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Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A 2007; 105:82-7. [PMID: 18162543 DOI: 10.1073/pnas.0709082105] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab-RNA complex at 1.95 A. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab-RNA interface also differs significantly from Fab-protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology.
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Wu S, Ke A, Doudna JA. A fast and efficient procedure to produce scFvs specific for large macromolecular complexes. J Immunol Methods 2006; 318:95-101. [PMID: 17126854 PMCID: PMC2920608 DOI: 10.1016/j.jim.2006.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 09/30/2006] [Accepted: 10/04/2006] [Indexed: 10/23/2022]
Abstract
We have expanded the application of antibody phage display to a new type of antigen: ribonucleoprotein (RNP) complexes. We describe a simple and efficient method for screening antibodies specific for large intact RNPs and individual components. We also describe a fast and easy method to overcome the abundance of amber stop codons in the positive phage clones. The resulting antibodies have been used in ELISA and Western blot analysis.
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Affiliation(s)
- Si Wu
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, USA
| | - Ailong Ke
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, USA
| | - Jennifer A Doudna
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Corresponding author. 301B/E Hildebrand Hall, University of California, Berkeley, CA 94720, USA. Tel: 510-643-0225; Fax: 510-643-0080. Email address:
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Leiro J, Siso MIG, Iglesias R, Ubeira FM, Sanmartín ML. Mouse antibody response to a microsporidian parasite following inoculation with a gene coding for parasite ribosomal RNA. Vaccine 2002; 20:2648-55. [PMID: 12034089 DOI: 10.1016/s0264-410x(02)00210-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This study found that a plasmid construct encoding the small-subunit ribosomal RNA (SSUrRNA) of the microsporidian Microgemma caulleryi generates a humoral response upon intramuscular inoculation in mice. The plasmid used was pCMV, following preliminary trials indicating efficient beta-galactosidase gene expression in mouse muscle cells transfected with pCMV/beta-Gal. The antibodies produced after inoculation with pCMV/SSUDNA recognized parasite spore antigens and reached maximum levels at 30 days postinoculation, subsequently remaining stable for at least 120 days. Due to the highly conserved sequence of the SSUrDNA in different microsporidian species, these results open up interesting prospects for broad-spectrum vaccination.
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Affiliation(s)
- J Leiro
- Laboratorio de Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Yu ZC, Ding J, Nie YZ, Fan DM, Zhang XY. Preparation of single chain variable fragment of MG 7 mAb by phage display technology. World J Gastroenterol 2001; 7:510-4. [PMID: 11819819 PMCID: PMC4688663 DOI: 10.3748/wjg.v7.i4.510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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
AIM: To develop the single chain variable fragment of MG7 murine anti-human gastric cancer monoclonal antibody using the phage display technology for obtaining a tumor-targeting mediator.
METHODS: mRNA was isolated from MG7 producing murine hybridoma cell line and converted into cDNA. The variable fragments of heavy and light chain were amplified separately and assembled into ScFv with a specially constructed DNA linker by PCR. The ScFvs DNA was ligated into the phagmid vector pCANTAB5E and the ligated sample was transformed into competent E. Coli TG1. The transformed cells were infected with M13K07 helper phage to form MG7 recombinant phage antibody library. The volume and recombinant rate of the library were evaluated by means of bacterial colony count and restriction analysis. After two rounds of panning with gastric cancer cell line KATOIII of highly expressing MG7-binding antigen, the phage clones displaying ScFv of the antibody were selected by ELISA from the enriched phage clones. The antigen binding affinity of the positive clone was detected by competition ELISA. HB2151 E.coli was transfected with the positive phage clone demonstrated by competition ELISA for production of a soluble form of the MG7 ScFv. ELISA assay was used to detect the antigen-binding affinity of the soluble MG7 ScFv. Finally, the relative molecular mass of soluble MG7 ScFv was measured by SDS-PAGE.
RESULTS: The V-H, V-L and ScFv DNAs were about 340 bp, 320 bp and 750 bp, respectively. The volume of the library was up to 2 × 106 and 8 of 11 random clones were recombinants. Two phage clones could strongly compete with the original MG7 antibody for binding to the antigen expressed on KATOIII cells. Within 2 strong positive phage clones, the soluble MG7 ScFv from one clone was found to have the binding activity with KATOIII cells. SDS-PAGE showed that the relative molecular weight of soluble MG7 ScFv was 32.
CONCLUSION: The MG7 ScFv was successfully produced by phage antibody technology, which may be useful for broadening the scope of application of the antibody.
