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Peptide Regulation of Gene Expression: A Systematic Review. Molecules 2021; 26:molecules26227053. [PMID: 34834147 PMCID: PMC8619776 DOI: 10.3390/molecules26227053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/22/2022] Open
Abstract
Peptides are characterized by their wide range of biological activity: they regulate functions of the endocrine, nervous, and immune systems. The mechanism of such action of peptides involves their ability to regulate gene expression and protein synthesis in plants, microorganisms, insects, birds, rodents, primates, and humans. Short peptides, consisting of 2-7 amino acid residues, can penetrate into the nuclei and nucleoli of cells and interact with the nucleosome, the histone proteins, and both single- and double-stranded DNA. DNA-peptide interactions, including sequence recognition in gene promoters, are important for template-directed synthetic reactions, replication, transcription, and reparation. Peptides can regulate the status of DNA methylation, which is an epigenetic mechanism for the activation or repression of genes in both the normal condition, as well as in cases of pathology and senescence. In this context, one can assume that short peptides were evolutionarily among the first signaling molecules that regulated the reactions of template-directed syntheses. This situation enhances the prospects of developing effective and safe immunoregulatory, neuroprotective, antimicrobial, antiviral, and other drugs based on short peptides.
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2
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Markowska A, Markowski AR, Jarocka-Karpowicz I. The Importance of 6-Aminohexanoic Acid as a Hydrophobic, Flexible Structural Element. Int J Mol Sci 2021; 22:12122. [PMID: 34830000 PMCID: PMC8618066 DOI: 10.3390/ijms222212122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
6-aminohexanoic acid is an ω-amino acid with a hydrophobic, flexible structure. Although the ω-amino acid in question is mainly used clinically as an antifibrinolytic drug, other applications are also interesting and important. This synthetic lysine derivative, without an α-amino group, plays a significant role in chemical synthesis of modified peptides and in the polyamide synthetic fibers (nylon) industry. It is also often used as a linker in various biologically active structures. This review concentrates on the role of 6-aminohexanoic acid in the structure of various molecules.
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Affiliation(s)
- Agnieszka Markowska
- Department of Analytical Chemistry, Medical University of Bialystok, 15-089 Bialystok, Poland;
| | - Adam Roman Markowski
- Department of Internal Medicine and Gastroenterology, Polish Red Cross Memorial Municipal Hospital, 79 Henryk Sienkiewicz Street, 15-003 Bialystok, Poland;
| | - Iwona Jarocka-Karpowicz
- Department of Analytical Chemistry, Medical University of Bialystok, 15-089 Bialystok, Poland;
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Li Z, Qiao J, Jia Z, Meng S. Synthesis of the Pyridine Hydrazones as Metal-free Artificial Nucleases. CHEM LETT 2015. [DOI: 10.1246/cl.150428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zhifen Li
- School of Chemical and Environmental Engineering, Datong University
| | - Jun Qiao
- School of Chemical and Environmental Engineering, Datong University
| | - Zhifang Jia
- School of Chemical and Environmental Engineering, Datong University
| | - Shuangming Meng
- School of Chemical and Environmental Engineering, Datong University
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Lee YH, Chang SF, Liaw J. Anti-Apoptotic Gene Delivery with cyclo-(d-Trp-Tyr) Peptide Nanotube via Eye Drop Following Corneal Epithelial Debridement. Pharmaceutics 2015; 7:122-36. [PMID: 26193308 PMCID: PMC4588189 DOI: 10.3390/pharmaceutics7030122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 01/20/2023] Open
Abstract
Corneal keratocyte apoptosis triggered by cornel debridement is one mechanism of corneal disorders. In this study, the feasibility of cyclo-(d-Trp-Tyr) peptide nanotubes (PNTs) as carriers of caspase 3 silence shRNA delivery was assessed. A model of epithelial injury by epithelial debridement was applied to investigate the feasibility of PNTs as gene delivery carriers on corneal injury. First, the PNTs were found within 2 μm in length and 300 nm in width by an atomic force microscope and confocal laser microscope system. Plasmid DNAs were observed to be associated with PNTs by atomic force microscope and confocal laser scanning microscope. The plasmids were associated with tyrosine of PNTs with a binding constant of 2.7 × 108 M-1. The stability of plasmid DNA with PNTs against the DNase was found at 60 min. Using thioflavin T pre-stained PNTs on the corneal eye drop delivery, the distribution of PNTs was in the epithelial and stroma regions. After corneal debridement, the rhodamine-labeled plasmid DNA and thioflavin T pre-stained PNTs were also delivered and could be observed in the stroma of cornea. PNTs complexed with anti-apoptotic plasmid caspase 3 silencing shRNA eye drop delivery decreased 41% of caspase 3 activity after the first dose by caspase 3 activity and Western blot analysis.
