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Pattelli ON, Valdivia EM, Beyersdorf MS, Regan CS, Rivas M, Hebert KA, Merajver SD, Cierpicki T, Mapp AK. A Lipopeptidomimetic of Transcriptional Activation Domains Selectively Disrupts the Coactivator Med25 Protein-Protein Interactions. Angew Chem Int Ed Engl 2024; 63:e202400781. [PMID: 38527936 PMCID: PMC11134611 DOI: 10.1002/anie.202400781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium-chain, branched fatty acid to the N-terminus of one such heptameric lipopeptidomimetic (LPPM-8) increases the affinity for the coactivator Med25 >20-fold (Ki >100 μM to 4 μM), rendering it an effective inhibitor of Med25 protein-protein interactions (PPIs). The lipid structure, the peptide sequence, and the C-terminal functionalization of the lipopeptidomimetic each influence the structural propensity of LPPM-8 and its effectiveness as an inhibitor. LPPM-8 engages Med25 through interaction with the H2 face of its activator interaction domain and in doing so stabilizes full-length protein in the cellular proteome. Further, genes regulated by Med25-activator PPIs are inhibited in a cell model of triple-negative breast cancer. Thus, LPPM-8 is a useful tool for studying Med25 and mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator-coactivator complexes.
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Affiliation(s)
- Olivia N. Pattelli
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Estefanía Martínez Valdivia
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Matthew S. Beyersdorf
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Clint S. Regan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mónica Rivas
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Sofia D. Merajver
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Tomasz Cierpicki
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Anna K. Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
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2
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Philips SJ, Danda A, Ansari AZ. Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review. Methods 2024; 225:20-27. [PMID: 38471600 PMCID: PMC11055675 DOI: 10.1016/j.ymeth.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant gene expression underlies numerous human ailments. Hence, developing small molecules to target and remedy dysfunctional gene regulation has been a long-standing goal at the interface of chemistry and medicine. A major challenge for designing small molecule therapeutics aimed at targeting desired genomic loci is the minimization of widescale disruption of genomic functions. To address this challenge, we rationally design polyamide-based multi-functional molecules, i.e., Synthetic Genome Readers/Regulators (SynGRs), which, by design, target distinct sequences in the genome. Herein, we briefly review how SynGRs access chromatin-bound and chromatin-free genomic sites, then highlight the methods for the study of chromatin processes using SynGRs on positioned nucleosomes in vitro or disease-causing repressive genomic loci in vivo.
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Affiliation(s)
- Steven J Philips
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adithi Danda
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aseem Z Ansari
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Mohammed A, Waddell MB, Sutkeviciute I, Danda A, Philips SJ, Lang W, Slavish PJ, Kietlinska SJ, Kaulage M, Sourav D, Ansari AZ. Domain-Selective BET Ligands Yield Next-Generation Synthetic Genome Readers/Regulators with Nonidentical Cellular Functions. J Am Chem Soc 2023. [PMID: 37923569 DOI: 10.1021/jacs.3c06297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
SynTEF1, a prototype synthetic genome reader/regulator (SynGR), was designed to target GAA triplet repeats and restore the expression of frataxin (FXN) in Friedreich's ataxia patients. It achieves this complex task by recruiting BRD4, via a pan-BET ligand (JQ1), to the GAA repeats by using a sequence-selective DNA-binding polyamide. When bound to specific genomic loci in this way, JQ1 functions as a chemical prosthetic for acetyl-lysine residues that are natural targets of the two tandem bromodomains (BD1 and BD2) in bromo- and extra-terminal domain (BET) proteins. As next-generation BET ligands were disclosed, we tested a select set with improved physicochemical, pharmacological, and bromodomain-selective properties as substitutes for JQ1 in the SynGR design. Here, we report two unexpected findings: (1) SynGRs bearing pan-BET or BD2-selective ligands license transcription at the FXN locus, whereas those bearing BD1-selective ligands do not, and (2) rather than being neutral or inhibitory, an untethered BD1-selective ligand (GSK778) substantively enhances the activity of all active SynGRs. The failure of BD1-selective SynGRs to recruit BRD4/BET proteins suggests that rather than functioning as "epigenetic/chromatin mimics," active SynGRs mimic the functions of natural transcription factors in engaging BET proteins through BD2 binding. Moreover, the enhanced activity of SynGRs upon cotreatment with the BD1-selective ligand suggests that natural transcription factors compete for a limited pool of nonchromatin-bound BET proteins, and blocking BD1 directs pan-BET ligands to more effectively engage BD2. Taken together, SynGRs as chemical probes provide unique insights into the molecular recognition principles utilized by natural factors to precisely regulate gene expression, and they guide the design of more sophisticated synthetic gene regulators with greater therapeutic potential.
