Molecular Recognition of DNA by Rigid [n]-Polynorbornane-Derived Bifunctional Intercalators: Synthesis and Evaluation of Their Binding Properties
We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are...
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Published in | Journal of medicinal chemistry Vol. 50; no. 10; pp. 2326 - 2340 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
WASHINGTON
American Chemical Society
17.05.2007
Amer Chemical Soc |
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Abstract | We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27° and a binding constant of about 8 μM. 9-Aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding. |
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AbstractList | We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27 degree and a binding constant of about 8 mu M. 9-Aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding. We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27 degrees and a binding constant of about 8 microM. 9-aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding. We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27° and a binding constant of about 8 μM. 9-Aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding. We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27 degrees and a binding constant of about 8 mu M. 9-Aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding. |
Author | Pfeffer, Frederick M Foley, Patrick J Liu, Ligong Waring, Michael J Van Vliet, Liisa D Russell, Richard A Warrener, Ronald N Hollfelder, Florian Ellis, Tom |
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Keywords | ANTITUMOR AGENTS CONSTANTS TRIOSTIN-A AMINO-ACIDS SEQUENCE EQUILIBRIUM COMPLEXES DIACRIDINES UNWINDING ANGLES DITERCALINIUM Molecular rigidity Imide Intercalating agent Acridine derivatives DNA Epoxide Molecular recognition Steric hindrance Stability constant Chemical synthesis |
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Snippet | We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with... |
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SubjectTerms | Acridines - chemical synthesis Acridines - chemistry Amides - chemical synthesis Amides - chemistry Aminoacridines - chemical synthesis Aminoacridines - chemistry Analytical, structural and metabolic biochemistry Biological and medical sciences Chemistry, Medicinal Deoxyribonucleases - chemistry Dialysis DNA - chemistry Dna, deoxyribonucleoproteins Electrophoresis, Gel, Two-Dimensional Fundamental and applied biological sciences. Psychology Intercalating Agents - chemical synthesis Intercalating Agents - chemistry Life Sciences & Biomedicine Medical sciences Miscellaneous Naphthalimides - chemical synthesis Naphthalimides - chemistry Norbornanes - chemical synthesis Norbornanes - chemistry Nucleic acids Pharmacology & Pharmacy Pharmacology. Drug treatments Science & Technology Structure-Activity Relationship |
Title | Molecular Recognition of DNA by Rigid [n]-Polynorbornane-Derived Bifunctional Intercalators: Synthesis and Evaluation of Their Binding Properties |
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