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Shiraishi JI, Shimakura N, Kimura K, Egusa AS, Ohta Y. Embryonic Cadaverine Signaling: Implications for Plasma Free Amino Acid and Skeletal Muscle Energy Metabolism in Newly Hatched Chicks. J Poult Sci 2024; 61:2024017. [PMID: 38846485 PMCID: PMC11150007 DOI: 10.2141/jpsa.2024017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/19/2024] [Indexed: 06/09/2024] Open
Abstract
Cadaverine is a bioactive substance derived from lysine degradation by lysine decarboxylase and has gained attention for its physiological effects. Studies in rodents have revealed its role as a cell growth regulator, particularly intestinal bacterial-produced cadaverine. However, the nutritional and physiological roles of cadaverine during the embryonic period remain unclear, especially considering the immature state of the gut microbiota and digestive functions during this stage. This study explored the potential functions of cadaverine as a nutritional and metabolic signal during chicken embryonic development. Experiments were conducted using an in ovo administration method to evaluate the effects of nutritional bioactive substances on developing chicken embryos. Although there were no observable changes in body or organ weights of newly hatched chicks following in ovo cadaverine administration to day 18 chick embryos, plasma tryptophan, Nτ-methylhistidine, and Nπ-methylhistidine concentrations decreased and the gene expression of insulin/insulin-like growth factor 1 signaling in skeletal muscle was upregulated. These findings imply that cadaverine influences tryptophan metabolism and skeletal muscle catabolism during the embryonic period, suggesting its role as a bioactive factor contributing to energy metabolism signaling in skeletal muscle.
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Affiliation(s)
- Jun-ichi Shiraishi
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, Musashino 180-8602, Japan
| | - Naoko Shimakura
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, Musashino 180-8602, Japan
| | - Kazuki Kimura
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, Musashino 180-8602, Japan
| | - Ai-Saiga Egusa
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, Musashino 180-8602, Japan
| | - Yoshiyuki Ohta
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, Musashino 180-8602, Japan
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Hoshino H, Kasahara Y, Obika S. Polyamines promote xenobiotic nucleic acid synthesis by modified thermophilic polymerase mutants. RSC Chem Biol 2024; 5:467-472. [PMID: 38725908 PMCID: PMC11078213 DOI: 10.1039/d4cb00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
The enzymatic synthesis of xenobiotic nucleic acids (XNA), which are artificially sugar-modified nucleic acids, is essential for the preparation of XNA libraries. XNA libraries are used in the in vitro selection of XNA aptamers and enzymes (XNAzymes). Efficient enzymatic synthesis of various XNAs can enable the screening of high-quality XNA aptamers and XNAzymes by expanding the diversity of XNA libraries and adding a variety of properties to XNA aptamers and XNAzymes. However, XNAs that form unstable duplexes with DNA, such as arabino nucleic acid (ANA), may dissociate during enzyme synthesis at temperatures suitable for thermophilic polymerases. Thus, such XNAs are not efficiently synthesised by the thermophilic polymerase mutants at the end of the sequence. This undesirable bias reduces the possibility of generating high-quality XNA aptamers and XNAzymes. Here, we demonstrate that polyamine-induced DNA/ANA duplex stabilisation promotes ANA synthesis that is catalysed by thermophilic polymerase mutants. Several polyamines, including spermine, spermidine, cadaverine, and putrescine promote ANA synthesis. The negative effect of polyamines on the fidelity of ANA synthesis was negligible. We also showed that polyamines promote the synthesis of other XNAs, including 2'-amino-RNA/2'-fluoro-RNA mixture and 2'-O-methyl-RNA. In addition, we found that polyamine promotes DNA synthesis from the 2'-O-methyl-RNA template. Polyamines, with the use of thermophilic polymerase mutants, may allow further development of XNA aptamers and XNAzymes by promoting the transcription and reverse transcription of XNAs.
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Affiliation(s)
- Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita 565-0871 Osaka Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita 565-0871 Osaka Japan
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3
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Ortega JA, Sasselli IR, Boccitto M, Fleming AC, Fortuna TR, Li Y, Sato K, Clemons TD, Mckenna ED, Nguyen TP, Anderson EN, Asin J, Ichida JK, Pandey UB, Wolin SL, Stupp SI, Kiskinis E. CLIP-Seq analysis enables the design of protective ribosomal RNA bait oligonucleotides against C9ORF72 ALS/FTD poly-GR pathophysiology. SCIENCE ADVANCES 2023; 9:eadf7997. [PMID: 37948524 PMCID: PMC10637751 DOI: 10.1126/sciadv.adf7997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 10/11/2023] [Indexed: 11/12/2023]
Abstract
Amyotrophic lateral sclerosis and frontotemporal dementia patients with a hexanucleotide repeat expansion in C9ORF72 (C9-HRE) accumulate poly-GR and poly-PR aggregates. The pathogenicity of these arginine-rich dipeptide repeats (R-DPRs) is thought to be driven by their propensity to bind low-complexity domains of multivalent proteins. However, the ability of R-DPRs to bind native RNA and the significance of this interaction remain unclear. Here, we used computational and experimental approaches to characterize the physicochemical properties of R-DPRs and their interaction with RNA. We find that poly-GR predominantly binds ribosomal RNA (rRNA) in cells and exhibits an interaction that is predicted to be energetically stronger than that for associated ribosomal proteins. Critically, modified rRNA "bait" oligonucleotides restore poly-GR-associated ribosomal deficits and ameliorate poly-GR toxicity in patient neurons and Drosophila models. Our work strengthens the hypothesis that ribosomal function is impaired by R-DPRs, highlights a role for direct rRNA binding in mediating ribosomal dysfunction, and presents a strategy for protecting against C9-HRE pathophysiological mechanisms.
