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Zonjić I, Radić Stojković M, Crnolatac I, Tomašić Paić A, Pšeničnik S, Vasilev A, Kandinska M, Mondeshki M, Baluschev S, Landfester K, Glavaš-Obrovac L, Jukić M, Kralj J, Brozovic A, Horvat L, Tumir LM. Styryl dyes with N-Methylpiperazine and N-Phenylpiperazine Functionality: AT-DNA and G-quadruplex binding ligands and theranostic agents. Bioorg Chem 2022; 127:105999. [DOI: 10.1016/j.bioorg.2022.105999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022]
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2
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Velagapudi SP, Vummidi BR, Disney MD. Small molecule chemical probes of microRNA function. Curr Opin Chem Biol 2014; 24:97-103. [PMID: 25500006 DOI: 10.1016/j.cbpa.2014.10.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/27/2014] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as progress is made in understanding small molecule recognition of RNA.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458, United States
| | - Balayeshwanth R Vummidi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458, United States.
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3
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Bahal R, Sahu B, Rapireddy S, Lee CM, Ly DH. Sequence-unrestricted, Watson-Crick recognition of double helical B-DNA by (R)-miniPEG-γPNAs. Chembiochem 2011; 13:56-60. [PMID: 22135012 DOI: 10.1002/cbic.201100646] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
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4
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NIELSEN PE. ChemInform Abstract: Design of Sequence-Specific DNA-Binding Ligands. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/chin.199728282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Zhou CY, Wu YB, Yang P. Synthesis, characterization, and studies on DNA binding of the complex Fe(Sal2dienNO3·H2O). BIOCHEMISTRY (MOSCOW) 2010; 75:505-493. [DOI: 10.1134/s0006297910040152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Biron E, Voyer N. Towards sequence selective DNA binding: design, synthesis and DNA binding studies of novel bis-porphyrin peptidic nanostructures. Org Biomol Chem 2008; 6:2507-15. [DOI: 10.1039/b803281e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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Fujimoto K, Matsuda S, Yoshimura Y, Ami T, Saito I. Reversible photopadlocking on double-stranded DNA. Chem Commun (Camb) 2007:2968-70. [PMID: 17622447 DOI: 10.1039/b707524c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a highly efficient method for reversible photocircularization of oligonucleotide (ODN) on a double-stranded DNA template: 5-carboxyvinyl-2'-deoxyuridine-containing ODN was reversibly circularized around the target sequence of the double-stranded plasmid DNA resulting in formation of a catenated plasmid.
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Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, 923-1292, Japan.
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9
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Liu B, Han Y, Ferdous A, Corey DR, Kodadek T. Transcription activation by a PNA-peptide chimera in a mammalian cell extract. ACTA ACUST UNITED AC 2004; 10:909-16. [PMID: 14583257 DOI: 10.1016/j.chembiol.2003.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Bo Liu
- Center for Biomedical Inventions, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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10
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Toth JL, Price CA, Madsen EC, Handl HL, Hudson SJ, Hubbard RB, Bowen JP, Kiakos K, Hartley JA, Lee M. Sequence selective recognition of DNA by hairpin conjugates of a racemic seco-cyclopropaneindoline-2-benzofurancarboxamide and polyamides. Bioorg Med Chem Lett 2002; 12:2245-8. [PMID: 12127548 DOI: 10.1016/s0960-894x(02)00341-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conjugates of racemic seco-cyclopropaneindoline-2-benzofurancarboxamide (CI-Bf) and four diamides (ImIm 1, ImPy 2, PyIm 3, and PyPy 4, where Py is pyrrole, and Im is imidazole), linked by a gamma-aminobutyrate group were synthesized. In addition to alkylating at adenine-N3 positions within an A(5) sequence, the imidazole-containing compounds 1 and 2 were found to also alkylate purine-N3 positions within a sequence 3'-GGGGGGA(888)CTGCTC(894)-5'. A model for the binding of hairpin conjugates 1 and 2 with the 3'-GACT-5' sequence is proposed.
