Abstract
In addition to the canonical B-form structure, DNA can adopt alternative conformations including Z DNA, triplex DNA, as well as G4 and i-Motif quadruplex structures. Such structures have been shown to form in cells in a dynamic manner. Monoclonal antibodies against such structures represent key tools to study the biological functions of these structures. Here we provide protocols for the generation of antibody fragments against structured DNA using phage display selections.
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References
Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171(4356):737–738
Sun D, Hurley LH (2009) The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression. J Med Chem 52(9):2863–2874. https://doi.org/10.1021/jm900055s
Gessner RV, Frederick CA, Quigley GJ, Rich A, Wang AH (1989) The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG). J Biol Chem 264(14):7921–7935
Frank-Kamenetskii MD, Mirkin SM (1995) Triplex DNA structures. Annu Rev Biochem 64:65–95. https://doi.org/10.1146/annurev.bi.64.070195.000433
Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417(6891):876–880. https://doi.org/10.1038/nature755
Phan AT, Gueron M, Leroy JL (2000) The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere. J Mol Biol 299(1):123–144. https://doi.org/10.1006/jmbi.2000.3613
Bochman ML, Paeschke K, Zakian VA (2012) DNA secondary structures: stability and function of G-quadruplex structures. Nat Rev Genet 13(11):770–780. https://doi.org/10.1038/nrg3296
Huppert JL, Balasubramanian S (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33(9):2908–2916. https://doi.org/10.1093/nar/gki609
Bedrat A, Lacroix L, Mergny JL (2016) Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res 44(4):1746–1759. https://doi.org/10.1093/nar/gkw006
Wells RD (2007) Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci 32(6):271–278. https://doi.org/10.1016/j.tibs.2007.04.003
Zeraati M, Moye AL, Wong JW, Perera D, Cowley MJ, Christ DU, Bryan TM, Dinger ME (2017) Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression. Sci Rep 7(1):708. https://doi.org/10.1038/s41598-017-00739-y
Balasubramanian S, Hurley LH, Neidle S (2011) Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov 10(4):261–275. https://doi.org/10.1038/nrd3428
Collie GW, Parkinson GN (2011) The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 40(12):5867–5892. https://doi.org/10.1039/c1cs15067g
Li Q, Xiang JF, Yang QF, Sun HX, Guan AJ, Tang YL (2013) G4LDB: a database for discovering and studying G-quadruplex ligands. Nucleic Acids Res 41(Database issue):D1115–D1123. https://doi.org/10.1093/nar/gks1101
Day HA, Pavlou P, Waller ZA (2014) i-Motif DNA: structure, stability and targeting with ligands. Bioorg Med Chem 22(16):4407–4418. https://doi.org/10.1016/j.bmc.2014.05.047
Schaffitzel C, Berger I, Postberg J, Hanes J, Lipps HJ, Pluckthun A (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc Natl Acad Sci U S A 98(15):8572–8577. https://doi.org/10.1073/pnas.141229498
Biffi G, Tannahill D, McCafferty J, Balasubramanian S (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem 5(3):182–186. https://doi.org/10.1038/nchem.1548
Zeraati M, Langley DB, Schofield P, Moye AL, Rouet R, Hughes WE, Bryan TM, Dinger ME, Christ D (2018) I-motif DNA structures are formed in the nuclei of human cells. Nature Chemistry 10(6):631–637
Kristensen P, Winter G (1998) Proteolytic selection for protein folding using filamentous bacteriophages. Fold Des 3(5):321–328
Rouet R, Dudgeon K, Christie M, Langley D, Christ D (2015) Fully human VH single domains that rival the stability and cleft recognition of camelid antibodies. J Biol Chem 290(19):11905–11917. https://doi.org/10.1074/jbc.M114.614842
Rouet R, Lowe D, Dudgeon K, Roome B, Schofield P, Langley D, Andrews J, Whitfeld P, Jermutus L, Christ D (2012) Expression of high-affinity human antibody fragments in bacteria. Nat Protoc 7(2):364–373. https://doi.org/10.1038/nprot.2011.448
Lee CM, Iorno N, Sierro F, Christ D (2007) Selection of human antibody fragments by phage display. Nat Protoc 2(11):3001–3008
de Wildt RM, Mundy CR, Gorick BD, Tomlinson IM (2000) Antibody arrays for high-throughput screening of antibody-antigen interactions. Nat Biotechnol 18(9):989–994. https://doi.org/10.1038/79494
Kypr J, Kejnovska I, Renciuk D, Vorlickova M (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 37(6):1713–1725. https://doi.org/10.1093/nar/gkp026
Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1(4):263–282
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Zeraati, M., Dinger, M.E., Christ, D. (2018). Selection of Antibody Fragments Against Structured DNA by Phage Display. In: Nevoltris, D., Chames, P. (eds) Antibody Engineering. Methods in Molecular Biology, vol 1827. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8648-4_11
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DOI: https://doi.org/10.1007/978-1-4939-8648-4_11
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