1
|
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z. Syntheses of Pyrimidine-Modified Seleno-DNAs as Stable Antisense Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539140. [PMID: 37205589 PMCID: PMC10187239 DOI: 10.1101/2023.05.02.539140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chemically modified antisense oligonucleotides (ASO) currently in pre-clinical and clinical experiments mainly focus on the 2'-position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2'-modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO's binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno-modification at 5-position of thymidine, as well as its Se-oligonucleotides. Via X-ray crystal structural study, we found that the Se-modification was located in the major groove of nucleic acid duplex and didn't cause the thermal and structural perturbations. Surprisingly, our nucleobase-modified Se-DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. This affords a novel avenue for potential antisense modification in the form of Se-antisense oligonucleotides (Se-ASO).
Collapse
Affiliation(s)
- Ziyuan Fang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Cen Chen
- Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, 618000, P. R. China
| |
Collapse
|
2
|
Duschmalé J, Schäublin A, Funder E, Schmidt S, Kiełpiński ŁJ, Nymark H, Jensen K, Koch T, Duschmalé M, Koller E, Møller MR, Schadt S, Husser C, Brink A, Sewing S, Minz T, Wengel J, Bleicher K, Li M. Investigating discovery strategies and pharmacological properties of stereodefined phosphorodithioate LNA gapmers. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:176-188. [PMID: 35860384 PMCID: PMC9271985 DOI: 10.1016/j.omtn.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jörg Duschmalé
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Adrian Schäublin
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erik Funder
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Steffen Schmidt
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Łukasz J. Kiełpiński
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Helle Nymark
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Klaus Jensen
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Troels Koch
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erich Koller
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Marianne Ravn Møller
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Simone Schadt
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Christophe Husser
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Andreas Brink
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Sabine Sewing
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Tanja Minz
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Konrad Bleicher
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Meiling Li
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
- Corresponding author Meiling Li, Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland.
| |
Collapse
|
3
|
Huber HF, Jaberi-Douraki M, DeVader S, Aparicio-Lopez C, Nava-Chavez J, Xu X, Millagaha Gedara NI, Gaudreault NN, Delong RK. Targeting SARS-CoV-2 Variants with Nucleic Acid Therapeutic Nanoparticle Conjugates. Pharmaceuticals (Basel) 2021; 14:1012. [PMID: 34681236 PMCID: PMC8539335 DOI: 10.3390/ph14101012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of SARS-CoV-2 variants is cause for concern, because these may become resistant to current vaccines and antiviral drugs in development. Current drugs target viral proteins, resulting in a critical need for RNA-targeted nanomedicines. To address this, a comparative analysis of SARS-CoV-2 variants was performed. Several highly conserved sites were identified, of which the most noteworthy is a partial homopurine palindrome site with >99% conservation within the coding region. This sequence was compared among recently emerged, highly infectious SARS-CoV-2 variants. Conservation of the site was maintained among these emerging variants, further contributing to its potential as a regulatory target site for SARS-CoV-2. RNAfold was used to predict the structures of the highly conserved sites, with some resulting structures being common among coronaviridae. An RNA-level regulatory map of the conserved regions of SARS-CoV-2 was produced based on the predicted structures, with each representing potential target sites for antisense oligonucleotides, triplex-forming oligomers, and aptamers. Additionally, homopurine/homopyrimidine sequences within the viral genome were identified. These sequences also demonstrate appropriate target sites for antisense oligonucleotides and triplex-forming oligonucleotides. An experimental strategy to investigate these is summarized along with potential nanoparticle types for delivery, and the advantages and disadvantages of each are discussed.
Collapse
Affiliation(s)
- Hanah F. Huber
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Majid Jaberi-Douraki
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Sarah DeVader
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Cesar Aparicio-Lopez
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Juliet Nava-Chavez
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Xuan Xu
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Nuwan Indika Millagaha Gedara
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA;
| | - Robert K. Delong
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| |
Collapse
|
4
|
DeLong RK, Cheng YH, Pearson P, Lin Z, Coffee C, Mathew EN, Hoffman A, Wouda RM, Higginbotham ML. Translating Nanomedicine to Comparative Oncology-the Case for Combining Zinc Oxide Nanomaterials with Nucleic Acid Therapeutic and Protein Delivery for Treating Metastatic Cancer. J Pharmacol Exp Ther 2019; 370:671-681. [PMID: 31040175 DOI: 10.1124/jpet.118.256230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/04/2019] [Indexed: 01/16/2023] Open
Abstract
The unique anticancer, biochemical, and immunologic properties of nanomaterials are becoming a new tool in biomedical research. Their translation into the clinic promises a new wave of targeted therapies. One nanomaterial of particular interest are zinc oxide (ZnO) nanoparticles (NPs), which has distinct mechanisms of anticancer activity including unique surface, induction of reactive oxygen species, lipid oxidation, pH, and also ionic gradients within cancer cells and the tumor microenvironment. It is recognized that ZnO NPs can serve as a direct enzyme inhibitor. Significantly, ZnO NPs inhibit extracellular signal-regulated kinase (ERK) and protein kinase B (AKT) associated with melanoma progression, drug resistance, and metastasis. Indeed, direct intratumoral injection of ZnO NPs or a complex of ZnO with RNA significantly suppresses ERK and AKT phosphorylation. These data suggest ZnO NPs and their complexes or conjugates with nucleic acid therapeutic or anticancer protein may represent a potential new strategy for the treatment of metastatic melanoma, and potentially other cancers. This review focuses on the anticancer mechanisms of ZnO NPs and what is currently known about its biochemical effects on melanoma, biologic activity, and pharmacokinetics in rodents and its potential for translation into large animal, spontaneously developing models of melanoma and other cancers, which represent models of comparative oncology.