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Affiliation(s)
- Juan A. Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Pathology and Experimental Therapy, Institute of Neurosciences, University of Barcelona, Barcelona 08907, Spain
| | - Ivan R. Sasselli
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Centro de Fisica de Materiales (CFM), CSIC-UPV/EHU, 20018 San Sebastián, Spain
| | - Marco Boccitto
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Andrew C. Fleming
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tyler R. Fortuna
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Yichen Li
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kohei Sato
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - Tristan D. Clemons
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth D. Mckenna
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Thao P. Nguyen
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric N. Anderson
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Jesus Asin
- Department of Statistical Methods, School of Engineering, University of Zaragoza, Zaragoza 50018, Spain
| | - Justin K. Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Udai B. Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Sandra L. Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Samuel I. Stupp
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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4
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Polyamines conjugated to deoxyribonucleic acid-protein in cell nucleus from filling grain embryos were involved in tolerance of wheat to drought. J Biosci 2022. [DOI: 10.1007/s12038-022-00319-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Exploring the DNA interactions, FGF growth receptor interaction and biological screening of metal(II) complexes of NNN donor ligand derived from 2‑(aminomethyl)benzimidazole. Int J Biol Macromol 2019; 126:1303-1317. [DOI: 10.1016/j.ijbiomac.2018.09.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 11/22/2022]
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6
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Synthesis, Structure, DNA Interaction, and SOD Activity of Three Nickel(II) Complexes Containing L-Phenylalanine Schiff Base and 1,10-Phenanthroline. Bioinorg Chem Appl 2018; 2018:8478152. [PMID: 30073020 PMCID: PMC6057355 DOI: 10.1155/2018/8478152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/28/2018] [Indexed: 01/03/2023] Open
Abstract
Three hexacoordinated octahedral nickel(II) complexes, [Ni(sal-L-phe)(phen)(CH3OH)]·CH3OH (1), [Ni(naph-L-phe)(phen)(CH3OH)] (2), and [Ni(o-van-L-phe)(phen)(CH3OH)]·5CH3OH (3) (sal-L-phe = a Schiff base derived from salicylaldehyde and L-phenylalanine, naph-L-phe = a Schiff base derived from 2-hydroxy-1-naphthaldehyde and L-phenylalanine, o-van-L-phe = a Schiff base derived from o-vanillin and L-phenylalanine, and phen = 1,10-phenanthroline), have been synthesized and characterized by elemental analysis, IR spectra, and single-crystal X-ray diffraction. The interactions of these complexes with CT-DNA were studied by UV-Vis absorption spectroscopy, fluorescence spectroscopy, circular dichroism spectroscopy, and viscosity measurements. The binding constant (Kb) values of 1.82 × 104 M−1 for 1, 1.96 × 104 M−1 for 2, and 2.02 × 104 M−1 for 3 suggest that each of these complexes could bind with DNA in a moderate intercalative mode. Complex 3 exhibited a stronger interaction with CT-DNA than complexes 1 and 2. In addition, the superoxide scavenging activity of these complexes was investigated by the nitrotetrazolium blue chloride (NBT) light reduction method, and the results showed that they exhibited a significant superoxide scavenging activity with the IC50 values of 4.4 × 10−5 M for complex 1, 5.6 × 10−5 M for complex 2, and 3.1 × 10−5 M for complex 3, respectively.
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7
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Menzi M, Wild B, Pradère U, Malinowska AL, Brunschweiger A, Lightfoot HL, Hall J. Towards Improved Oligonucleotide Therapeutics Through Faster Target Binding Kinetics. Chemistry 2017; 23:14221-14230. [PMID: 28746731 DOI: 10.1002/chem.201701670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 01/19/2023]
Abstract
When used as inhibitors of gene expression in vivo, oligonucleotides require modification of their structures to boost their binding affinity for complementary target RNAs. To date, hundreds of modifications have been designed and tested but few have proven to be useful. Among those investigated are mono- and polyamino-groups. These are positively charged at physiological pH and have been appended to oligonucleotides in an effort to reduce electrostatic repulsion during hybridization to RNAs, but have generally shown relatively minor benefits to binding. We conjugated spermine to uracils in oligonucleotides via a triazole linker so that the polyamine fits in the major groove of a subsequently formed RNA-duplex. The modifications produced large increases in target-binding affinity of the oligonucleotides. Using surface plasmon resonance-based assays, we showed that the increases derived mainly from faster annealing (kon ). We propose that the spermine fragments play a similar role to that of natural polyamines during oligonucleotide-target interactions in cells, and may be advantageous for oligonucleotides that operate catalytic mechanisms.
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Affiliation(s)
- Mirjam Menzi
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Bettina Wild
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Anna L Malinowska
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Helen L Lightfoot
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
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8
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Wei Q, Dong J, Zhao P, Li M, Cheng F, Kong J, Li L. DNA binding, BSA interaction and SOD activity of two new nickel(II) complexes with glutamine Schiff base ligands. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 161:355-67. [DOI: 10.1016/j.jphotobiol.2016.03.053] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/10/2016] [Accepted: 03/24/2016] [Indexed: 12/31/2022]
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9
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Thomas TJ, Tajmir-Riahi HA, Thomas T. Polyamine–DNA interactions and development of gene delivery vehicles. Amino Acids 2016; 48:2423-31. [DOI: 10.1007/s00726-016-2246-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/27/2016] [Indexed: 12/11/2022]
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10
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Brzezinska J, Markiewicz WT. Non-Nucleosidic Analogues of Polyaminonucleosides and Their Influence on Thermodynamic Properties of Derived Oligonucleotides. Molecules 2015; 20:12652-69. [PMID: 26184145 PMCID: PMC6332422 DOI: 10.3390/molecules200712652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 11/22/2022] Open
Abstract
The rationale for the synthesis of cationic modified nucleosides is higher expected nuclease resistance and potentially better cellular uptake due to an overall reduced negative charge based on internal charge compensation. Due to the ideal distance between cationic groups, polyamines are perfect counterions for oligodeoxyribonucleotides. We have synthesized non-nucleosidic analogues built from units that carry different diol structures instead of sugar residues and functionalized with polyamines. The non-nucleosidic analogues were attached as internal or 5′-terminal modifications in oligodeoxyribonucleotide strands. The thermodynamic studies of these polyaminooligonucleotide analogues revealed stabilizing or destabilizing effects that depend on the linker or polyamine used.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
| | - Wojciech T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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11