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Affiliation(s)
- Ashraf Mohammed
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ieva Sutkeviciute
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Adithi Danda
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Steven J Philips
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Walter Lang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - P Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Sandra J Kietlinska
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Mangesh Kaulage
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Das Sourav
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Aseem Z Ansari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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4
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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Pattelli ON, Valdivia EM, Beyersdorf MS, Regan CS, Rivas M, Merajver SD, Cierpicki T, Mapp AK. A lipopeptidomimetic of transcriptional activation domains selectively disrupts Med25 PPIs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534168. [PMID: 36993479 PMCID: PMC10055422 DOI: 10.1101/2023.03.24.534168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium-chain, branched fatty acid to the N-terminus of one such heptameric lipopeptidomimetic (34913-8) increases the affinity for the coactivator Med25 >10-fold ( Ki >>100 μM to 10 μM). Importantly, the selectivity of 34913-8 for Med25 compared to other coactivators is excellent. 34913-8 engages Med25 through interaction with the H2 face of its Ac tivator I nteraction D omain and in doing so stabilizes full-length protein in the cellular proteome. Further, genes regulated by Med25-activator PPIs are inhibited in a cell model of triple-negative breast cancer. Thus, 34913-8 is a useful tool for studying Med25 and the Mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator-coactivator complexes.
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6
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Ryzowicz C, Yildirim N. Differential roles of transcriptional and translational negative autoregulations in protein dynamics. Mol Omics 2023; 19:60-71. [PMID: 36399028 DOI: 10.1039/d2mo00222a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cells continuously respond to stimuli to function properly by employing a wide variety of regulatory mechanisms that often involve protein up or down regulations. This study focuses on dynamics of a protein with negative autoregulations in E. coli, and assumes that the input signal up-regulates the protein, and then the protein down-regulates its own production via 2 distinct types of mechanisms. The mathematical models describe the dynamics of mRNA and protein for 3 scenarios: (i) a simplistic model with no regulation, (ii) a model with transcriptional negative autoregulation, and (iii) a model with translational negative autoregulation. Our analysis shows that the negative autoregulation models produce faster responses and quicker return times to the input signals compared to the model with no regulation, while the transcriptional autoregulation model is the only model capable of producing oscillatory dynamics. The stochastic simulations predict that the transcriptional autoregulation model is the noisiest followed by the simplistic model, and the translational autoregulation model has the least noise. The noise level depends on the strength of inhibition. Furthermore, the transcriptional autoregulation model filters out the noise in the input signal for longer periods of time, and this time increases as the strength of the feedback gets stronger.
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Affiliation(s)
- Christopher Ryzowicz
- Division of Natural Sciences, New College of Florida, 5800 Bayshore Road, Sarasota, FL 34243, USA.
| | - Necmettin Yildirim
- Division of Natural Sciences, New College of Florida, 5800 Bayshore Road, Sarasota, FL 34243, USA.
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7
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Jana P, Samanta K, Ehlers M, Zellermann E, Bäcker S, Stauber RH, Schmuck C, Knauer SK. Impact of Peptide Sequences on Their Structure and Function: Mimicking of Virus-Like Nanoparticles for Nucleic Acid Delivery. Chembiochem 2023; 24:e202200519. [PMID: 36314419 PMCID: PMC10099937 DOI: 10.1002/cbic.202200519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/30/2022] [Indexed: 01/05/2023]
Abstract
We rationally designed a series of amphiphilic hepta-peptides enriched with a chemically conjugated guanidiniocarbonylpyrrole (GCP) unit at the lysine side chain. All peptides are composed of polar (GCP) and non-polar (cyclohexyl alanine) residues but differ in their sequence periodicity, resulting in different secondary as well as supramolecular structures. CD spectra revealed the assembly of β-sheet-, α-helical and random structures for peptides 1, 2 and 3, respectively. Consequently, this enabled the formation of distinct supramolecular assemblies such as fibres, nanorod-like or spherical aggregates. Notably, all three cationic peptides are equipped with the anion-binding GCP unit and thus possess a nucleic acid-binding centre. However, only the helical (2) and the unstructured (3) peptide were able to assemble into small virus-like DNA-polyplexes and effectively deliver DNA into cells. Notably, as both peptides (2 and 3) were also capable of siRNA-delivery, they could be utilized to downregulate expression of the caner-relevant protein Survivin.
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Affiliation(s)
- Poulami Jana
- Department of Chemistry, Kaliachak College Sultanganj, Malda, 732201-, West Bengal, India
| | - Krishnananda Samanta
- Department of Chemistry, Balurghat College Dakshin Dinajpur, 733101-, West Bengal, India
| | - Martin Ehlers
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Elio Zellermann
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Sandra Bäcker
- Molecular Biology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology, ENT Department, University Mainz Medical Center, 55131, Mainz, Germany
| | - Carsten Schmuck
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology, University of Duisburg-Essen, 45117, Essen, Germany
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8
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Boral A, Khamaru M, Mitra D. Designing synthetic transcription factors: A structural perspective. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:245-287. [PMID: 35534109 DOI: 10.1016/bs.apcsb.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this chapter, we discuss different design strategies of synthetic proteins, especially synthetic transcription factors. Design and engineering of synthetic transcription factors is particularly relevant for the need-based manipulation of gene expression. With recent advances in structural biology techniques and with the emergence of other precision biochemical/physical tools, accurate knowledge on structure-function relations is increasingly becoming available. Besides discussing the underlying principles of design, we go through individual cases, especially those involving four major groups of transcription factors-basic leucine zippers, zinc fingers, helix-turn-helix and homeodomains. We further discuss how synthetic biology can come together with structural biology to alter the genetic blueprint of life.