Collapse
Affiliation(s)
- R K DeLong
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Yi-Hsien Cheng
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Paige Pearson
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Zhoumeng Lin
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Calli Coffee
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Elza Neelima Mathew
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Amanda Hoffman
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Raelene M Wouda
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Mary Lynn Higginbotham
- Department of Anatomy and Physiology, Nanotechnology Innovation Center (R.K.D., P.P., E.N.M., A.H.), Department of Anatomy and Physiology, Institute for Computational Comparative Medicine (Y.-H.C., Z.L.), and Department of Clinical Sciences (C.C., R.M.W., M.L.H.), College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| |
Collapse
|
5
|
Yang X. Solid-Phase Synthesis of Oligodeoxynucleotide Analogs Containing Phosphorodithioate Linkages. ACTA ACUST UNITED AC 2016; 66:4.71.1-4.71.14. [PMID: 27584703 DOI: 10.1002/cpnc.13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The oligodeoxynucleotide phosphorodithioate modification (PS2-ODN) uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphordiester backbone linkage. Like a natural phosphodiester ODN backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-ODNs are highly stable to nucleases and numerous in vitro assays have demonstrated their biological activity. For example, PS2-ODNs activated RNase H in vitro, strongly inhibited human immunodeficiency virus (HIV) reverse transcriptase, induced B-cell proliferation and differentiation, and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-ODNs has spawned a variety of strategies for synthesizing, isolating, and characterizing this compounds. ODN-thiophosphoramidite monomers are commercially available from either AM Biotechnologies or Glen Research and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of ODNs having PS2 internucleotide linkages. © 2016 by John Wiley & Sons, Inc.
Collapse
|
6
|
|
7
|
Nath RK, Xiong W, Humphries AD, Beri R. Treatment with antisense oligonucleotide reduces the expression of type I collagen in a human-skin organ-wound model: implications for antifibrotic gene therapy. Ann Plast Surg 2008; 59:699-706. [PMID: 18046156 DOI: 10.1097/sap.0b013e31803bf66c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Increased collagen expression during wound healing causes scar formation, abnormal contracture, low tensile strength, functional impairment, and disfigurement. A novel ex vivo wound-injury model demonstrated that AS60, an antisense oligonucleotide (ASO) to type I collagen, reduced the mRNA and protein expression of type 1 collagen. Following a cutaneous wound injury in a human-skin organ culture, AS60 injection resulted in a 36% (P < 0.001) and 30% decrease (P < 0.001) in type 1 collagen mRNA and protein expression after 7 days. Similarly, transfection of cultured human fibroblasts with ASO resulted in a 36% decrease (P < 0.001) and a 31% decrease (P < 0.001) in type 1 collagen mRNA and protein expression. Immunofluorescence of human skin organ culture treated with ASO showed a specific reduction in collagen expression. Using AS60 to reduce collagen expression in human skin may have implications for its use as a gene therapy agent to reduce the formation of fibrotic scarring.
Collapse
Affiliation(s)
- Rahul K Nath
- Texas Nerve and Paralysis Institute, Houston, TX 77030, USA.