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Affiliation(s)
- Z C Yu
- Department of Gastroenterology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
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Degen WG, Pieffers M, Welin-Henriksson E, van den Hoogen FH, van Venrooij WJ, Raats JM. Characterization of recombinant human autoantibody fragments directed toward the autoantigenic U1-70K protein. Eur J Immunol 2000; 30:3029-38. [PMID: 11069087 DOI: 10.1002/1521-4141(200010)30:10<3029::aid-immu3029>3.0.co;2-j] [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: 12/14/2022]
Abstract
The U1-70K protein is specifically bound to stemloop I of the U1 small nuclear RNA contained in the U1 small nuclear ribonucleoprotein complex (U1 snRNP), which is involved in the splicing of pre-mRNA. All components of the U1 snRNP complex, including the U1-70K protein, are important autoantigens in patients with systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD). Here we describe for the first time the selection and characterization of recombinant human anti-U1-70K single chain autoantibody fragments (anti-hU1-70K scFv) from autoimmune patient-derived phage display antibody libraries. All scFv specifically recognize parts of the hU1-70K protein and its apoptotic 40-kDa cleavage product. In Western blotting assays a number of scFv preferentially recognize the 40-kDa apoptotic cleavage fragment of the U1-70K protein, suggesting a possible involvement of this apoptotic cleavage product in the autoimmune response of patients. The germline gene usage of these recombinant autoantibodies was also determined. Using several U1-70K deletion and point mutants of both human (h) and Drosophila melanogaster (Dm) origin, it was established that the U1-70K epitope that is recognized by the anti-hU1-70K scFv is located within the RNA binding domain.
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Affiliation(s)
- W G Degen
- Department of Biochemistry, University of Nijmegen, The Netherlands
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Degen WG, Pruijn GJ, Raats JM, van Venrooij WJ. Caspase-dependent cleavage of nucleic acids. Cell Death Differ 2000; 7:616-27. [PMID: 10889506 DOI: 10.1038/sj.cdd.4400672] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Autoimmune diseases are frequently characterized by the presence of autoantibodies directed against nucleic acid-protein complexes present in the nucleus of the cell. The mechanisms by which these autoantigenic molecules escape immunological tolerance are largely unknown, although a number of recent observations suggest that modified self-proteins generated during apoptosis may play an important role in the development of autoimmunity. It has been hypothesized that the recognition of these modified self-proteins by the immune system may promote autoantibody production. While apoptosis is specifically characterized by posttranslational modification of proteins, recent findings also show that nucleic acids are modified. This review summarizes the specific cleavages of some of these key nucleic acids, i.e. chromosomal DNA, ribosomal RNA and small structural RNAs (U1 snRNA, Y RNA), in apoptotic cells.
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Affiliation(s)
- W G Degen
- Department of Biochemistry, University of Nijmegen, P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands
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Degen WG, Aarssen Y, Pruijn GJ, Utz PJ, van Venrooij WJ. The fate of U1 snRNP during anti-Fas induced apoptosis: specific cleavage of the U1 snRNA molecule. Cell Death Differ 2000; 7:70-9. [PMID: 10713722 DOI: 10.1038/sj.cdd.4400617] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
During apoptosis, the U1-70K protein, a component of the spliceosomal U1 snRNP complex, is specifically cleaved by the enzyme caspase-3, converting it into a C-terminally truncated 40-kDa fragment. In this study, we show that the 40-kDa U1-70K fragment is still associated with the complete U1 snRNP complex, and that no obvious modifications occur with the U1 snRNP associated proteins U1A, U1C and Sm-B/B'. Furthermore, it is described for the first time that the U1 snRNA molecule, which is the backbone of the U1 snRNP complex, is modified during apoptosis by the specific removal of the first 5 - 6 nucleotides including the 2,2, 7-trimethylguanosine (TMG) cap. The observations that U1 snRNA cleavage is very specific (no such modifications were detected for the other U snRNAs tested) and that U1 snRNA cleavage is markedly inhibited in the presence of caspase inhibitors, indicate that an apoptotically activated ribonuclease is responsible for the specific modification of U1 snRNA during apoptosis.
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Affiliation(s)
- W G Degen
- Department of Biochemistry, University of Nijmegen, NL-6500 HB Nijmegen, The Netherlands.