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Affiliation(s)
- Aparna Boral
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Madhurima Khamaru
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
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9
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Redirection of the Transcription Factor SP1 to AT Rich Binding Sites by a Synthetic Adaptor Molecule. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Abstract
The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
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Affiliation(s)
- John D Bagert
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Tom W Muir
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
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11
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Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome. PLoS One 2020; 15:e0243905. [PMID: 33351840 PMCID: PMC7755219 DOI: 10.1371/journal.pone.0243905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 01/21/2023] Open
Abstract
Pyrrole–imidazole (Py–Im) polyamides are synthetic molecules that can be rationally designed to target specific DNA sequences to both disrupt and recruit transcriptional machinery. While in vitro binding has been extensively studied, in vivo effects are often difficult to predict using current models of DNA binding. Determining the impact of genomic architecture and the local chromatin landscape on polyamide-DNA sequence specificity remains an unresolved question that impedes their effective deployment in vivo. In this report we identified polyamide–DNA interaction sites across the entire genome, by covalently crosslinking and capturing these events in the nuclei of human LNCaP cells. This technique confirms the ability of two eight ring hairpin-polyamides, with similar architectures but differing at a single ring position (Py to Im), to retain in vitro specificities and display distinct genome-wide binding profiles.
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12
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Abstract
The dynamic nature of histone post-translational modifications such as methylation or acetylation makes possible the alteration of disease associated epigenetic states through the manipulation of the associated epigenetic machinery. One approach is through small molecule perturbation. Chemical probes of epigenetic reader domains have been critical in improving our understanding of the biological consequences of modulating their targets, while also enabling the development of novel probe-based reagents. By appending a functional handle to a reader domain probe, a chemical toolbox of reagents can be created to facilitate chemiprecipitation of epigenetic complexes, evaluate probe selectivity, develop in vitro screening assays, visualize cellular target localization, enable target degradation and recruit epigenetic machinery to a site within the genome in a highly controlled fashion.
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13
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Yu Z, Ai M, Samanta SK, Hashiya F, Taniguchi J, Asamitsu S, Ikeda S, Hashiya K, Bando T, Pandian GN, Isaacs L, Sugiyama H. A synthetic transcription factor pair mimic for precise recruitment of an epigenetic modifier to the targeted DNA locus. Chem Commun (Camb) 2020; 56:2296-2299. [DOI: 10.1039/c9cc09608f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
ePIP–HoGu not only mimics the transcription factor operation as pairs but is also capable of recruiting the epigenetic modifiers to a particular DNA locus.
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14
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Liu B, Bashkin JK, Poon GMK, Wang S, Wang S, Wilson WD. Modulating DNA by polyamides to regulate transcription factor PU.1-DNA binding interactions. Biochimie 2019; 167:1-11. [PMID: 31445072 DOI: 10.1016/j.biochi.2019.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022]
Abstract
Hairpin polyamides are synthetic small molecules that bind DNA minor groove sequence-selectively and, in many sequences, induce widening of the minor groove and compression of the major groove. The structural distortion of DNA caused by polyamides has enhanced our understanding of the regulation of DNA-binding proteins via polyamides. Polyamides have DNA binding affinities that are comparable to those proteins, therefore, can potentially be used as therapeutic agents to treat diseases caused by aberrant gene expression. In fact, many diseases are characterized by over- or under-expressed genes. PU.1 is a transcription factor that regulates many immune system genes. Aberrant expression of PU.1 has been associated with the development of acute myeloid leukemia (AML). We have, therefore, designed and synthesized ten hairpin polyamides to investigate their capacity in controlling the PU.1-DNA interaction. Our results showed that nine of the polyamides disrupt PU.1-DNA binding and the inhibition capacity strongly correlates with binding affinity. One molecule, FH1024, was observed forming a FH1024-PU.1-DNA ternary complex instead of inhibiting PU.1-DNA binding. This is the first report of a small molecule that is potentially a weak agonist that recruits PU.1 to DNA. This finding sheds light on the design of polyamides that exhibit novel regulatory mechanisms on protein-DNA binding.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - James K Bashkin
- Department of Chemistry & Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, MO, 63121, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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P311, a novel intrinsically disordered protein, regulates adipocyte development. Biochem Biophys Res Commun 2019; 515:234-240. [PMID: 31146912 PMCID: PMC6561663 DOI: 10.1016/j.bbrc.2019.05.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
Adipocyte development and adipose tissue expansion have many implications for human diseases, including obesity. Obesity is a debilitating disorder and a risk factor for metabolic disorders including insulin resistance and diabetes mellitus, due in part to an overabundance of adipocytes and adipocyte dysfunction. In recent years, obesity has become a global pandemic with approximately one-third of US adults classified as obese. Adipose tissue has recently been identified as a major metabolic organ, classified into white adipose tissue (WAT) and brown adipose tissue (BAT). Other than lifestyle modifications and invasive surgeries, only a very limited number of drugs are available to treat obesity and overweight. P311 has been shown to play a key role in blood pressure regulation, vascular contractility and tissue remodeling. Here we present a role for P311 in adipogenesis using a 3T3-L1 cell culture model. P311 expression is initiated with the induction of adipogenesis and increased during adipogenesis. This increase correlates with an increase in the expression of the key adipogenic transcriptional factors PPARγ2 and C/EBPα. In addition, siRNA-mediated P311 knockdown inhibits adipogenic differentiation in 3T3-L1 cells. Finally, P311 binds to the PPARγ2 promoter, implicating P311 mediates adipogenesis partly through PPARγ activation.
