Å and more, which our preliminary nuclear magnetic resonance (NMR) experiments show are free of distortion (AG, T. Zaliznyak, C. de los Santos, ODS, unpublished data). ICL formation was found to be most efficient with nondistorting ICLs (10.8–13.2 Å), followed by those with minor (8.4–9.6 Å) and moderate distortion (7.2–8.4 Å) (Figure 5). The higher nucleophilicity and reactivity of hydrazine allowed for the formation of more distorted ICLs. The major groove ICLs reported here inducing no, minor and moderate distortion in DNA duplexes (Figure 6) will be invaluable for advancing studies elucidating structure–function relationships in ICL repair.


Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors.

Mukherjee S, Guainazzi A, Schärer OD - Nucleic Acids Res. (2014)

Models of structures of nitrogen mustard ICLs. A. C1/C2/HY ICL isosteric to a native nitrogen mustard ICL with a bridge length of 7.2 Å inducing a 20° bend in the DNA as predicted by molecular modeling studies (22); B. C2/C3/NH3 ICL with a bridge length of 8.4 Å, inducing a distortion in the DNA. C. C3/C3/NH3 ICL with a bridge length of 9.6 Å without DNA distortion. The structure in (A) was calculated using molecular dynamic simulations (22), (B) and (C) were manually generated using VMD 1.9 (42).
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Figure 6: Models of structures of nitrogen mustard ICLs. A. C1/C2/HY ICL isosteric to a native nitrogen mustard ICL with a bridge length of 7.2 Å inducing a 20° bend in the DNA as predicted by molecular modeling studies (22); B. C2/C3/NH3 ICL with a bridge length of 8.4 Å, inducing a distortion in the DNA. C. C3/C3/NH3 ICL with a bridge length of 9.6 Å without DNA distortion. The structure in (A) was calculated using molecular dynamic simulations (22), (B) and (C) were manually generated using VMD 1.9 (42).
Mentions: We used oligonucleotides with 7-deazaguanine residues having alkyl aldehyde chains of different lengths (C1, C2, C3) at the 7 position and studied ICL formation with ammonia, hydrazine and DMEDA using a reductive amination reaction. The efficiency of ICL formation was found to be correlated with the length of the ICL and the reactivity of the amine (summarized in Figure 5). We were able to form ICLs with bridge lengths ranging from 7.2 Å, for which our molecular modeling studies predict a bend of about 20° in the DNA duplex (22), to those of 10.8 Å and more, which our preliminary nuclear magnetic resonance (NMR) experiments show are free of distortion (AG, T. Zaliznyak, C. de los Santos, ODS, unpublished data). ICL formation was found to be most efficient with nondistorting ICLs (10.8–13.2 Å), followed by those with minor (8.4–9.6 Å) and moderate distortion (7.2–8.4 Å) (Figure 5). The higher nucleophilicity and reactivity of hydrazine allowed for the formation of more distorted ICLs. The major groove ICLs reported here inducing no, minor and moderate distortion in DNA duplexes (Figure 6) will be invaluable for advancing studies elucidating structure–function relationships in ICL repair.

Bottom Line: Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs.We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation.Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.

Show MeSH
Related in: MedlinePlus