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Charles I, Davis E, Arya DP. Efficient stabilization of phosphodiester (PO), phosphorothioate (PS), and 2'-O-methoxy (2'-OMe) DNA·RNA hybrid duplexes by amino sugars. Biochemistry 2012; 51:5496-505. [PMID: 22639785 DOI: 10.1021/bi3004507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Antisense strategies that target DNA·RNA hybrid structures offer potential for the development of new therapeutic drugs. The α-sarcin loop region of the 23S [corrected] rRNA domain has been shown to be a high value target for such strategies. Herein, aminoglycoside interaction with three RNA·DNA α-sarcin targeted duplexes (rR·dY, rR·S-dY, and rR·2'OMe-rY) have been investigated to determine the overall effect of aminoglycoside interaction on the stability, affinity, and conformation of these hybrid duplexes. To this end, UV thermal denaturation, circular dichroism spectroscopy, fluorescence intercalator displacement, and ITC as well as DSC calorimetry experiments were carried out. The results suggest the following. (1) Of all the aminoglycosides studied, neomycin confers the highest thermal stability on all three hybrid duplexes studied. (2) There is no appreciable difference in aminoglycoside-induced thermal stability between the unmodified rR·dY and phophorothioate modified rR·S-dY duplexes. (3) The rR·2'OMe-rY duplexes thermal stability is slightly less than the other two hybrids. (4) In all three duplexes, aminoglycoside-induced thermal stability decreased as the number of amino groups decreased. (5) CD scans revealed similar spectra for the rR·dY and rR·S-dY duplexes as well as a more pronounced A-form signal for the rR·2'OMe-rY duplex. (6) FID assays paralleled the CD results, yielding similar affinity values between the rR·dY and rR·S-dY duplexes and higher affinities with the rR·2'OMe-rY duplex. (7) The overall affinity trend between aminoglycosides and the three duplexes was determined to be neomycin > paromomycin > neamine > ribostamycin. (8) ITC K(a) values revealed similar binding constants for the rR·dY and rR·S-dY duplexes with rR·dY having a K(1) of (1.03 ± 0.58) × 10(7) M(-1) and K(2) of (1.13 ± 0.07) × 10(5) M(-1) while rR·S-dY produced a K(1) of (1.17 ± 0.54) × 10(7) M(-1) and K(2) of (1.27 ± 0.69) × 10(5) M(-1). (8) The rR·2'OMe-rY produced a slightly higher binding constant values with a K(1) of (1.25 ± 0.24) × 10(7) M(-1) and K(2) of (3.62 ± 0.18) × 10(5) M(-1). (9) The ΔT(m)-derived K(Tm) of 3.81 × 10(7) M(-1) for rR·S-dY was in relative agreement with the corresponding K(1) of 1.17 × 10(7) M(-1) derived constant from the fitted ITC. These results illustrate that the increased DNA·RNA hybrid duplex stability in the presence of aminoglycosides can help extend the roles of aminoglycosides in designing modified ODNs for targeting RNA.
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Affiliation(s)
- I Charles
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, South Carolina 29634, United States
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12
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Chang YM, Chen CKM, Hou MH. Conformational changes in DNA upon ligand binding monitored by circular dichroism. Int J Mol Sci 2012; 13:3394-3413. [PMID: 22489158 PMCID: PMC3317384 DOI: 10.3390/ijms13033394] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 11/16/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future.
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Affiliation(s)
- Yu-Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; E-Mails: (Y.-M.C.); (C.K.-M.C.)
| | - Cammy K.-M. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; E-Mails: (Y.-M.C.); (C.K.-M.C.)
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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Kedracki D, Safir I, Gour N, Ngo KX, Vebert-Nardin C. DNA–Polymer Conjugates: From Synthesis, Through Complex Formation and Self-assembly to Applications. BIO-SYNTHETIC POLYMER CONJUGATES 2012. [DOI: 10.1007/12_2012_181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Effects of cationic and anionic nanoparticles on the stability of the secondary structure of DNA. Colloid Polym Sci 2011. [DOI: 10.1007/s00396-011-2453-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Liu Y, Stepanov VG, Strych U, Willson RC, Jackson GW, Fox GE. DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli. BMC Biotechnol 2010; 10:85. [PMID: 21134283 PMCID: PMC3019158 DOI: 10.1186/1472-6750-10-85] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/06/2010] [Indexed: 01/24/2023] Open
Abstract
Background Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3×pen aRNA) was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.
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Affiliation(s)
- Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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16
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Tapia MJ, Montserín M, Valente AJM, Burrows HD, Mallavia R. Binding of polynucleotides to conjugated polyelectrolytes and its applications in sensing. Adv Colloid Interface Sci 2010; 158:94-107. [PMID: 19836007 DOI: 10.1016/j.cis.2009.09.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 09/10/2009] [Accepted: 09/24/2009] [Indexed: 12/31/2022]
Abstract
We provide a brief overview of the structural characteristics of the main groups of conjugated polyelectrolytes (CPEs) as well as the methods of synthesis and their behaviour in solution. Their tendency to form aggregates in solution, which is one of the key points to be taken into account for them to be used in polynucleotide sensing, is also considered and the various strategies adopted to avoid it will be discussed. These include the synthetic one (with the incorporation of charged and/or bulky substituents), the use of organic co-solvents and the addition of surfactants. The main physical chemical changes (optical, photophysical, electrical conductivity and viscosity) observed upon direct binding between polynucleotide and CPE, the kind of interactions involved and their applicability in sensing are considered as a function of the CPE structural rigidity. Moreover, more complex devices developed in CPE-polynucleotide sensing with the involvement of additional spectroscopic probes to induce Förster resonant energy transfer processes (FRET) or superquenching phenomena are reviewed. Finally, the main CPE applications in biosensing and the potential use of these systems in understanding DNA compaction and possible extension to the construction of supramolecular oligonucleotide structures are summarized.
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Affiliation(s)
- Maria J Tapia
- Departamento de Química, Universidad de Burgos, Plaza Misael Bañuelos, Burgos 09001, Spain.
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Zulkefeli M, Sogon T, Takeda K, Kimura E, Aoki S. Design and synthesis of a stable supramolecular trigonal prism formed by the self-assembly of a linear tetrakis(Zn2+-cyclen) complex and trianionic trithiocyanuric acid in aqueous solution and its complexation with DNA (cyclen = 1,4,7,10-tetraazacyclododecane). Inorg Chem 2010; 48:9567-78. [PMID: 19743814 DOI: 10.1021/ic901407d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new supramolecular complex, {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+), was designed and synthesized by the 3:4 self-assembly of a linear tetrakis(Zn(2+)-cyclen) complex (Zn(4)L(4))(8+) and trianionic trithiocyanurate (TCA(3-)) in aqueous solution (cyclen = 1,4,7,10-tetraazacyclododecane). The {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+) complex, which should have a trigonal prism configuration, was found to be very stable in aqueous solution at neutral pH and 25 degrees C, as evidenced by (1)H NMR titration, potentiometric pH and UV titrations, and MS measurements. The complex does not dissociate into the starting building blocks in the presence of Zn(2+)-binding anions such as phosphates and double-stranded DNA. The results of the competitive binding assays with ethidium bromide and calf-thymus DNA, thermal melting experiments, gel mobility shift assays, and dynamic light-scattering data strongly indicated that the trigonal prism functions as a polycationic template to induce the aggregation of double-stranded DNA.
