Abstract
The identification of binding sites for small molecules in the genome space is important for various applications. Previously, we demonstrated rapid transcriptional activation by our small molecule SAHA-PIPs. However, it was not clear whether the strong biological effects exerted by SAHA-PIP were due to its binding specificity. Here, we used high-throughput sequencing (Bind-n-seq) to identify the binding specificity of SAHA-PIPs. Firstly sequence specificity bias was determined with SAHA-PIPs (3 and 4), which showed enhanced 6-bp sequence-specific binding compared with hairpin PIPs (1 and 2). This finding allowed us to investigate the role of β-alanine that links SAHA with PIP, which led to the design of ββ-PIPs (5 and 6). ββ-PIPs showed enhanced binding specificity. Overall, we demonstrated the importance of β-moieties for the binding specificity of PIPs, and the utilization of cost-effective high-throughput screening of these small molecules to the minor groove.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Berdasco M, Esteller M (2010) Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 19:698–711
Wade WS, Mrksich M, Dervan PB (1992) Design of peptides that bind in the minor groove of DNA at 5′-(A, T)G(A, T)C(A, T)-3′ sequences by a dimeric side-by-side motif. J Am Chem Soc 114:8783–8794. doi:10.1021/ja00049a006
Wemmer DE, Dervan PB (1997) Targeting the minor groove of DNA. Curr Opin Struct Biol 7:355–361. doi:10.1016/S0959-440X(97)80051-6
Dervan PB, Edelson BS (2003) Recognition of the DNA minor groove by pyrrole-imidazole polyamides. Curr Opin Struct Biol 13:284–299
Pelton JG, Wemmer DE (1989) Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR. Proc Natl Acad Sci U S A 86:5723–5727. doi:10.1073/pnas.86.15.5723
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Ohtsuki A, Kimura MT, Minoshima M et al (2009) Synthesis and properties of PI polyamide-SAHA conjugate. Tetrahedron Lett 50:7288–7292. doi:10.1016/j.tetlet.2009.10.034
Pandian GN, Shinohara KI, Ohtsuki A et al (2011) Synthetic small molecules for epigenetic activation of pluripotency genes in mouse embryonic fibroblasts. ChemBioChem 12:2822–2828. doi:10.1002/cbic.201100597
Pandian GN, Ohtsuki A, Bando T et al (2012) Development of programmable small DNA-binding molecules with epigenetic activity for induction of core pluripotency genes. Bioorg Med Chem 20:2656–2660. doi:10.1016/j.bmc.2012.02.032
Pandian GN, Nakano Y, Sato S et al (2012) A synthetic small molecule for rapid induction of multiple pluripotency genes in mouse embryonic fibroblasts. Sci Rep 2:1–8. doi:10.1038/srep00544
Pandian GN, Taniguchi J, Junetha S et al (2014) Distinct DNA-based epigenetic switches trigger transcriptional activation of silent genes in human dermal fibroblasts. Sci Rep 4:3843. doi:10.1038/srep03843
Meier JL, Yu A, Korf I et al (2012) Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc 134:17814–17822. doi:10.1021/ja308888c
Kang JS, Meier JL, Dervan PB (2014) Design of sequence-specific DNA binding molecules for DNA methyltransferase inhibition. J Am Chem Soc 136:3687–3694. doi:10.1021/ja500211z
Han L, Pandian GN, Junetha S et al (2013) A synthetic small molecule for targeted transcriptional activation of germ cell genes in a human somatic cell. Angew Chem Int Ed 52:13410–13413
Zykovich A, Korf I, Segal DJ (2009) Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res 37:e151. doi:10.1093/nar/gkp802
Bailey TL (2011) DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27:1653–1659. doi:10.1093/bioinformatics/btr261
Workman CT, Yin Y, Corcoran DL et al (2005) enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. doi:10.1093/nar/gki439
Morinaga H, Bando T, Takagaki T et al (2011) Cysteine cyclic pyrrole-imidazole polyamide for sequence-specific recognition in the DNA minor groove. J Am Chem Soc 133:18924–18930. doi:10.1021/ja207440p
Minoshima M, Bando T, Sasaki S et al (2008) Pyrrole-imidazole hairpin polyamides with high affinity at 5′-CGCG-3′ DNA sequence; influence of cytosine methylation on binding. Nucleic Acids Res 36:2889–2894. doi:10.1093/nar/gkn116
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2018 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Chandran, A. (2018). Next Generation Sequencing Studies Guide the Design of Pyrrole-Imidazole Polyamides with Improved Binding Specificity by the Addition of β-Alanine. In: Advancing Development of Synthetic Gene Regulators. Springer Theses. Springer, Singapore. https://doi.org/10.1007/978-981-10-6547-7_2
Download citation
DOI: https://doi.org/10.1007/978-981-10-6547-7_2
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-6546-0
Online ISBN: 978-981-10-6547-7
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)