Sequence-Selective Recognition of Duplex DNA through Covalent Interstrand Cross-Linking: Kinetic and Molecular Modeling Studies with Pyrrolobenzodiazepine Dimers
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- 作者：Melissa Smellie ; Deravander S. Bose ; Andrew S. Thompson ; Terence C. Jenkins ; John A. Hartley ; and David E. Thurston
- 刊名：Biochemistry
- 出版年：2003
- 出版时间：July 15, 2003
- 年：2003
- 卷：42
- 期：27
- 页码：8232 - 8239
- 全文大小：295K
- 年卷期：v.42,no.27(July 15, 2003)
- ISSN：1520-4995
文摘
Members of a homologous series of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimers withC8-O-(CH2)n-O-C8' diether linkages (n = 3-6 for 2a-d, respectively) have been studied for their abilityto interact with oligonucleotide duplexes containing potential target binding sites. The results confirmearlier predictions that the n = 3 analogue (2a, DSB-120) will covalently bind to a 5'-Pu-GATC-Py sequenceby cross-linking opposite-strand guanines separated by 2 bp. Preference for this DNA sequence is shownusing oligonucleotides with altered bases between and/or flanking these guanines. The more extendedPBD dimer 2c (n = 5) can span an extra base pair and cross-link the 5'-Pu-GA(T/A)TC-Py sequence. Theability of each homologue to cross-link linear plasmid DNA has been determined, with a rank order thatcorrelates with the reported order of in vitro cytotoxicity: n = 3 (2a) > n = 5 (2c) > n = 6 (2d) > n= 4 (2b). The n = 3 homologue (2a) is >300-fold more efficient at cross-linking DNA than the clinicallyused cross-linking agent melphalan under the same conditions. Kinetic studies reveal that the n = 3 and5 dimers achieve faster cross-linking to plasmid DNA (108 and 81% cross-linking h-1 
M-1 at 37 
C,respectively), whereas the n = 4 and 6 homologues are significantly less efficient at 10.3 and 23% cross-linking h-1 M-1, respectively. Alternating activity for the odd n and even n dimers is probably due toconfigurational factors governed by the spatial separation of the PBD subunits and the flexible characterof the tethering linkage. Molecular modeling confirms the order of cross-linking reactivity, and highlightsthe role of linker length in dictating sequence recognition for this class of DNA-reactive agent.
M-1 at 37 C,respectively), whereas the n = 4 and 6 homologues are significantly less efficient at 10.3 and 23% cross-linking h-1 M-1, respectively. Alternating activity for the odd n and even n dimers is probably due toconfigurational factors governed by the spatial separation of the PBD subunits and the flexible characterof the tethering linkage. Molecular modeling confirms the order of cross-linking reactivity, and highlightsthe role of linker length in dictating sequence recognition for this class of DNA-reactive agent.