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Affiliation(s)
- Mohd Zulkefeli
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan
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18
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ACHYUTHAN KE, WHITTEN DG, BRANCH DW. Supramolecular Self-Assembling Cyanine as an Alternative to Ethidium Bromide Displacement in DNA-Drug Model Interactions during High Throughput Screening. ANAL SCI 2010; 26:55-61. [DOI: 10.2116/analsci.26.55] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - David G. WHITTEN
- Department of Chemical and Nuclear Engineering, University of New Mexico
| | - Darren W. BRANCH
- Biosensors and Nanomaterials Department, Sandia National Laboratories
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19
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N’soukpoé-Kossi CN, Ouameur AA, Thomas T, Shirahata A, Thomas TJ, Tajmir-Riahi HA. DNA Interaction with Antitumor Polyamine Analogues: A Comparison with Biogenic Polyamines. Biomacromolecules 2008; 9:2712-8. [DOI: 10.1021/bm800412r] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- C. N. N’soukpoé-Kossi
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - A. Ahmed Ouameur
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - T. Thomas
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - A. Shirahata
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - T. J. Thomas
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - H. A. Tajmir-Riahi
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
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20
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Oligonucleotide-polyamine conjugates: influence of length and position of 2'-attached polyamines on duplex stability and antisense effect. Eur J Med Chem 2008; 44:670-7. [PMID: 18617292 DOI: 10.1016/j.ejmech.2008.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 04/15/2008] [Accepted: 05/19/2008] [Indexed: 11/22/2022]
Abstract
Tethering cationic ligands to oligonucleotides results in zwitterionic molecules with often improved target affinity and better cell membrane permeation. Due to the ideal distance between cationic groups, polyamines are perfect counter ions for oligonucleotides. Using an easy and versatile procedure for attaching ligands to the 2'-position, polyamines were conjugated to distinct terminal and internal positions of oligonucleotides. With polyamines attached to terminal nucleosides, the affinity to complementary DNA or RNA strands increased with growing number of cationic amines. Tethering polyamines to an internal nucleoside of wild type DNA oligonucleotides resulted in a considerable decrease in duplex stability, but in phosphorothioates, no significant decrease was detected. Conjugates exhibited progressively higher target downregulation ability with increasing polyamine chain length in a human melanoma cell culture assay.
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21
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Marques MPM, Batista de Carvalho LAE. Vibrational spectroscopy studies on linear polyamines. Biochem Soc Trans 2007; 35:374-80. [PMID: 17371281 DOI: 10.1042/bst0350374] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Vibrational spectroscopy [both Raman and INS (inelastic neutron scattering)], coupled to quantum mechanical calculations, was used in order to perform a thorough structural analysis of linear polyamines and polynuclear polyamine metal chelates [e.g. with Pt(II) and Pd(II)] with potential anticancer activity. The complementarity of the Raman and INS spectroscopies was exploited in order to gain a better knowledge of the conformational behaviour of these systems. Moreover, the conjugation of the experimental spectroscopic data to the theoretical results allows us to obtain valuable information on the structural preferences of this kind of system, which may lead to the establishment of SARs (structure–activity relationships) ruling their biological activity. Some of the most significant results obtained by the ‘Molecular Physical-Chemistry’ Research Group of the University of Coimbra (Portugal) are reviewed here.
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Affiliation(s)
- M P M Marques
- Research Unit Molecular Physical-Chemistry, University of Coimbra, 3000 Coimbra, Portugal.
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22
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Vijayanathan V, Thomas TJ, Nair SK, Shirahata A, Gallo MA, Thomas T. Bending of the estrogen response element by polyamines and estrogen receptors alpha and beta: a fluorescence resonance energy transfer study. Int J Biochem Cell Biol 2006; 38:1191-1206. [PMID: 16767802 DOI: 10.1016/j.biocel.2005.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Estrogenic regulation of gene expression is mediated by the binding of the hormone to its receptors (ERalpha and ERbeta) followed by their binding to estrogen response element (ERE). Previous studies showed that natural polyamines -- putrescine, spermidine, and spermine -- facilitated ERalpha.ERE recognition. We determined the effects of natural and synthetic polyamines on the bending of a 27-mer oligonucleotide (ODN) harboring the ERE (ERE-ODN), using fluorescence resonance energy transfer (FRET) technique. Complementary strands of the ERE-ODN were labeled with fluorescein and tetramethylrhodamine, as donor and acceptor, respectively. The ERE-ODN was intrinsically bent with an end-to-end distance of 76 +/- 2 Angstrom, compared to a theoretical value of 98 Angstrom. The end-to-end distance of the ERE-ODN was reduced to 64 Angstrom in the presence of 250 microM spermine. A control ODN with scrambled sequence did not show intrinsic bending or spermine-induced bending. Alkyl substitution at the pendant amino groups reduced the ability of spermine to bend the ERE-ODN. Both ERalpha and ERbeta decreased the end-to-end distance of the ERE-ODN, although ERalpha was more efficient than ERbeta in inducing ERE bending. Spermine-induced bending of the ERE-ODN was significantly increased by ERalpha. Fluorescence anisotropy measurement showed that the equilibrium association constant of ERalpha-ERE binding increased by 12-fold in the presence of 250 microM spermine compared to control. The free energy change (Delta G) of ERalpha.ERE complex formation was -13.1 kcal/mol at 22 degrees C in the presence of spermine. Our results suggest that polyamine-induced bending of the ERE might be a mechanism for enhancing ERalpha-ERE binding affinity and thereby fine-tuning the transcriptional response of estrogen-responsive genes.
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Affiliation(s)
- Veena Vijayanathan
- Department of Medicine, University of Medicine and Dentistry of New Jersey--Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
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23
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Martin GR, Beck PL, Sigalet DL. Gut hormones, and short bowel syndrome: The enigmatic role of glucagon-like peptide-2 in the regulation of intestinal adaptation. World J Gastroenterol 2006; 12:4117-29. [PMID: 16830359 PMCID: PMC4087358 DOI: 10.3748/wjg.v12.i26.4117] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Short bowel syndrome (SBS) refers to the malabsorption of nutrients, water, and essential vitamins as a result of disease or surgical removal of parts of the small intestine. The most common reasons for removing part of the small intestine are due to surgical intervention for the treatment of either Crohn's disease or necrotizing enterocolitis. Intestinal adaptation following resection may take weeks to months to be achieved, thus nutritional support requires a variety of therapeutic measures, which include parenteral nutrition. Improper nutrition management can leave the SBS patient malnourished and/or dehydrated, which can be life threatening. The development of therapeutic strategies that reduce both the complications and medical costs associated with SBS/long-term parenteral nutrition while enhancing the intestinal adaptive response would be valuable.