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16
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Yu Z, Pandian GN, Hidaka T, Sugiyama H. Therapeutic gene regulation using pyrrole-imidazole polyamides. Adv Drug Deliv Rev 2019; 147:66-85. [PMID: 30742856 DOI: 10.1016/j.addr.2019.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/22/2018] [Accepted: 02/04/2019] [Indexed: 12/13/2022]
Abstract
Recent innovations in cutting-edge sequencing platforms have allowed the rapid identification of genes associated with communicable, noncommunicable and rare diseases. Exploitation of this collected biological information has facilitated the development of nonviral gene therapy strategies and the design of several proteins capable of editing specific DNA sequences for disease control. Small molecule-based targeted therapeutic approaches have gained increasing attention because of their suggested clinical benefits, ease of control and lower costs. Pyrrole-imidazole polyamides (PIPs) are a major class of DNA minor groove-binding small molecules that can be predesigned to recognize specific DNA sequences. This programmability of PIPs allows the on-demand design of artificial genetic switches and fluorescent probes. In this review, we detail the progress in the development of PIP-based designer ligands and their prospects as advanced DNA-based small-molecule drugs for therapeutic gene modulation.
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17
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Geel TM, Ruiters MHJ, Cool RH, Halby L, Voshart DC, Andrade Ruiz L, Niezen-Koning KE, Arimondo PB, Rots MG. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170077. [PMID: 29685979 PMCID: PMC5915719 DOI: 10.1098/rstb.2017.0077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- T M Geel
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - M H J Ruiters
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - R H Cool
- Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - L Halby
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - D C Voshart
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Andrade Ruiz
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - K E Niezen-Koning
- Laboratory of Metabolic Diseases, Dept Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - P B Arimondo
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - M G Rots
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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18
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Roy K, Mazumder A, Ghosh P, Naiya G, Ghosh B, Roy S. A peptide-based synthetic transcription factor selectively activates transcription in a mammalian cell. Chem Commun (Camb) 2018; 54:1611-1614. [PMID: 29369310 DOI: 10.1039/c7cc09279b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A peptide-based cell permeable synthetic transcription factor is reported, which binds to its target site with high affinity and specificity. When linked to a HAT-binding peptide, it causes significant upregulation of gene expression in a mammalian cell. Such molecules may be developed for selectively activating repressed genes in mammalian cells.
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Affiliation(s)
- Koushik Roy
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.Mullick Road, Kolkata 700032, India
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19
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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20
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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21
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N. N, Thimmalapura VM, Hosamani B, Prabhu G, Kumar LR, Sureshbabu VV. Thioacids – synthons for amide bond formation and ligation reactions: assembly of peptides and peptidomimetics. Org Biomol Chem 2018; 16:3524-3552. [DOI: 10.1039/c8ob00512e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of α-amino thioacids and peptide thioacids and their applications in chemoselective amide bond formation, ligation of peptides/proteins/glycopeptides and synthesis of peptidomimetics are reviewed.
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Affiliation(s)
- Narendra N.
- Department of Chemistry
- University College of Science
- Tumkur University
- Tumkur 572 103
- India
| | - Vishwanatha M. Thimmalapura
- Room No. 109
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
| | - Basavaprabhu Hosamani
- Room No. 109
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
| | - Girish Prabhu
- Room No. 109
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
| | - L. Roopesh Kumar
- Room No. 109
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
| | - Vommina V. Sureshbabu
- Room No. 109
- Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
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22
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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23
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Rathnam C, Chueng STD, Yang L, Lee KB. Advanced Gene Manipulation Methods for Stem Cell Theranostics. Theranostics 2017; 7:2775-2793. [PMID: 28824715 PMCID: PMC5562215 DOI: 10.7150/thno.19443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022] Open
Abstract
In the field of tissue engineering, autologous cell sources are ideal to prevent adverse immune responses; however, stable and reliable cell sources are limited. To acquire more reliable cell sources, the harvesting and differentiation of stem cells from patients is becoming more and more common. To this end, the need to control the fate of these stem cells before transplantation for therapeutic purposes is urgent. Since transcription factors orchestrate all of the gene activities inside of a cell, researchers have developed engineered and synthetic transcription factors to precisely control the fate of stem cells allowing for safer and more effective cell sources. Engineered transcription factors, mutant fusion proteins of naturally occurring proteins, comprise the three main domains of natural transcription factors including DNA binding domains, transcriptional activation domains, and a linker domain. Several key advancements of engineered zinc finger proteins, transcriptional activator-like effectors, and deficient cas9 proteins have revolutionized the field of engineered transcription factors allowing for precise control of gene regulation. Synthetic transcription factors are chemically made transcription factor mimics that use small molecule based moieties to replicate the main functions of natural transcription factors. These include hairpin polyamides, triple helix forming oligonucleotides, and nanoparticle-based methods. Synthetic transcription factors allow for non-viral delivery and greater spatiotemporal control of gene expression. The developments in engineered and synthetic transcription factors have lowered the risk of tumorigenicity and improved differentiation capability of stem cells, as well as facilitated many key discoveries in the fields of cancer and stem cell biology, thus providing a stepping stone to advance regenerative medicine in the clinic for cell replacement therapies.