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Hoet RMA, Pieffers M, Stassen MHW, Raats J, de Wildt R, Pruijn GJM, van den Hoogen F, van Venrooij WJ. The Importance of the Light Chain for the Epitope Specificity of Human Anti-U1 Small Nuclear RNA Autoantibodies Present in Systemic Lupus Erythematosus Patients. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.163.6.3304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Abs to U1 RNA are frequently found in patients suffering from systemic lupus erythematosus overlap syndromes and Ab titers correlate with disease activity. We describe the isolation of the first human anti-U1 RNA autoantibodies from a combinatorial IgG library made from the bone marrow of a systemic lupus erythematosus patient. With the use of phage display technology, two anti-U1 RNA single-chain variable fragment (scFv) Abs were selected. Both high affinity anti-U1 RNA Ab fragments (Kd ∼ 1 nM) recognize stem II of U1 RNA and were derived from the same heavy chain gene (VH3–11) and the same λ (3r) light chain gene although somatic mutations, predominantly present in the complementarity-determining regions, are different. Experiments, in which the heavy chain genes of both anti-U1 RNA scFvs were reshuffled with the original light chain repertoire of the patient resulted, after selection on stem loop II, in a large number of RNA-binding Ab fragments. All these stem loop II-specific RNA binding clones used a similar, but not identical, 3r λ light chain. When scFvs were selected from the reshuffled libraries by stem loop IV, representing the other autoantigenic site of U1 RNA, most selected Ab clones did react with stem loop IV, but no longer with stem loop II. The stem loop IV-reactive Ab clones contained different, not 3r-related, light chains. These results point to a major role for the light chain in determining the sequence specificity of these disease-related anti-U1 RNA Abs. The possibility that secondary light chain rearrangements are involved in this autoimmune response is discussed.
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Affiliation(s)
- René M. A. Hoet
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
- ‡Department of Pathology, University Hospital Maastricht, Maastricht, The Netherlands
| | - Martijn Pieffers
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
| | - Maurice H. W. Stassen
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
| | - Jos Raats
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
| | - Ruud de Wildt
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
| | - Ger J. M. Pruijn
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
| | - Frank van den Hoogen
- ‡Department of Pathology, University Hospital Maastricht, Maastricht, The Netherlands
| | - Walther J. van Venrooij
- *Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands; Department of Rheumatology, University Hospital Nijmegen, Nijmegen, The Netherlands; and
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Becker HF, Corda Y, Mathews MB, Fourrey JL, Grosjean H. Inosine and N1-methylinosine within a synthetic oligomer mimicking the anticodon loop of human tRNA(Ala) are major epitopes for anti-PL-12 myositis autoantibodies. RNA (NEW YORK, N.Y.) 1999; 5:865-875. [PMID: 10411130 PMCID: PMC1369811 DOI: 10.1017/s1355838299990118] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sera of some patients afflicted with the inflammatory disease myositis contain antibodies of the anti-PL-12 type. A fraction of these polyclonal autoantibodies specifically precipitates the fully matured human tRNA(Ala) bearing the anticodon IGC (PL-12 antigen). Earlier work (Bunn & Mathews, 1987, Science 238:116-119) had shown that the epitopes are located entirely within the anticodon stem-loop of the tRNA(Ala). Here we demonstrate that human anti-tRNA(Ala) autoantibodies immunoprecipitate a synthetic polyribonucleotide containing inosine (I) and N1-methylinosine (m1I) separated by 2 nt as in the anticodon stem-loop of human tRNA(Ala). The shortest polyribonucleotide that can be immunoprecipitated corresponds to the pentanucleotide IpGpCpm1IpUp, which corresponds to part of the anticodon loop of human tRNA(Ala) and lacks the stem-loop structure. The efficiency of immunoprecipitation was about four times greater with longer polyribonucleotides capable of forming a stem-loop structure, and was abolished by altering the relative positions of I and m1I within the synthetic polynucleotide. Synthetic oligodeoxyribonucleotide analogs of the tRNA(Ala) stem-loop, containing the sequence dIpdGdCdm1Ip, are not antigenic. Our results show that human anti-tRNA(Ala) autoantibodies selectively recognize chemical details of modified nucleotides (the 6-keto group of inosine-34 and the 6-keto group and the N1-methyl groups of N1-methylinosine-37) within an anticodon loop structure of a tRNA molecule. We also describe the chemical synthesis of the phosphoramidite derivatives corresponding to N1-methylinosine and N1-methyl-2'-deoxyinosine for use in the automatic chemical synthesis of oligonucleotides containing N1-methylinosine and N1-methyl-2'-deoxyinosine.
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Affiliation(s)
- H F Becker
- Laboratoire d'Enzymologie et Biochimie Structurales, Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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