Affinity and kinetic modulation of polyamide-DNA interactions by N-modification of the heterocycles
Synthetic N‐methyl imidazole and N‐pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules t...
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| Published in: | Biopolymers Vol. 99; no. 8; pp. 497 - 507 |
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| Main Authors: | , , , , , , , , , , , , , , |
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01-08-2013
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| Abstract | Synthetic N‐methyl imidazole and N‐pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f‐ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5′‐ACGCGT‐3′. The synthesis and biophysical characterization of six f‐ImPy*Im were determined by CD, ΔTM, DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f‐ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5′‐ACGCGT‐3′, and with strong affinity, Keq = 2.8 × 108 M−1 and Keq = 6.2 × 107 M−1, respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 497–507, 2013. |
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| AbstractList | Synthetic N‐methyl imidazole and N‐pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f‐ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5′‐ACGCGT‐3′. The synthesis and biophysical characterization of six f‐ImPy*Im were determined by CD, ΔTM, DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f‐ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5′‐ACGCGT‐3′, and with strong affinity, Keq = 2.8 × 108 M−1 and Keq = 6.2 × 107 M−1, respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 497–507, 2013. Synthetic N‐methyl imidazole and N‐pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f‐ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5′‐ACGCGT‐3′. The synthesis and biophysical characterization of six f‐ImPy*Im were determined by CD, ΔT M , DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f‐ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5′‐ACGCGT‐3′, and with strong affinity, K eq = 2.8 × 10 8 M −1 and K eq = 6.2 × 10 7 M −1 , respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 497–507, 2013. Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form "stacked" dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f-ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5'-ACGCGT-3'. The synthesis and biophysical characterization of six f-ImPy*Im were determined by CD, ΔTM, DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f-ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5'-ACGCGT-3', and with strong affinity, Keq = 2.8 × 10(8) M(-1) and Keq = 6.2 × 10(7) M(-1), respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f-ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5′-ACGCGT-3′. The synthesis and biophysical characterization of six f-ImPy*Im were determined by CD, ΔT M , DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f-ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5′-ACGCGT-3′, and with strong affinity, K eq = 2.8 × 10 8 M −1 and K eq = 6.2 × 10 7 M −1 , respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form "stacked" dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f-ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5'-ACGCGT-3'. The synthesis and biophysical characterization of six f-ImPy*Im were determined by CD, Delta T sub(M), DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f-ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5'-ACGCGT-3', and with strong affinity, K sub(eq) = 2.8 10 super(8) M super(-1) and K sub(eq) = 6.2 10 super(7) M super(-1), respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. [copy 2013 Wiley Periodicals, Inc. Biopolymers 99: 497-507, 2013. |
| Author | Wang, Shuo Lee, Megan Babu, Balaji Lin, Shicai Liu, Yang Tzou, Samuel Savagian, Mia Hartley, John A. Ferguson, Amanda Kiakos, Konstantinos Wilson, W. David Ramos, Joseph P. Chavda, Sameer Plaunt, Adam Lee, Moses |
| AuthorAffiliation | 2 Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423 3 Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK 1 Department of Chemistry, Georgia State University, Atlanta, GA 30303 |
| AuthorAffiliation_xml | – name: 2 Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423 – name: 1 Department of Chemistry, Georgia State University, Atlanta, GA 30303 – name: 3 Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK |
| Author_xml | – sequence: 1 givenname: Joseph P. surname: Ramos fullname: Ramos, Joseph P. organization: Department of Chemistry, Georgia State University, GA, 30303, Atlanta – sequence: 2 givenname: Balaji surname: Babu fullname: Babu, Balaji organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 3 givenname: Sameer surname: Chavda fullname: Chavda, Sameer organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 4 givenname: Yang surname: Liu fullname: Liu, Yang organization: Department of Chemistry, Georgia State University, GA, 30303, Atlanta – sequence: 5 givenname: Adam surname: Plaunt fullname: Plaunt, Adam organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 6 givenname: Amanda surname: Ferguson fullname: Ferguson, Amanda organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 7 givenname: Mia surname: Savagian fullname: Savagian, Mia organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 8 givenname: Megan surname: Lee fullname: Lee, Megan organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 9 givenname: Samuel surname: Tzou fullname: Tzou, Samuel organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 10 givenname: Shicai surname: Lin fullname: Lin, Shicai organization: Cancer Research, UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O' Gorman Building, 72 Huntley Street, WCIE 6BT, London, UK – sequence: 11 givenname: Konstantinos surname: Kiakos fullname: Kiakos, Konstantinos organization: Cancer Research, UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O' Gorman Building, 72 Huntley Street, WCIE 6BT, London, UK – sequence: 12 givenname: Shuo surname: Wang fullname: Wang, Shuo organization: Department of Chemistry, Georgia State University, GA, 30303, Atlanta – sequence: 13 givenname: Moses surname: Lee fullname: Lee, Moses email: wdw@gsu.edu organization: Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI, 49423 – sequence: 14 givenname: John A. surname: Hartley fullname: Hartley, John A. organization: Cancer Research, UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O' Gorman Building, 72 Huntley Street, WCIE 6BT, London, UK – sequence: 15 givenname: W. David surname: Wilson fullname: Wilson, W. David email: wdw@gsu.edu organization: Department of Chemistry, Georgia State University, GA, 30303, Atlanta |
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| Cites_doi | 10.1073/pnas.86.15.5723 10.1021/bi102028a 10.1016/S1074-5521(97)90243-X 10.1016/j.ymeth.2006.09.009 10.1016/S0968-0896(01)00262-0 10.1158/1535-7163.MCT-08-0130 10.1093/oso/9780198558972.001.0001 10.1021/ja044359p 10.1093/nar/gki238 10.1016/S0378-1119(98)00094-8 10.1016/j.bbrc.2010.12.073 10.1021/ja01145a113 10.1021/bc980008m 10.1021/bi061245c 10.1021/bi000474a 10.1021/ja00160a016 10.1097/CAD.0b013e328334d8f9 10.1158/1535-7163.MCT-06-0503 10.1002/1097-0282(1999)52:4<197::AID-BIP1004>3.0.CO;2-U 10.1093/nass/nrp035 10.1073/pnas.0906532106 10.1080/00397910701648785 10.2174/1568011054222346 10.1021/bi201010g 10.1016/j.antiviral.2011.05.014 10.4155/fmc.12.52 10.1016/S0959-440X(97)80051-6 10.1016/S0959-440X(03)00081-2 10.1021/ar0101032 10.1016/j.bmc.2011.12.010 10.1021/ar030287f 10.1107/S0907444998012475 10.1016/S1367-5931(99)00027-7 10.1073/pnas.88.16.7155 10.1038/sj.onc.1205914 10.1021/ja016154b |
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| Snippet | Synthetic N‐methyl imidazole and N‐pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA... Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form "stacked" dimers can be programmed to target and bind to specific DNA... Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA... |
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| SubjectTerms | ACGCGT Base Sequence binding affinity cell-cycle box Circular Dichroism diamino dicationic DNA DNA - chemistry gene control imidazole kinetics MCB minor groove binder Mlu1 Nylons polyamides pyrrole sequence selectivity Surface Plasmon Resonance |
| Title | Affinity and kinetic modulation of polyamide-DNA interactions by N-modification of the heterocycles |
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