Currently, therapeutic options available for the treatment of SBS are limited. There are many potential stimulators of intestinal adaptation including peptide hormones, growth factors, and neuronally-derived components. Glucagon-like peptide-2 (GLP-2) is one potential treatment for gastrointestinal disorders associated with insufficient mucosal function. A significant body of evidence demonstrates that GLP-2 is a trophic hormone that plays an important role in controlling intestinal adaptation. Recent data from clinical trials demonstrate that GLP-2 is safe, well-tolerated, and promotes intestinal growth in SBS patients. However, the mechanism of action and the localization of the glucagon-like peptide-2 receptor (GLP-2R) remains an enigma. This review summarizes the role of a number of mucosal-derived factors that might be involved with intestinal adaptation processes; however, this discussion primarily examines the physiology, mechanism of action, and utility of GLP-2 in the regulation of intestinal mucosal growth.
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Affiliation(s)
- G-R Martin
- Department of Gastrointestinal Sciences, Faculty of Medicine, University of Calgary, 3330 Hospital Drive NW., Calgary, Alberta T2N 4N1, Canada.
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24
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Liu H, Ji X, Yu B, Liu Y. Relationship between osmotic stress and polyamines conjugated to the deoxyribonucleic acid-protein in wheat seedling roots. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2006; 49:12-7. [PMID: 16544571 DOI: 10.1007/s11427-004-5084-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The contents of covalently conjugated polyamines (CC-PAs) and noncovalently conjugated polyamines (NCC-PAs) to deoxyribonucleic acid-protein (DNP) isolated from wheat (Triticum aestivum L.) seedling roots under osmotic stress were detected. Results showed thatafter osmotic stress treatment for 7 d, the levels in NCC-spermine (NCC-Spm) and NCC-spermidine (NCC-Spd) of drought-tolerant Yumai No. 18 cv. increased more markedly than that of drought-sensitive Yangmai No. 9 cv., while the NCC-putrescine (NCC-Put) could not be statistically detected in two cultivars. Exogenous Spm treatment alleviated osmotic stress injury to Yangmai No. 9 cv. seedlings, coupled with marked increases of NCC-Spm and NCC-Spd levels of this cultivar. Under PEG osmotic stress, the concomitant treatment of drought-tolerant Yumai No. 18 cv.seedlings with methylglyoxyl-bis (guanylhydrazone) (MGBG), an inhibitor of S-adenosylmethionine decarboxylase (SAMDC), aggravated osmotic stress injury to this cultivar, coupled with market decreases of the NCC-Spm and NCC-Spd levels. The levels in CC-Put and CC-Spd of drought-tolerant Yumai No. 18 cv. increased more markedly than that of drought-sensitive Yangmai No. 9 cv. Under osmotic stress. The treatment of drought-tolerant Yumai No. 18 cv. seedlings with phenanthrolin (o-Phen), an inhibitor of transglutaminase (TGase), aggravated osmotic stress injury to this cultivar, coupled with a reduction of sum contents of CC-Put+CC-Spd. These results suggested that NCC-Spm and NCC-Spd, together with CC-Put and CC-Spd, in DNP of roots could enhance tolerance of the wheat seedlings to osmotic stress.
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Affiliation(s)
- Huaipan Liu
- Ministry of Agriculture Key Laboratory of Crop Growth Regulation, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
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25
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Abstract
Nuclear aggregates of polyamines (NAPs) are cyclic supramolecular compounds made of polyamines and phosphate groups. Three different aggregates, s-NAP, m-NAP and l-NAP, with a molecular weight of 1035, 5175 and 9552 Da, respectively, are described. These molecules interact with genomic DNA. In consequence of this interaction, NAPs not only protect DNA from nucleases with extraordinarily greater efficiency than single polyamines (spermine, spermidine and putrescine), but also induce noticeable changes in DNA condensation status, as shown by temperature-dependent modifications of DNA electrophoretic properties. The biochemical characterization of these compounds has allowed the definition of a structural model for each NAP. According to this model, five s-NAPs assemble together to form a m-NAP unit. We hypothesize that the complexation of s-NAP into m-NAP favours the transition to Z-DNA through the progressive widening of DNA strands and the exposure of bases. We propose that NAPs, by wrapping the DNA helixes, form supramolecular tunnel-like structures that confer efficient protection without affecting DNA elasticity.
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Affiliation(s)
- Luciano D'Agostino
- Department of Clinical and Experimental Medicine, "Federico II" University of Naples, Italy.
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26
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Qin Y, Pang JY, Chen WH, Cai Z, Jiang ZH. Synthesis, DNA-binding affinities, and binding mode of berberine dimers. Bioorg Med Chem 2006; 14:25-32. [PMID: 16169735 DOI: 10.1016/j.bmc.2005.07.069] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Revised: 07/26/2005] [Accepted: 07/27/2005] [Indexed: 10/25/2022]
Abstract
Six novel berberine dimers (3a-f) were synthesized in 37-84% yield from the reaction of berberrubine (2) with dihaloalkanes of varying lengths from two to seven carbons. Their interactions with calf thymus (CT) DNA and three double helical oligodeoxynucleotides, d(AAGAATTCTT)2, d(AAGCATGCTT)2, and d(TAAGAATTCTTA)2, were investigated by means of fluorometric titration and ethidium bromide (EB) displacement experiments. Compared with the monomeric parent berberine (1), these dimers' DNA-binding affinities increased up to approximately 100-fold, suggesting a cooperative interaction of the two berberine subunits in the molecules. Furthermore, these dimers linked by different spacers show a prominent structure-activity relationship when bound with oligodeoxynucleotides. The relative binding affinities are in the order of 3b>3a>3c>3d>3e>3f with d(AAGAATTCTT)2 and d(TAAGAATTCTTA)2, and 3b>3c>3a>3d>3e>3f with d(AAGCATGCTT)2. Dimer 3b, linked with a propyl chain, exhibits the highest binding affinity. This suggests that a propyl chain may be the most suitable spacer to bridge the two berberine units for DNA binding. Spectrophotometric titration and competitive EB displacement of berberine (1) and dimer 3b indicate that both berberine and its dimers form intercalating complexes with duplex DNA. A larger redshift, a stronger hypochromic effect, and a much higher EB displacement ratio, observed in 3b, indicate that the dimer is in more intimate contact with DNA than berberine. In addition, no obvious binding of canadine (4), a hydrogenated product of berberine, with CT DNA was observed, suggesting critical roles of the quaternary ammonium cation and planar structure in the DNA-binding of berberine.