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24
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Chakraborty M, Roy S. A peptide-based synthetic transcription factor selectively down-regulates the proto-oncogene CFOS in tumour cells and inhibits proliferation. Chem Commun (Camb) 2017; 53:376-379. [DOI: 10.1039/c6cc08086c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A synthetic transcription factor targeted against Elk-1 inhibits expression of CFOS and other genes selectively in Ras-mutated tumour cells.
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Affiliation(s)
| | - Siddhartha Roy
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
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25
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Reprogramming cell fate with a genome-scale library of artificial transcription factors. Proc Natl Acad Sci U S A 2016; 113:E8257-E8266. [PMID: 27930301 DOI: 10.1073/pnas.1611142114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1). Cognate site identification, global transcriptional profiling, and identification of ATF binding sites reveal that the ATFs do not directly target Oct4; instead, they target distinct nodes that converge to stimulate the endogenous pluripotency network. This forward genetic approach enables cell type conversions without a priori knowledge of potential key regulators and reveals unanticipated gene network dynamics that drive cell fate choices.
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26
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Synthetic genome readers target clustered binding sites across diverse chromatin states. Proc Natl Acad Sci U S A 2016; 113:E7418-E7427. [PMID: 27830652 DOI: 10.1073/pnas.1604847113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to "read" specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells. This genome-wide view from live cells reveals that polyamide-based synthetic genome readers bind cognate sites that span a range of binding affinities. Polyamides can access cognate sites within repressive heterochromatin. The occupancy patterns suggest that polyamides could be harnessed to target loci within regions of the genome that are inaccessible to other DNA-targeting molecules.
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27
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Zabidi MA, Stark A. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet 2016; 32:801-814. [PMID: 27816209 DOI: 10.1016/j.tig.2016.10.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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28
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Castaneda CH, Scuderi MJ, Edwards TG, Harris GD, Dupureur CM, Koeller KJ, Fisher C, Bashkin JK. Improved Antiviral Activity of a Polyamide Against High-Risk Human Papillomavirus Via N-Terminal Guanidinium Substitution. MEDCHEMCOMM 2016; 7:2076-2082. [PMID: 27840672 DOI: 10.1039/c6md00371k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the synthesis of two novel pyrrole-imidazole polyamides with N-terminal guanidinium or tetramethylguanidinium groups and evaluate their antiviral activity against three cancer-causing human papillomavirus strains. Introduction of guanidinium improves antiviral activity when compared to an unsubstituted analog, especially in IC90 values. These substitutions change DNA-binding preferences, while binding affinity remains unchanged.
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Affiliation(s)
- C H Castaneda
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - M J Scuderi
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - T G Edwards
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - G D Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C M Dupureur
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - K J Koeller
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C Fisher
- NanoVir, LLC, Kalamazoo, MI 49008 (USA)
| | - J K Bashkin
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA; NanoVir, LLC, Kalamazoo, MI 49008 (USA)
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29
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Erkina TY, Erkine AM. Nucleosome distortion as a possible mechanism of transcription activation domain function. Epigenetics Chromatin 2016; 9:40. [PMID: 27679670 PMCID: PMC5029090 DOI: 10.1186/s13072-016-0092-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022] Open
Abstract
After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct recruitment by ADs of co-activators and basal transcriptional machinery components, however, is not always compatible with the short size yet very high degree of sequence randomness and intrinsic structural disorder of natural and synthetic ADs. In this review, we formulate the basis for an alternative and complementary model, whereby sequence randomness and intrinsic structural disorder of ADs are necessary for transient distorting interactions with promoter nucleosomes, triggering promoter nucleosome translocation and subsequently gene activation.