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Affiliation(s)
- Yu-Hsing Lee
- School of Pharmacy, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan.
| | - Shwu-Fen Chang
- Graduate Institute of Medical Sciences, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan.
| | - Jiahorng Liaw
- School of Pharmacy, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan.
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5
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Antitumor and antimicrobial activity of some cyclic tetrapeptides and tripeptides derived from marine bacteria. Mar Drugs 2015; 13:3029-45. [PMID: 25988520 PMCID: PMC4446616 DOI: 10.3390/md13053029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 04/22/2015] [Accepted: 05/06/2015] [Indexed: 11/25/2022] Open
Abstract
Marine derived cyclo(Gly-l-Ser-l-Pro-l-Glu) was selected as a lead to evaluate antitumor-antibiotic activity. Histidine was chosen to replace the serine residue to form cyclo(Gly-l-His-l-Pro-l-Glu). Cyclic tetrapeptides (CtetPs) were then synthesized using a solution phase method, and subjected to antitumor and antibiotic assays. The benzyl group protected CtetPs derivatives, showed better activity against antibiotic-resistant Staphylococcus aureus in the range of 60–120 μM. Benzyl group protected CtetPs 3 and 4, exhibited antitumor activity against several cell lines at a concentration of 80–108 μM. However, shortening the size of the ring to the cyclic tripeptide (CtriP) scaffold, cyclo(Gly-l-Ser-l-Pro), cyclo(Ser-l-Pro-l-Glu) and their analogues showed no antibiotic or antitumor activity. This phenomenon can be explained from their backbone structures.
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6
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Ma C, Chen H, Li C, Zhang J, Qiao R. An IDB-containing low molecular weight short peptide as an efficient DNA cleavage reagent. Org Biomol Chem 2015; 13:4524-31. [DOI: 10.1039/c4ob02518k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present poly(aspartic acid) grafting bis-amine conjugates as artificial nucleases, which can effectively induce double-strand DNA cleavage.
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Affiliation(s)
- Chunying Ma
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Huan Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Jin Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
- State Key Laboratory of Medicinal Chemical Biology
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Chakraborty S, Tyagi P, Tai DF, Lee GH, Peng SM. A lead (II) 3D coordination polymer based on a marine cyclic peptide motif. Molecules 2013; 18:4972-85. [PMID: 23624650 PMCID: PMC6270303 DOI: 10.3390/molecules18054972] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/16/2013] [Accepted: 04/24/2013] [Indexed: 11/23/2022] Open
Abstract
The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-L-Ser-L-Pro-L-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network in the crystalline state. The polymerization of a heavy metal ion with a rigid asymmetric cyclic tetrapeptide represents the first example of a new class of macrocyclic complexes.