| | | | | | | |
Collapse
|
8
|
Abstract
Advances in molecular and cell biology have led to further understanding of the mechanisms of malignant growth and metastasis in human breast cancer cells. Initiation and progression of breast cancer results from mutations and the abnormal expression of many genes that control cellular proliferation, differentiation, invasion, metastasis and sensitivity to therapy (chemotherapy and radiation therapy). Inhibition of host immunity also plays a role in breast cancer progression. Many genes have been selected as targets for antisense therapy, including HER-2/neu, PKA, TGF-alpha, EGFR, TGF-beta, IGFIR, P12, MDM2, BRCA, Bcl-2, ER, VEGF, MDR, ferritin, transferrin receptor, IRE, C-fos, HSP27, C-myc, C-raf and metallothionein genes. The strategy behind antisense therapy is the development of specific therapeutic agents that aim to correct the mutations and abnormal expression of cellular genes in breast tumour cells by decreasing gene expression, inducing degradation of target mRNA and causing premature termination of transcription. Many in vitro and in vivo studies have investigated the therapeutic efficacy of oligonucleotides and antisense RNAs. These studies have demonstrated specific inhibition of tumour cell growth by antisense therapy and have shown synergistic inhibitory effects between antisense oligonucleotides or antisense RNA and conventional chemotherapeutic drugs used in the treatment of breast cancer. Antisense oligonucleotides have been modified to improve their ability to penetrate cells, bind to gene sequences and downregulate target gene function. Many delivery systems for antisense RNA and antisense oligonucleotides have been developed, including virus vectors (retrovirus, adenovirus and adeno-associate virus) and liposomes, to carry the antisense RNA or oligonucleotides through the cell membrane into the cytoplasm and nucleus of the tumour cells. However, in order to determine their feasibility antisense therapies need to be further investigated to determine their antitumour activity, pharmacokinetics and toxicity in breast cancer patients.
Collapse
Affiliation(s)
- Ding Cheng Yang
- Mastology Research Institute, Head Breast Cancer Research and Treatment Center, Baton Rouge, LA 70816, USA
| | | | | |
Collapse
|
9
|
Mou TC, Gray DM. The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications. Nucleic Acids Res 2002; 30:749-58. [PMID: 11809888 PMCID: PMC100283 DOI: 10.1093/nar/30.3.749] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the problems that hamper the use of antisense DNAs as effective drugs is the non-specific binding of chemically-modified oligonucleotides to cellular proteins. We previously showed that the affinity of a model ssDNA-binding protein, the Ff gene 5 protein (g5p), was >300-fold higher for phosphorothioate-modified DNA (S-DNA) than for unmodified dA(36), consistent with the propensity of S-DNA to bind indiscriminately to proteins. The current work shows that g5p binding is also sensitive to sugar and pyrimidine modifications used in antisense oligomers. Binding affinities of g5p for 10 36mer oligomers were quantitated using solution circular dichroism measurements. The oligomers contained C-5-propyne (prC), 2'-O-methyl (2'-O-Me) or 2'-OH (RNA) groups, alone or combined with the phosphorothioate modification. In agreement with reported increases in antisense activity, the addition of prC or 2'-O-Me modifications substantially reduced the affinity of oligomers for g5p by approximately 2-fold compared with the same DNA oligomer sequences containing only phosphorothioate linkages. That is, such modifications moderated the propensity of the phosphorothioate group to bind tightly to the g5p. The Ff g5p could be a useful model protein for assessing non-specific binding effects of antisense oligomer modifications.
Collapse
Affiliation(s)
- Tung-Chung Mou
- Department of Molecular and Cell Biology, Mail Stop FO31, The University of Texas at Dallas, PO Box 830688, Richardson, TX 75083-0688, USA
| | | |
Collapse
|
10
|
Mou TC, Gray CW, Terwilliger TC, Gray DM. Ff gene 5 protein has a high binding affinity for single-stranded phosphorothioate DNA. Biochemistry 2001; 40:2267-75. [PMID: 11329296 DOI: 10.1021/bi002136f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gene 5 protein (g5p) of Ff bacteriophages is a well-studied model ssDNA-binding protein that binds cooperatively to the Ff ssDNA genome and single-stranded polynucleotides. Its affinity, K omega (the intrinsic binding constant times a cooperativity factor), can differ by several orders of magnitude for ssDNAs of different nearest-neighbor base compositions [Mou, T. C., Gray, C. W., and Gray, D. M. (1999) Biophys. J. 76, 1537-1551]. We found that the DNA backbone can also dramatically affect the binding affinity. The K omega for binding phosphorothioate-modified S-d(A)(36) was >300-fold higher than for binding unmodified P-d(A)(36) at 0.2 M NaCl. CD titrations showed that g5p bound phosphorothioate-modified oligomers with the same stoichiometry as unmodified oligomers. The CD spectrum of S-d(A)(36) underwent the same qualitative change upon protein binding as did the spectrum of unmodified DNA, and the phosphorothioate-modified DNA appeared to bind in the normal g5p binding site. Oligomers of d(A)(36) with different proportions of phosphorothioate nucleotides had binding affinities and CD perturbations intermediate to those of the fully modified and unmodified sequences. The influence of phosphorothioation on binding affinity was nearly proportional to the extent of the modification, with a small nearest-neighbor dependence. These and other results using d(ACC)(12) oligomers and mutant proteins indicated that the increased binding affinity of g5p for phosphorothioate DNA was not a polyelectrolyte effect and probably was not an effect due to the altered nucleic acid structure, but was more likely a general effect of the properties of the sulfur in the context of the phosphorothioate group.