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Affiliation(s)
- James L Toth
- Department of Chemistry, Furman University, Greenville, SC 29613, USA
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11
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12
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Guelev VM, Cubberley MS, Murr MM, Lokey RS, Iverson BL. Design, synthesis, and characterization of polyintercalating ligands. Methods Enzymol 2001; 340:556-70. [PMID: 11494870 DOI: 10.1016/s0076-6879(01)40442-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- V M Guelev
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
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13
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Nguyen DH, Szewczyk JW, Baird EE, Dervan PB. Alternative heterocycles for DNA recognition: an N-methylpyrazole/N-methylpyrrole pair specifies for A.T/T.A base pairs. Bioorg Med Chem 2001; 9:7-17. [PMID: 11197348 DOI: 10.1016/s0968-0896(00)00219-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Side-by-side pairs of three five-membered rings, N-methylpyrrole (Py), N-methylimidazole (Im), and N-methylhydroxy-pyrrole (Hp), have been demonstrated to distinguish each of the four Watson Crick base pairs in the minor groove of DNA. However, not all DNA sequences targeted by these pairing rules achieve affinities and specificities comparable to DNA binding proteins. We have initiated a search for new heterocycles which can expand the sequence repetoire currently available. Two heterocyclic aromatic amino acids. N-methylpyrazole (Pz) and 4-methylthiazole (Th), were incorporated into a single position of an eight-ring polyamide of sequence ImImXPy-gamma-lmPyPyPy-beta-Dp to examine the modulation of affinity and specificity for DNA binding by a Pz/Py pair and or a Th/Py pair. The X/Py pairings Pz/Py and Th/Py were evaluated by quantitative DNase I footprint titrations on a DNA fragment with the four sites 5'-TGGNCA-3' (N=T, A, G, C). The Pz/Py pair binds T.A and A.T with similar affinity to a Py/Py pair but with improved specificity. disfavoring both G.C and C.G by about 100-fold. The Th/Py pair binds poorly to all four Watson Crick base pairs. These results demonstrate that in some instances new heterocyclic aromatic amino acid pairs can be incorporated into imidazole-pyrrole polyamides to mimic the DNA specificity of Py/Py pairs which may be relevant as biological criteria in animal studies become important.
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Affiliation(s)
- D H Nguyen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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14
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Weck M, Choi IS, Jeon NL, Whitesides GM. Assembly of Mesoscopic Analogues of Nucleic Acids. J Am Chem Soc 2000. [DOI: 10.1021/ja994099p] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcus Weck
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
| | - Insung S. Choi
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
| | - Noo Li Jeon
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138
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Guelev VM, Harting MT, Lokey RS, Iverson BL. Altered sequence specificity identified from a library of DNA-binding small molecules. CHEMISTRY & BIOLOGY 2000; 7:1-8. [PMID: 10662682 DOI: 10.1016/s1074-5521(00)00007-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The ability to target specific DNA sequences using small molecules has major implications for basic research and medicine. Previous studies revealed that a bis-intercalating molecule containing two 1,4,5,8-napthalenetetracarboxylic diimides separated by a lysine-tris-glycine linker binds to DNA cooperatively, in pairs, with a preference for G + C-rich sequences. Here we investigate the binding properties of a library of bis-intercalating molecules that have partially randomized peptide linkers. RESULTS A library of bis-intercalating derivatives with varied peptide linkers was screened for sequence specificity using DNase I footprinting on a 231 base pair (bp) restriction fragment. The library mixtures produced footprints that were generally similar to the parent bis-intercalator, which bound within a 15 bp G + C-rich repeat above 125 nM. Nevertheless, subtle differences in cleavage enhancement bands followed by library deconvolution revealed a derivative with novel specificity. A lysine-tris-beta-alanine derivative was found to bind preferentially within a 19 bp palindrome, without substantial loss of affinity. CONCLUSIONS Synthetically simple changes in the bis-intercalating compounds can produce derivatives with novel sequence specificity. The large size and symmetrical nature of the preferred binding sites suggest that cooperativity may be retained despite modified sequence specificity. Such findings, combined with structural data, could be used to develop versatile DNA ligands of modest molecular weight that target relatively long DNA sequences in a selective manner.