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Affiliation(s)
| | - Pooja Tyagi
- Department of Chemistry, National Dong-Hwa University, Hualien 974, Taiwan
| | - Dar-Fu Tai
- Department of Chemistry, National Dong-Hwa University, Hualien 974, Taiwan
| | - Gene-Hsiang Lee
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Shie-Ming Peng
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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Hsieh WH, Chang SF, Chen HM, Chen JH, Liaw J. Oral gene delivery with cyclo-(D-Trp-Tyr) peptide nanotubes. Mol Pharm 2012; 9:1231-49. [PMID: 22480317 DOI: 10.1021/mp200523n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The feasibility of cyclo-(D-Trp-Tyr) peptide nanotubes (PNTs) as oral gene delivery carriers was investigated in nude mice with eight 40 μg doses of pCMV-lacZ in 2 days at 3 h intervals. The association between DNA and PNTs, the DNase I stability of PNTs-associated DNA, and in vitro permeability of DNA were estimated. The results showed that the cyclo-(D-Trp-Tyr) PNTs self-associated at concentrations above 0.01 mg/mL. Plasmid DNA associated with PNTs with a binding constant of 3.2 × 10(8) M(-1) calculated by a fluorescence quenching assay. PNTs were able to protect DNA from DNase I, acid, and bile digestion for 50 min, 60 min, and 180 min, respectively. The in vitro duodenal apparent permeability coefficient of pCMV-lacZ calculated from a steady state flux was increased from 49.2 ± 21.6 × 10(-10) cm/s of naked DNA to 395.6 ± 142.2 × 10(-10) cm/s of pCMV-lacZ/PNT formulation. The permeation of pCMV-lacZ formulated with PNTs was found in an energy-dependent process. Furthermore, β-galatosidase (β-Gal) activity in tissues was quantitatively assessed using chlorophenol red-β-D-galactopyranoside (CPRG) and was significantly increased by 41% in the kidneys at 48 h and by 49, 63, and 46% in the stomach, duodenum, and liver, respectively, at 72 h after the first dose of oral delivery of pCMV-lacZ/PNT formulation. The organs with β-Gal activity were confirmed for the presence of pCMV-lacZ DNA with Southern blotting analysis and intracellular tracing the TM-rhodamine-labeled DNA and the presence of mRNA by reverse transcription-real time quantitative PCR (RT-qPCR). Another plasmid (pCMV-hRluc) encoding Renilla reniformis luciferase was used to confirm the results. An increased hRluc mRNA and luciferase in stomach, duodenum, liver, and kidney were detected by RT-qPCR, ex vivo bioluminescence imaging, luciferase activity quantification, and immunostaining, respectively.
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Affiliation(s)
- Wei-Hsien Hsieh
- College of Pharmacy, Taipei Medical University, 250 Wu Hsing Street, Taipei 110, Taiwan
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Li ZF, Chen HL, Zhang LJ, Lu ZL. Synthesis of [12]aneN3-dipeptide conjugates as metal-free DNA nucleases. Bioorg Med Chem Lett 2012; 22:2303-7. [PMID: 22364814 DOI: 10.1016/j.bmcl.2012.01.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/16/2012] [Accepted: 01/20/2012] [Indexed: 11/28/2022]
Abstract
In this Letter, a series of macrocyclic polyamine [12]aneN(3)-dipeptide conjugates as a new type of metal-free nucleases were synthesized and fully characterized with (1)H NMR, (13)C NMR, IR, and HR-MS. Results indicate that these conjugates can bind to calf thymus DNA mainly through electrostatic interaction and can cleave the plasmid DNA at 200 μM (pH 7.2, 37°C), with an acceleration of 10(6)-fold via hydrolytic pathway.
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Affiliation(s)
- Zhi-Fen Li
- College of Chemistry, Beijing Normal University, Beijing, China
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Alkhader S, Ezra A, Kasparkova J, Brabec V, Yavin E. A Metal-Free DNA Nuclease Based on a Cyclic Peptide Scaffold. Bioconjug Chem 2010; 21:1425-31. [DOI: 10.1021/bc900543b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shadad Alkhader
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 61265 Brno, Czech Republic
| | - Aviva Ezra
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 61265 Brno, Czech Republic
| | - Jana Kasparkova
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 61265 Brno, Czech Republic
| | - Viktor Brabec
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 61265 Brno, Czech Republic
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 61265 Brno, Czech Republic
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12
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Patra AK, Nethaji M, Chakravarty AR. Red-light photosensitized cleavage of DNA by (l-lysine)(phenanthroline base)copper(ii) complexes. Dalton Trans 2005:2798-804. [PMID: 16075123 DOI: 10.1039/b506310h] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ternary copper(II) complexes [Cu(l-lys)B(ClO4)](ClO4)(1-4), where B is a heterocyclic base, viz. 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 3) and dipyrido[3,2-a:2',3'-c]phenazene (dppz, 4), are prepared and their DNA binding and photo-induced DNA cleavage activity studied (l-lys =l-lysine). Complex 2, structurally characterized by X-ray crystallography, shows a square-pyramidal (4 + 1) coordination geometry in which the N,O-donor l-lysine and N,N-donor heterocyclic base bind at the basal plane and the perchlorate ligand is bonded at the elongated axial site. The crystal structure shows the presence of a pendant cationic amine moiety -(CH2)4NH3+ of l-lysine. The one-electron paramagnetic complexes display a d-d band in the range of 598-762 nm in DMF and exhibit cyclic voltammetric response due to Cu(II)/Cu(I) couple in the range of 0.07 to -0.20 V vs. SCE in DMF-Tris-HCl buffer. The complexes having phenanthroline bases display good binding propensity to the calf thymus DNA giving an order: 4 (dppz) > 3 (dpq) > 2 (phen)>> 1 (bpy). Control cleavage experiments using pUC19 supercoiled DNA and distamycin suggest major groove binding for the dppz and minor groove binding for the other complexes. Complexes 2-4 show efficient DNA cleavage activity on UV (365 nm) or visible light (694 nm ruby laser) irradiation via a mechanistic pathway involving formation of singlet oxygen as the reactive species. The amino acid l-lysine bound to the metal shows photosensitizing effect at red light, while the heterocyclic bases are primarily DNA groove binders. The dpq and dppz ligands display red light-induced photosensitizing effects in copper-bound form.