Collapse
Affiliation(s)
- T C Mou
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688, USA
| | | | | | | |
Collapse
|
11
|
Teulade-Fichou MP, Fauquet M, Baudoin O, Vigneron JP, Lehn JM. DNA double helix destabilizing properties of cyclobisintercaland compounds and competition with a single strand binding protein. Bioorg Med Chem 2000; 8:215-22. [PMID: 10968280 DOI: 10.1016/s0968-0896(99)00283-7] [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: 11/16/2022]
Abstract
The DNA helix destabilizing activity of a series of cyclobisintercaland compounds (CBIs) has been evaluated by measuring their ability to displace a 32P-labelled oligonucleotide primer (17-mer) hybridized to the single stranded DNA of M13. This destabilizing activity appears to be strongly dependent on the cyclic structure (the linear acyclic references are inactive) and the size of the macrocycle; both features being known to determine the preferential binding of the compound to ssDNA. Interestingly, CBIs induced the dissociation of the duplex template in a concentration range (0.5-1 microM) close to that required for the destabilizing activity of single stranded DNA binding proteins (SSBs). Therefore competition experiments between CBIs and an SSB protein (Eco SSB) for binding to a single stranded oligonucleotide target (36-mer) have been performed through gel electrophoresis and nitrocellulose binding assays and strong inhibitory effects on the formation of the SSB:36-mer complex have been observed.
Collapse
Affiliation(s)
- M P Teulade-Fichou
- Laboratoire de Chimie des Iteractions Molécullaires, CNRS UPR 285, Collège de France, Paris
| | | | | | | | | |
Collapse
|
12
|
Baker BF, Monia BP. Novel mechanisms for antisense-mediated regulation of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:3-18. [PMID: 10806993 DOI: 10.1016/s0167-4781(99)00146-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- B F Baker
- Department of Molecular Pharmacology, Isis Pharmaceuticals, Carlsbad, CA 92008, USA
| | | |
Collapse
|
13
|
Antony T, Thomas T, Shirahata A, Thomas TJ. Selectivity of polyamines on the stability of RNA-DNA hybrids containing phosphodiester and phosphorothioate oligodeoxyribonucleotides. Biochemistry 1999; 38:10775-84. [PMID: 10451373 DOI: 10.1021/bi990180t] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RNA-DNA hybrid stabilization is an important factor in the efficacy of oligonucleotide-based antisense gene therapy. We studied the ability of natural polyamines, putrescine, spermidine, and spermine, and a series of their structural analogues to stabilize RNA-DNA hybrids using melting temperature (Tm) measurements, circular dichroism (CD) spectroscopy, and the ethidium bromide (EB) displacement assay. Phosphodiester (PO) and phosphorothioate (PS) oligodeoxyribonucleotides (ODNs) (21-mer) targeted to the initiation codon region of c-myc mRNA and the corresponding complementary RNA oligomer were used for this study. In the absence of polyamines, the Tm values of RNA-PODNA and RNA-PSDNA helices were 41 +/- 1 and 35 +/- 1 degrees C, respectively, in 10 mM sodium cacodylate buffer. In the presence of a hexamine analogue of spermine at a concentration of 25 microM, the hybrids were stabilized with Tm values of 80 and 78 degrees C, for RNA-PODNA and RNA-PSDNA, respectively. The d(Tm)/d(log[polyamine]) values, representing the concentration-dependent stabilization of hybrid helices by polyamines, increased from 10 to 24 for both the RNA-PODNA and RNA-PSDNA helices. Bisethyl substitution of the primary amino groups of the polyamines reduced the hybrid stabilizing potential of the polyamines. Among the homologues of spermidine [H2N(CH2)3NH(CH2)nNH2, where n = 2-8; n = 4 for spermidine] and spermine [H)N(CH2)3NH(CH2)nNH(CH2)3NH2, where n = 2-8; n = 4 for spermine], spermidine and spermine were the most effective agents for stabilizing the hybrid helices. At a physiologically compatible concentration of 150 mM NaCl, the hybrid helix formed from PODNA was more stable than that formed from PSDNA in the presence of polyamines. CD spectroscopic studies showed that the hybrids were stabilized in a conformation close to A-DNA in the presence of polyamines. The relative binding affinity of the polyamine homologues for the hybrid helices, as measured by the EB displacement assay, followed the same order in which they stabilized the hybrids. These results are important in the antisense context and in the general context of polyamine-nucleic acid interactions, and suggest that pentamine and hexamine analogues of spermine might be useful in improving the efficacy of therapeutic ODNs.
Collapse
Affiliation(s)
- T Antony
- Department of Medicine, Environmental and Occupational Health Sciences Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick 08903, USA
| | | | | | | |
Collapse
|