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Affiliation(s)
- Yong Qin
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
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27
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Terui Y, Ohnuma M, Hiraga K, Kawashima E, Oshima T. Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus. Biochem J 2005; 388:427-33. [PMID: 15673283 PMCID: PMC1138949 DOI: 10.1042/bj20041778] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. To clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) DNAs and tRNA in response to thermal denaturation, as measured by differential scanning calorimetry. Linear polyamines stabilized dsDNA in proportion to the number of amino nitrogen atoms within their molecular structure. We used the empirical results to derive formulae that estimate the melting temperature of dsDNA in the presence of polyamines of a particular molecular composition. ssDNA and tRNA were stabilized more effectively by tetrakis(3-aminopropyl)ammonium than any of the other polyamines tested. We propose that long linear polyamines are effective to stabilize DNA, and tetrakis(3-aminopropyl)ammonium plays important roles in stabilizing RNAs in thermophile cells.
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Affiliation(s)
- Yusuke Terui
- *Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
| | - Mio Ohnuma
- *Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
| | - Kaori Hiraga
- *Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
| | - Etsuko Kawashima
- †Department of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
| | - Tairo Oshima
- *Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
- To whom correspondence should be addressed (email )
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Chen N, Zinchenko AA, Murata S, Yoshikawa K. Specific Formation of Beads-on-a-Chain Structures on Giant DNA Using a Designed Polyamine Derivative. J Am Chem Soc 2005; 127:10910-6. [PMID: 16076197 DOI: 10.1021/ja042509q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence microscopy was used to study the folding transition of giant DNAs, T4 DNA (ca. 166 kbp), and lambda DNA (ca. 48 kbp), which proceeds through intermediates with intramolecular segregation induced by pteridine-polyamine conjugates, i.e., 2-amino-6,7-dimethyl-4-(4,9,13-triazatridecylamino)pteridine and -4-(3-(aminopropyl)amino)pteridine. According to the results of DNA denaturation, UV and fluorescent spectroscopy, and transmission electron microscopic observations, it became clear that DNA folding induced by the polyamine derivative is not a continuous shrinking process but a combination of discontinuous processes.
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Affiliation(s)
- Ning Chen
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601 Japan
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29
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D'Agostino L, di Pietro M, Di Luccia A. Nuclear aggregates of polyamines are supramolecular structures that play a crucial role in genomic DNA protection and conformation. FEBS J 2005; 272:3777-87. [PMID: 16045750 DOI: 10.1111/j.1742-4658.2005.04782.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a previous study we showed that natural polyamines interact in the nuclear environment with phosphate groups to form molecular aggregates [nuclear aggregates of polyamines (NAPs)] with estimated molecular mass values of 8000, 4800 and 1000 Da. NAPs were found to interact with genomic DNA, influence its conformation and interfere with the action of nucleases. In the present work, we demonstrated that NAPs protect naked genomic DNA from DNase I, whereas natural polyamines (spermine, spermidine and putrescine) fail to do so. In the context of DNA protection, NAPs induced noticeable changes in DNA conformation, which were revealed by temperature-dependent modifications of DNA electrophoretic properties. In addition, we presented, for NAPs, a structural model of polyamine aggregation into macropolycyclic compounds. We believe that NAPs are the sole biological forms by which polyamines efficiently protect genomic DNA against DNase I, while maintaining its dynamic structure.
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Affiliation(s)
- Luciano D'Agostino
- Department of Clinical and Experimental Medicine, Federico II University of Naples, Italy.
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30
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Roth CM, Sundaram S. Engineering synthetic vectors for improved DNA delivery: insights from intracellular pathways. Annu Rev Biomed Eng 2004; 6:397-426. [PMID: 15255775 DOI: 10.1146/annurev.bioeng.6.040803.140203] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Significant progress has been made in the area of nonviral gene delivery to date. Yet, synthetic vectors remain less efficient by orders of magnitude than their viral counterparts. Research continues toward unraveling and overcoming various barriers to the efficient delivery of DNA, whether in plasmid form encoding a gene or as an oligonucleotide for the selective inhibition of target gene expression. Novel components for overcoming these hurdles are continually being incorporated into the design of synthetic vectors, leading to increasingly more virus-like particles. Despite these advances, general principles defining the design of synthetic vectors are yet to be developed fully. A more quantitative analysis of the cellular uptake and intracellular processing of these vectors is required for the rational manipulation of vector design. Mathematical frameworks with a more conceptual basis will help obtain an integrated perspective on these complex systems. In this review, we critically examine the progress made toward the improved design of synthetic vectors by the strategic exploitation of intracellular mechanisms and explore newer possibilities to overcome obstacles in the practical realization of this field.
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Affiliation(s)
- Charles M Roth
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA.
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31
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Koculi E, Lee NK, Thirumalai D, Woodson SA. Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J Mol Biol 2004; 341:27-36. [PMID: 15312760 DOI: 10.1016/j.jmb.2004.06.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 05/28/2004] [Accepted: 06/02/2004] [Indexed: 11/21/2022]
Abstract
Polyamines are abundant metabolites that directly influence gene expression. Although the role of polyamines in DNA condensation is well known, their role in RNA folding is less understood. Non-denaturing gel electrophoresis was used to monitor the equilibrium folding transitions of the Tetrahymena ribozyme in the presence of polyamines. All of the polyamines tested induce near-native structures that readily convert to the native conformation in Mg(2+). The stability of the folded structure increases with the charge of the polyamine and decreases with the size of the polyamine. When the counterion excluded volume becomes large, the transition to the native state does not go to completion even under favorable folding conditions. Brownian dynamics simulations of a model polyelectrolyte suggest that the kinetics of counterion-mediated collapse and the dimensions of the collapsed RNA chains depend on the structure of the counterion. The results are consistent with delocalized condensation of polyamines around the RNA. However, the effective charge of the counterions is lowered by their excluded volume. The stability of the folded RNA is enhanced when the spacing between amino groups matches the distance between adjacent phosphate groups. These results show how changes in intracellular polyamine concentrations could alter RNA folding pathways.