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Affiliation(s)
- V M Guelev
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Lohse J, Dahl O, Nielsen PE. Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA. Proc Natl Acad Sci U S A 1999; 96:11804-8. [PMID: 10518531 PMCID: PMC18367 DOI: 10.1073/pnas.96.21.11804] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudocomplementary PNAs containing diaminopurine.thiouracil base pairs have been prepared and are shown to bind with high specificity and efficiency to complementary targets in double-stranded DNA by a mechanism termed "double duplex invasion" in which the duplex is unwound and both DNA strands are targeted simultaneously, each by one of the two pseudocomplementary peptide nucleic acids (PNAs). On the basis of our results we predict that (for decameric targets) more than 80% of all sequences can be targeted by straightforward Watson-Crick base pairing by using this approach in its present form. Targeting of pseudocomplementary PNAs to the promoter of the T7 phage RNA polymerase effectively inhibits transcription initiation. These results have important implications in the development of gene therapeutic agents as well as for genetic diagnostic and molecular biology applications.
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Affiliation(s)
- J Lohse
- Center for Biomolecular Recognition, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen O, Denmark
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17
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Seitz O, Bergmann F, Heindl D. Eine konvergente Strategie zur Modifizierung von Peptidnucleinsäuren: neue PNA-Hybridisierungssonden zum Nachweis von Basen-Fehlpaarungen. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990802)111:15<2340::aid-ange2340>3.0.co;2-n] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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18
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19
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Tao ZF, Fujiwara T, Saito I, Sugiyama H. Sequenzspezifische DNA-Alkylierung durch Hybridmoleküle aus Segment A von Duocarmycin A und einem Pyrrol-Imidazol-Diamid. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990301)111:5<692::aid-ange692>3.0.co;2-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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König B, Rödel M. Synthesis of an FmocN-Methyl 1H-Pyrrole Amino Acid Pentafluoro-Phenol Ester. SYNTHETIC COMMUN 1999. [DOI: 10.1080/00397919908086056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Peptide nucleic acids. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1874-5113(99)80009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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22
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Fukutomi R, Tanatani A, Kakuta H, Tomioka N, Itai A, Hashimoto Y, Shudo K, Kagechika H. Aromatic layered guanidines bind sequence-specifically to DNA minor groove with precise fit. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01378-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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23
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Turner JM, Swalley SE, Baird EE, Dervan PB. Aliphatic/Aromatic Amino Acid Pairings for Polyamide Recognition in the Minor Groove of DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja980147e] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Denison C, Kodadek T. Small-molecule-based strategies for controlling gene expression. CHEMISTRY & BIOLOGY 1998; 5:R129-45. [PMID: 9653545 DOI: 10.1016/s1074-5521(98)90167-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A central goal in chemical biology is to gain control over biological pathways using small molecules, and the mRNA-synthesizing machinery is a particular important target. New advances in our understanding of transcriptional regulation suggests strategies to manipulate these pathways using small molecules.