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Affiliation(s)
- Tamara Y Erkina
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN 46208 USA
| | - Alexandre M Erkine
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN 46208 USA
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30
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Erwin GS, Grieshop MP, Bhimsaria D, Eguchi A, Rodríguez-Martínez JA, Ansari AZ. Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). J Vis Exp 2016:e53510. [PMID: 26863565 DOI: 10.3791/53510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to dose-limiting toxicity and many adverse side effects. Targeting the genome with sequence-specific small molecules may enable molecules with increased therapeutic index and fewer off-target effects. N-methylpyrrole/N-methylimidazole polyamides are molecules that can be rationally designed to target specific DNA sequences with exquisite precision. And unlike most natural transcription factors, polyamides can bind to methylated and chromatinized DNA without a loss in affinity. The sequence specificity of polyamides has been extensively studied in vitro with cognate site identification (CSI) and with traditional biochemical and biophysical approaches, but the study of polyamide binding to genomic targets in cells remains elusive. Here we report a method, the crosslinking of small molecules to isolate chromatin (COSMIC), that identifies polyamide binding sites across the genome. COSMIC is similar to chromatin immunoprecipitation (ChIP), but differs in two important ways: (1) a photocrosslinker is employed to enable selective, temporally-controlled capture of polyamide binding events, and (2) the biotin affinity handle is used to purify polyamide-DNA conjugates under semi-denaturing conditions to decrease DNA that is non-covalently bound. COSMIC is a general strategy that can be used to reveal the genome-wide binding events of polyamides and other genome-targeting chemotherapeutic agents.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison
| | | | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison; Department of Electrical and Computer Engineering, University of Wisconsin-Madison
| | - Asuka Eguchi
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison
| | | | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison; The Genome Center, University of Wisconsin-Madison;
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31
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Han YW, Sugiyama H, Harada Y. The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein–DNA complex formation. Biomater Sci 2016; 4:391-9. [DOI: 10.1039/c5bm00214a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescent conjugates of Py–Im polyamides are used as sequence-specific fluorescent probes and applied to the characterisation of protein–DNA complex dynamics.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Department of Chemistry
| | - Yoshie Harada
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Biostudies
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32
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Joo JY, Lee J, Ko HY, Lee YS, Heo H, Gu HN, Cho S, Kim S. VisuFect-mediated siRNA delivery into zygotes. Colloids Surf B Biointerfaces 2015; 135:646-651. [DOI: 10.1016/j.colsurfb.2015.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/12/2015] [Accepted: 08/17/2015] [Indexed: 11/25/2022]
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34
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Bahal R, Quijano E, McNeer NA, Liu Y, Bhunia DC, Lopez-Giraldez F, Fields RJ, Saltzman WM, Ly DH, Glazer PM. Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition. Curr Gene Ther 2015; 14:331-42. [PMID: 25174576 DOI: 10.2174/1566523214666140825154158] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 01/13/2023]
Abstract
Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peter M Glazer
- Yale School of Medicine, Dept. of Therapeutic Radiology, P.O. Box 208040, New Haven, Connecticut 06520-8040, USA.
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35
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Patel S, Chueng STD, Yin PT, Dardir K, Song Z, Pasquale N, Kwan K, Sugiyama H, Lee KB. Induction of stem-cell-derived functional neurons by NanoScript-based gene repression. Angew Chem Int Ed Engl 2015; 54:11983-8. [PMID: 26292201 PMCID: PMC5568028 DOI: 10.1002/anie.201504902] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 01/22/2023]
Abstract
Even though gene repression is a powerful approach to exogenously regulate cellular behavior, developing a platform to effectively repress targeted genes, especially for stem-cell applications, remains elusive. Herein, we introduce a nanomaterial-based platform that is capable of mimicking the function of transcription repressor proteins to downregulate gene expression at the transcriptional level for enhancing stem-cell differentiation. We developed the "NanoScript" platform by integrating multiple gene repression molecules with a nanoparticle. First, we show a proof-of-concept demonstration using a GFP-specific NanoScript to knockdown GFP expression in neural stem cells (NSCs-GFP). Then, we show that a Sox9-specific NanoScript can repress Sox9 expression to initiate enhanced differentiation of NSCs into functional neurons. Overall, the tunable properties and gene-knockdown capabilities of NanoScript enables its utilization for gene-repression applications in stem cell biology.
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Affiliation(s)
- Sahishnu Patel
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Sy-Tsong Dean Chueng
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Perry T Yin
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA)
| | - Kholud Dardir
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Zhichao Song
- Department of Cell Biology & Neuroscience, W. M. Keck Center for Collaborative Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA)
| | - Nicholas Pasquale
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Kelvin Kwan
- Department of Cell Biology & Neuroscience, W. M. Keck Center for Collaborative Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8501 (Japan)
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/.
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA).
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36
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Patel S, Chueng STD, Yin PT, Dardir K, Song Z, Pasquale N, Kwan K, Sugiyama H, Lee KB. Induction of Stem-Cell-Derived Functional Neurons by NanoScript-Based Gene Repression. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Janssen BMG, van Ommeren SPFI, Merkx M. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation. Int J Mol Sci 2015; 16:12631-47. [PMID: 26053396 PMCID: PMC4490465 DOI: 10.3390/ijms160612631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/25/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023] Open
Abstract
The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py-Im) polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py-Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py-Im polyamides. The effect of Py-Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR). Although the synthesis of different protein-Py-Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py-Im-polyamide conjugates. The practical use of protein-Py-Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.