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Affiliation(s)
- Eda Koculi
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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32
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Vaish NK, Larralde R, Fraley AW, Szostak JW, McLaughlin LW. A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality. Biochemistry 2003; 42:8842-51. [PMID: 12873145 DOI: 10.1021/bi027354i] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An analogue of uridine triphosphate containing a cationic functional group was incorporated into a degenerate RNA library by enzymatic polymerization. In vitro selection experiments using this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner completely dependent on the presence of the cationic functionality. The consensus sequence and a secondary structure model for the ATP binding site were obtained by the analysis of functional sequences selected from a partially randomized pool based on the minimal parental sequence. Mutational studies of this receptor indicated that several of the modified uridines are critical for ATP binding. Analysis of the binding of ATP analogues revealed that the modified RNA receptor makes numerous contacts with ATP, including interactions with the triphosphate group. In contrast, the aptamer repeatedly isolated from natural RNA libraries does not interact with the triphosphate group of ATP. The incorporation of a cationic amine into nucleic acids clearly allows novel interactions to occur during the molecular recognition of ligands, which carries interesting implications for the RNA world hypothesis. In addition, new materials generated from such functionalized nucleic acids could be useful tools in research and diagnostics.
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Affiliation(s)
- Narendra K Vaish
- Department of Chemistry, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA.
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Turchanowa L, Shvetsov AS, Demin AV, Khomutov AR, Wallace HM, Stein J, Milovic V. Insufficiently charged isosteric analogue of spermine: interaction with polyamine uptake, and effect on Caco-2 cell growth. Biochem Pharmacol 2002; 64:649-55. [PMID: 12167484 DOI: 10.1016/s0006-2952(02)01225-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We characterised a novel, charge-insufficient isosteric analogue of spermine, 11-[(amino)oxy]-4,9-diaza-1-aminoundecane (AOSPM). This analogue was synthesised by displacing aminopropyl group by aminooxyethyl group, the latter having pK(a) of about 5. Charge deficiency of the AOSPM molecule was fixed at a definite atom, while pK(a) of the rest nitrogen was similar to the parent polyamine. AOSPM competed with putrescine, spermidine and spermine for the uptake into the cell, and was accumulated in the cells in high amounts when exogenous polyamine synthesis was impaired. It was not recognised by the cells as growth-promoting polyamine, since it was unable to restore growth arrest due to polyamine deprivation. Like natural spermine, this polyamine analogue prevented oxidative DNA damage. AOSPM could be used not only as a tool to study polyamine homeostasis in the cell, but may have distinct applications either as radiation protector, a stable and non-toxic inhibitor of polyamine uptake or, as an appropriate vector, to enhance the uptake of impermeable compounds into the cell.
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Affiliation(s)
- Lyudmila Turchanowa
- Second Department of Medicine, Johann Wolfgang Goethe University, Theodor Stern Kai 7, D-60590 Frankfurt am Main, Germany
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Vijayanathan V, Thomas T, Sigal LH, Thomas TJ. Direct measurement of the association constant of HER2/neu antisense oligonucleotide to its target RNA sequence using a molecular beacon. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2002; 12:225-33. [PMID: 12238811 DOI: 10.1089/108729002320351548] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A molecular beacon approach was developed to directly determine the association constant of RNA-DNA hybrid formation. The molecular beacon was composed of a 15-nt loop structure containing the antisense sequence that can hybridize with the AUG translational start site of the HER2/neu gene, which is overexpressed in a significant proportion of breast, ovarian, and lung tumors. The equilibrium association constant (Ka) of DNA binding to the RNA oligonucleotide was 6.4 +/- 0.14 x 10(7) M(-1) in the presence of 150 mM NaCl at 22 degrees C. The free energy change (AG) associated with RNA-DNA hybrid formation was -10.7 kcal/mole. The melting temperature (Tm) of RNA-DNA hybrid was 64.4 degrees C +/- 1 degree C in the presence of 150 mM NaCl. The RNA-DNA hybrid was more stable than the corresponding DNA-DNA duplex in 150 mM NaCl, as judged by both Ka and Tm data. We also determined the Ka, deltaG, and Tm values of RNA-DNA and DNA-DNA duplex formation in the presence of three monovalent cations, Li+, K+, and Cs+. The feasibility of this method was also investigated using a phosphorothioate molecular beacon. The information generated through this new approach for thermodynamic measurements might be useful for the design of oligonucleotides for antisense therapeutics.
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Affiliation(s)
- Veena Vijayanathan
- Department of Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick 08903, USA
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Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Bias of purine stretches in sequenced chromosomes. COMPUTERS & CHEMISTRY 2002; 26:531-41. [PMID: 12144181 DOI: 10.1016/s0097-8485(02)00013-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 bp or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine (pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.
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Affiliation(s)
- David Ussery
- Department of Biotechnology, Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby.
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Matsukura M, Okamoto T, Miike T, Sawai H, Shinozuka K. Selective binding of trisamine-modified phosphorothioate antisense DNA to target mRNA improves antisense activity and reduces toxicity. Biochem Biophys Res Commun 2002; 293:1341-7. [PMID: 12054660 DOI: 10.1016/s0006-291x(02)00383-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Antisense activity in living cells has been thought to occur via a mechanism involving both DNA-mediated hybridization arrest of target mRNA and RNase H-mediated mRNA digestion. Therefore an ideal antisense agent should be permeable to the cell and possess capacities (1) to form a thermally stable duplex in vivo with its target, (2) to discriminate between mRNAs with different degrees of complementarity, and (3) to form antisense/RNA complexes that are susceptible to RNase H hydrolysis. A trisamine-modified deoxyuridine derivative of a novel phosphorothioate DNA 15-mer that meets all these criteria is described here. Compared with the unmodified phosphorothioate oligomer, the phosphorothioate derivative exhibits a higher antisense activity as well as reduced cytotoxicity in cells infected with HIV-1. Our data suggest that the melting temperature (T(m)) between antisense DNA and the target mRNA is not only one of the factors contributing to this derivative's improved antisense activity. Also important are an enhanced ability to discriminate between sequences and an increased susceptibility of the DNA/mRNA complex to RNase H hydrolysis. These results will be useful in designing more active, clinically useful antisense drugs.