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Affiliation(s)
- C Denison
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas 75235-8573, USA
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25
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Cuenoud B, Casset F, Hüsken D, Natt F, Wolf R, Altmann KH, Martin P, Moser H. Zweifache Erkennung von doppelsträngiger DNA durch 2′-Aminoethoxy-modifizierte Oligonucleotide. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19980504)110:9<1350::aid-ange1350>3.0.co;2-o] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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26
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Bremer RE, Baird EE, Dervan PB. Inhibition of major-groove-binding proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch. CHEMISTRY & BIOLOGY 1998; 5:119-33. [PMID: 9545429 DOI: 10.1016/s1074-5521(98)90057-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gene-specific targeting of any protein-DNA complex by small molecules is a challenging goal at the interface of chemistry and biology. Polyamides containing N-methylimidazole and N-methylpyrrole amino acids are synthetic ligands that have an affinity and specificity for DNA comparable to many naturally occurring DNA-binding proteins. It has been shown that an eight-ring hairpin polyamide targeted to a specific minor-groove contact within a transcription factor binding site can inhibit protein-DNA binding and gene transcription. Polyamides and certain major-groove-binding proteins have been found to co-occupy the DNA helix, however. To expand the number of genes that can be targeted by pyrrole/imidazole polyamides, we set out to develop a class of polyamides that can selectively inhibit major-groove-binding proteins. RESULTS An eight-ring hairpin polyamide conjugated to a carboxy-terminal Arg-Pro-Arg tripeptide was designed to deliver a positive residue to the DNA backbone and interfere with protein-phosphate contacts. Gel mobility shift analysis demonstrated that a polyamide hairpin-Arg-Pro-Arg binding in the minor groove selectively inhibits binding of the transcription factor GCN4 (222-281) in the adjacent major groove. Substitution within the Arg-Pro-Arg revealed that each residue was required for optimal GCN4 inhibition. CONCLUSIONS A pyrrole-imidazole polyamide that binds to a predetermined site in the DNA minor groove and delivers a positive patch to the DNA backbone can selectively inhibit a DNA-binding protein that recognizes the adjacent major groove. A subtle alteration of the DNA microenvironment targeted to a precise location within a specific DNA sequence could achieve both gene-specific and protein-specific targeting.
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Affiliation(s)
- R E Bremer
- Arnold and Mabel Beckman Laboratory of Chemical Synthesis, California Institute of Technology, Pasadena 91125, USA
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27
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White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 1998; 391:468-71. [PMID: 9461213 DOI: 10.1038/35106] [Citation(s) in RCA: 292] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The design of synthetic ligands that read the information stored in the DNA double helix has been a long-standing goal at the interface of chemistry and biology. Cell-permeable small molecules that target predetermined DNA sequences offer a potential approach for the regulation of gene expression. Oligodeoxynucleotides that recognize the major groove of double-helical DNA via triple-helix formation bind to a broad range of sequences with high affinity and specificity. Although oligonucleotides and their analogues have been shown to interfere with gene expression, the triple-helix approach is limited to recognition of purines and suffers from poor cellular uptake. The subsequent development of pairing rules for minor-groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids offers a second code to control sequence specificity. An Im/Py pair distinguishes G x C from C x G and both of these from A x T/T x A base pairs. A Py/Py pair specifies A,T from G,C but does not distinguish AT from T x A. To break this degeneracy, we have added a new aromatic amino acid, 3-hydroxypyrrole (Hp), to the repertoire to test for pairings that discriminate A x T from T x A. We find that replacement of a single hydrogen atom with a hydroxy group in a Hp/Py pairing regulates affinity and specificity by an order of magnitude. By incorporation of this third amino acid, hydroxypyrrole-imidazole-pyrrole polyamides form four ring-pairings (Im/Py, Py/Im, Hp/Py and Py/Hp) which distinguish all four Watson-Crick base pairs in the minor groove of DNA.
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Affiliation(s)
- S White
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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Kuhn H, Demidov VV, Frank-Kamenetskii MD, Nielsen PE. Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA. Nucleic Acids Res 1998; 26:582-7. [PMID: 9421519 PMCID: PMC147306 DOI: 10.1093/nar/26.2.582] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such reagents extremely efficient for sequence-specific targeting of duplex DNA.
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Affiliation(s)
- H Kuhn
- Center for Biomolecular Recognition, Department for Biochemistry and Genetics Laboratory B, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
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Toshima K, Ouchi H, Okazaki Y, Kano T, Moriguchi M, Matsumura S, Asai A. Nichtnatürliche Anthrachinon-Kohlenhydrat-Hybride: Design, Synthese, DNA-Bindung und Cytotoxizität. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971092409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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