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Affiliation(s)
- Brian M G Janssen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Sven P F I van Ommeren
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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Ay A, Wilner N, Yildirim N. Mathematical modeling deciphers the benefits of alternatively-designed conserved activatory and inhibitory gene circuits. MOLECULAR BIOSYSTEMS 2015; 11:2017-30. [PMID: 25966646 DOI: 10.1039/c5mb00269a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells employ a variety of mechanisms as a response to external signals to maintain cellular homeostasis. In this study, we examine four activatory and four inhibitory protein synthesis mechanisms at both population and single cell level that can be triggered by a transient external signal. Activation mechanisms result from the assumption that cells can employ four different modes to temporarily increase the levels of a protein: decreased mRNA degradation, increased mRNA synthesis, decreased protein degradation and increased protein synthesis. For the inhibition mechanisms it is assumed that a cell can reduce a protein's level through four ways: increased mRNA degradation, reduced mRNA synthesis, increased protein degradation and reduced protein synthesis. Deterministic and stochastic models were developed to analyze the dynamic responses of these eight mechanisms to a transient signal. Three different response metrics were used to measure different aspects of the response. These metrics are (i) mid-protein abundance (mP), (ii) time required for the protein to reach the mid-protein level (mT), and (iii) duration of response (D), which is defined as the total time for which the protein (P) abundance are above or below of mid-protein level. Our simulations show that of the activation mechanisms, the signal-dependent increase in mRNA synthesis and protein synthesis are more effective and faster, than the signal dependent decrease in mRNA and protein degradation. On the other hand, the mechanism involving signal dependent increase in protein synthesis is noisier than the signal dependent increase in mRNA synthesis in regard to all metrics used. Of the four inhibition mechanisms, the signal-dependent increase in the protein degradation is the most effective and fastest of the four inhibition mechanisms. It is also noisiest of the four inhibition mechanisms before the protein levels reach a steady state around 100 minutes.
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Affiliation(s)
- Ahmet Ay
- Departments of Biology and Mathematics, Colgate University, 13 Oak Dr. Hamilton, NY 13346, USA
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Laughlin S, Wang S, Kumar A, Farahat AA, Boykin DW, Wilson WD. Resolution of mixed site DNA complexes with dimer-forming minor-groove binders by using electrospray ionization mass spectrometry: compound structure and DNA sequence effects. Chemistry 2015; 21:5528-39. [PMID: 25703690 PMCID: PMC4732565 DOI: 10.1002/chem.201406322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/18/2022]
Abstract
Small-molecule targeting of the DNA minor groove is a promising approach to modulate genomic processes necessary for normal cellular function. For instance, dicationic diamindines, a well-known class of minor groove binding compounds, have been shown to inhibit interactions of transcription factors binding to genomic DNA. The applications of these compounds could be significantly expanded if we understand sequence-specific recognition of DNA better and could use the information to design more sequence-specific compounds. Aside from polyamides, minor groove binders typically recognize DNA at A-tract or alternating AT base pair sites. Targeting sites with GC base pairs, referred to here as mixed base pair sequences, is much more difficult than those rich in AT base pairs. Compound 1 is the first dicationic diamidine reported to recognize a mixed base pair site. It binds in the minor groove of ATGA sequences as a dimer with positive cooperativity. Due to the well-characterized behavior of 1 with ATGA and AT rich sequences, it provides a paradigm for understanding the elements that are key for recognition of mixed sequence sites. Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to screen DNA complexes formed by analogues of 1 for specific recognition. We also report a novel approach to determine patterns of recognition by 1 for cognate ATGA and ATGA-mutant sequences. We found that functional group modifications and mutating the DNA target site significantly affect binding and stacking, respectively. Both compound conformation and DNA sequence directionality are crucial for recognition.
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Affiliation(s)
- Sarah Laughlin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Abdelbasset A. Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - David W. Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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40
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Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers. Biochem J 2014; 462:397-413. [PMID: 25145439 DOI: 10.1042/bj20140400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription factors control the fate of a cell by regulating the expression of genes and regulatory networks. Recent successes in inducing pluripotency in terminally differentiated cells as well as directing differentiation with natural transcription factors has lent credence to the efforts that aim to direct cell fate with rationally designed transcription factors. Because DNA-binding factors are modular in design, they can be engineered to target specific genomic sequences and perform pre-programmed regulatory functions upon binding. Such precision-tailored factors can serve as molecular tools to reprogramme or differentiate cells in a targeted manner. Using different types of engineered DNA binders, both regulatory transcriptional controls of gene networks, as well as permanent alteration of genomic content, can be implemented to study cell fate decisions. In the present review, we describe the current state of the art in artificial transcription factor design and the exciting prospect of employing artificial DNA-binding factors to manipulate the transcriptional networks as well as epigenetic landscapes that govern cell fate.
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41
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Patel S, Jung D, Yin PT, Carlton P, Yamamoto M, Bando T, Sugiyama H, Lee KB. NanoScript: a nanoparticle-based artificial transcription factor for effective gene regulation. ACS NANO 2014; 8:8959-67. [PMID: 25133310 PMCID: PMC4174092 DOI: 10.1021/nn501589f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 08/18/2014] [Indexed: 05/22/2023]
Abstract
Transcription factor (TF) proteins are master regulators of transcriptional activity and gene expression. TF-based gene regulation is a promising approach for many biological applications; however, several limitations hinder the full potential of TFs. Herein, we developed an artificial, nanoparticle-based transcription factor, termed NanoScript, which is designed to mimic the structure and function of TFs. NanoScript was constructed by tethering functional peptides and small molecules called synthetic transcription factors, which mimic the individual TF domains, onto gold nanoparticles. We demonstrate that NanoScript localizes within the nucleus and initiates transcription of a reporter plasmid by over 15-fold. Moreover, NanoScript can effectively transcribe targeted genes on endogenous DNA in a nonviral manner. Because NanoScript is a functional replica of TF proteins and a tunable gene-regulating platform, it has great potential for various stem cell applications.