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Affiliation(s)
- Makoto Matsukura
- Department of Child Development, Kumamoto University School of Medicine, Kumamoto City 860-0811, Japan.
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Marques MPM, Girão T, Pedroso De Lima MC, Gameiro A, Pereira E, Garcia P. Cytotoxic effects of metal complexes of biogenic polyamines. I. Platinum(II) spermidine compounds: prediction of their antitumour activity. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1589:63-70. [PMID: 11909641 DOI: 10.1016/s0167-4889(01)00186-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cytotoxicity and cell growth inhibition studies were performed for three distinct polynuclear platinum(II) complexes of spermidine, which showed to have significant cytotoxic and antiproliferative properties on the HeLa cancer cell line. The chemical environment of the metal centres in the drugs, as well as the coordination pattern of the ligand, were found to be strongly determinant of their cytotoxic ability. In the light of the results gathered, the most effective anticancer compound among the ones tested (IC50=5 microM) was found to be the one displaying three difunctional (PtCl2N2) moieties ((PtCl2)3(spd)2). Both the cytotoxic activity and the antiproliferative properties of the complexes studied showed to be irreversible for all the concentrations tested.
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Affiliation(s)
- M P M Marques
- Biochemistry Department, Faculty of Sciences and Technology, University Coimbra, Coimbra, Portugal.
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Hou MH, Lin SB, Yuann JM, Lin WC, Wang AH, Kan Ls L. Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure. Nucleic Acids Res 2001; 29:5121-8. [PMID: 11812845 PMCID: PMC97540 DOI: 10.1093/nar/29.24.5121] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The effects of ions (i.e. Na+, Mg2+ and polyamines including spermidine and spermine) on the stability of various DNA oligonucleotides in solution were studied. These synthetic DNA molecules contained sequences that mimic various cellular DNA structures, such as duplexes, bulged loops, hairpins and/or mismatched base pairs. Melting temperature curves obtained from the ultraviolet spectroscopic experiments indicated that the effectiveness of the stabilization of cations on the duplex formation follows the order of spermine > spermidine > Mg2+ > Na+ > Tris-HCl buffer alone at pH 7.3. Circular dichroism spectra showed that salts and polyamines did not change the secondary structures of those DNA molecules under study. Surface plasmon resonance (SPR) observations suggested that the rates of duplex formation are independent of the kind of cations used or the structure of the duplexes. However, the rate constants of DNA duplex dissociation decrease in the same order when those cations are involved. The enhancement of the duplex stability by polyamines, especially spermine, can compensate for the instability caused by abnormal structures (e.g. bulged loops, hairpins or mismatches). The effects can be so great as to make the abnormal DNAs as stable as the perfect duplex, both kinetically and thermodynamically. Our results may suggest that the interconversion of various DNA structures can be accomplished readily in the presence of polyamine. This may be relevant in understanding the role of DNA polymorphism in cells.
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Affiliation(s)
- M H Hou
- Institute of Chemistry, Academia Sinica, Taipei, 115 Taiwan
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Deng H, Bloomfield VA, Benevides JM, Thomas GJ. Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucleic Acids Res 2000; 28:3379-85. [PMID: 10954608 PMCID: PMC110699 DOI: 10.1093/nar/28.17.3379] [Citation(s) in RCA: 160] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2000] [Revised: 06/20/2000] [Accepted: 07/03/2000] [Indexed: 11/12/2022] Open
Abstract
Four genomic DNAs of differing GC content (Micrococcus luteus, 72% GC; Escherichia coli, 50% GC; calf thymus, 42% GC; Clostridium perfringens, 27% GC) have been employed as targets of interaction by the cationic polyamines spermidine ([H(3)N(CH(2))(3)NH(2)(CH(2))(4)NH(3)](3+)) and spermine ([(CH(2))(4)(NH(2)(CH(2))(3)NH(3))(2)](4+)). In solutions containing 60 mM DNA phosphate (approximately 20 mg DNA/ml) and either 1, 5 or 60 mM polyamine, only Raman bands associated with the phosphates exhibit large spectral changes, demonstrating that B-DNA phosphates are the primary targets of interaction. Phosphate perturbations, which are independent of base composition, are consistent with a model of non-specific cation binding in which delocalized polyamines diffuse along DNA while confined by the strong electrostatic potential gradient perpendicular to the helix axis. This finding provides experimental support for models in which polyamine-induced DNA condensation is driven by non-specific electrostatic binding. The Raman spectra also demonstrate that major groove sites (guanine N7 and thymine C5H(3)) are less affected than phosphates by polyamine-DNA interactions. Modest dependence of polyamine binding on genome base composition suggests that sequence context plays only a secondary role in recognition. Importantly, the results demonstrate that polyamine binding has a negligible effect on the native B-form secondary structure. The capability of spermidine or spermine to bind and condense genomic B-DNA without disrupting the native structure must be taken into account when considering DNA organization within bacterial nucleoids or cell nuclei.
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Affiliation(s)
- H Deng
- Department of Biochemistry, University of Minnesota, St Paul, MN 55108, USA
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Aich P, Thomas TJ, Lee JS. The role of polyamines, Na(+) and K(+) in the formation of triple helices between purine oligonucleotides and the promoter region of the human c-src proto-oncogene. Nucleic Acids Res 2000; 28:2307-10. [PMID: 10871361 PMCID: PMC102722 DOI: 10.1093/nar/28.12.2307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Binding constants for triplex formation between purine-rich oligonucleotides and a pyrimidine.purine tract of the human c-src proto-oncogene were measured by fluorescence polarization in the presence of polyamines, Na(+) and K(+). In both the hexamine and tetramine series, the longer polyamines had the larger binding constants for triplex formation at low concentrations of polyamine. At higher concentrations all values tended to plateau in the 10(9)/M range. In contrast to previous reports, K(+) did not inhibit triplex formation and at 150 mM the binding constants were again in the 10(9)/M range for both an 11mer and 22mer oligonucleotide. At 150 mM K(+) the addition of polyamines did not lead to any significant increase in the binding constants. It was determined that the lack of inhibition by K(+) was due to the low concentration (1 nM) of purine oligonucleotide required for the fluorescence polarization technique. At higher concentrations (1 microM) self-association of the oligonucleotide was observed. These results suggest that in vivo, at least for the c-src promoter, the inhibition of triplex formation by K(+) may not be detrimental. However, it may be difficult to achieve binding constants above approximately 10(9)/M even in the presence of polycations.
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Affiliation(s)
- P Aich
- Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
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