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Affiliation(s)
- Ashis K Patra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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Patra AK, Dhar S, Nethaji M, Chakravarty AR. Metal-assisted red light-induced DNA cleavage by ternary l-methionine copper(ii) complexes of planar heterocyclic bases. Dalton Trans 2005:896-902. [PMID: 15726142 DOI: 10.1039/b416711b] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ternary copper(II) complexes [Cu(l-met)B(Solv)](ClO4) (1-4), where B is a N,N-donor heterocyclic base like 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 3) and dipyrido[3,2-a:2'],3'-c]phenazene (dppz, 4), are prepared and their DNA binding and photo-induced DNA cleavage activity studied (L-Hmet =L-methionine). Complex 2, structurally characterized by X-ray crystallography, shows a square pyramidal (4 + 1) coordination geometry in which the N,O-donor L-methionine and N,N-donor heterocyclic base bind at the basal plane and a solvent molecule is coordinated at the axial site. The complexes display a d-d band at approximately 600 nm in DMF and exhibit a cyclic voltammetric response due to the Cu(II)/Cu(I) couple near -0.1 V in DMF-Tris-HCl buffer. The complexes display significant binding propensity to the calf thymus DNA in the order: 4(dppz) > 3(dpq) > 2(phen>> 1(bpy). Control cleavage experiments using pUC19 supercoiled DNA and distamycin suggest major groove binding for the dppz and minor groove binding for the other complexes. Complexes 2-4 show efficient DNA cleavage activity on UV (365 nm) or red light (632.8 nm) irradiation via a mechanistic pathway involving formation of singlet oxygen as the reactive species. The DNA cleavage activity of the dpq complex is found to be significantly more than its dppz and phen analogues.
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Affiliation(s)
- Ashis K Patra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
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Chang JC, Yang CH, Chou PY, Yang WH, Chou IC, Lu CT, Lin PH, Hou RCW, Jeng KCG, Cheng CC, Sheh L. DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs. Bioorg Med Chem 2004; 12:53-61. [PMID: 14697770 DOI: 10.1016/j.bmc.2003.10.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Three peptide amides, HPRK(Py)(4)HPRK-NH(2) (PyH-12), HPRK(Py)(3)HPRK-NH(2) (PyH-11) and HPRK(Py)(2)HPRK-NH(2) (PyH-10), incorporating two HPRK motifs and various 4-amino-1-methylpyrrole-2-carboxylic acid residues (Py) were synthesized by solid-phase peptide methodology. The binding of these three peptides to a 5'-32P-labeled 158-mer DNA duplex (Watson fragment) and to a 5'-32P-labeled 135-mer DNA duplex (complementary Crick fragment) was investigated by quantitative DNase I footprinting. On the 158-mer Watson strand, the most distinctive DNase I blockages seen with all three peptides occur around positions 105-112 and 76-79, corresponding to the sequences 5'-GAGAAAAT-3' and 5'-CGGT-3', respectively. However, on the complementary Crick strand, only PyH-12 strongly discriminates the 5'-TTT-3' site around positions 108-110 whereas both PyH-11 and PyH-10 have moderate binding around positions 102-112 comprising the sequence 5'-ATTTTCTCCTT-3'. Possible bidentate and single interactions of the side-chain functions and alpha-amino protons of the peptides with DNA bases are discussed.
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Affiliation(s)
- Jung-Cheng Chang
- Department of Chemistry, Tunghai Christian University, 407, ROC, Taichung, Taiwan
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