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Affiliation(s)
- Sahishnu Patel
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Dongju Jung
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Perry T. Yin
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Makoto Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Address correspondence to
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Erwin GS, Bhimsaria D, Eguchi A, Ansari AZ. Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angew Chem Int Ed Engl 2014; 53:10124-8. [PMID: 25066383 DOI: 10.1002/anie.201405497] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 01/04/2023]
Abstract
Targeting the genome with sequence-specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole-based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide-DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high-affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in vivo.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry and The Genome Center, University of Wisconsin - Madison, Madison, WI 53706 (USA)
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43
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Erwin GS, Bhimsaria D, Eguchi A, Ansari AZ. Mapping Polyamide-DNA Interactions in Human Cells Reveals a New Design Strategy for Effective Targeting of Genomic Sites. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405497] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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44
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Carrette LLG, Morii T, Madder A. Peptidosteroid Tweezers Revisited: DNA Binding Through an Optimised Design. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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DNA compaction induced by a cationic polymer or surfactant impact gene expression and DNA degradation. PLoS One 2014; 9:e92692. [PMID: 24671109 PMCID: PMC3966812 DOI: 10.1371/journal.pone.0092692] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/24/2014] [Indexed: 01/08/2023] Open
Abstract
There is an increasing interest in achieving gene regulation in biotechnological and biomedical applications by using synthetic DNA-binding agents. Most studies have so far focused on synthetic sequence-specific DNA-binding agents. Such approaches are relatively complicated and cost intensive and their level of sophistication is not always required, in particular for biotechnological application. Our study is inspired by in vivo data that suggest that DNA compaction might contribute to gene regulation. This study exploits the potential of using synthetic DNA compacting agents that are not sequence-specific to achieve gene regulation for in vitro systems. The semi-synthetic in vitro system we use include common cationic DNA-compacting agents, poly(amido amine) (PAMAM) dendrimers and the surfactant hexadecyltrimethylammonium bromide (CTAB), which we apply to linearized plasmid DNA encoding for the luciferase reporter gene. We show that complexing the DNA with either of the cationic agents leads to gene expression inhibition in a manner that depends on the extent of compaction. This is demonstrated by using a coupled in vitro transcription-translation system. We show that compaction can also protect DNA against degradation in a dose-dependent manner. Furthermore, our study shows that these effects are reversible and DNA can be released from the complexes. Release of DNA leads to restoration of gene expression and makes the DNA susceptible to degradation by Dnase. A highly charged polyelectrolyte, heparin, is needed to release DNA from dendrimers, while DNA complexed with CTAB dissociates with the non-ionic surfactant C12E5. Our results demonstrate the relation between DNA compaction by non-specific DNA-binding agents and gene expression and gene regulation can be achieved in vitro systems in a reliable dose-dependent and reversible manner.
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46
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Affiliation(s)
- Mark Ptashne
- From the Sloan-Kettering Institute, New York, New York 10065
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47
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Han YW, Tsunaka Y, Yokota H, Matsumoto T, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Sugiyama H, Harada Y. Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome. Biomater Sci 2014; 2:297-307. [DOI: 10.1039/c3bm60202h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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48
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Abstract
Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy-referring to the multiple pathways that a system recruits to achieve functional plasticity-is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability.
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49
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Abstract
In this contribution, we report studies of the nature of binding interactions and dynamics of protein histone I (H1) with ligands in solution and as a complex with DNA, an important biological process for the higher-order structure in chromatin. With femtosecond time resolution, we examined the role of solvation by water, the micropolarity at the interface of the binding site(s) of H1, and the rigidity of the complex structure. We used two biologically common fluorescent probes: 2-(p-toluidino)naphthalene-6-sulfonate (TNS) and 5-(dimethylamino)naphthalene-1-sulfonyl chloride (DC). By noncovalently attaching TNS and covalently adducting DC to the binding sites we found that the solvation dynamics, which occur within 1 ps, for the probe at the protein surface and in bulk solution are comparable, indicating the significant contribution of bulk water shells. However, the local polarity changes significantly, reflecting the change in dielectric properties at the protein/water interface. The binding structure of the protein-DNA complex was examined by the local orientational motion of the probe. The covalently bound DC molecule, sandwiched between the protein and DNA, was found to be frozen, revealing the very rigid structure at the recognition site, while, for noncovalently bound TNS, the complexes displace the probe. The dynamical rigidity of the complex, and the role of solvation and interface polarity, elucidate the strong recognition mechanism between DNA and the protein by electrostatic interactions, which are important to the compactness and to chromatin condensation in the biological function.
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Affiliation(s)
- D Zhong
- Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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50
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Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5′-GCGC-3′. Bioorg Med Chem 2013; 21:5436-41. [DOI: 10.1016/j.bmc.2013.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/27/2022]
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