Recognition study of double strand DNA with hairpin oligopolyamide_Journal of Biomedical Engineering

Authors：

LI Wenjia , SHI Huanhuan , DONG Bo [综述] ,  LIU Zhengchun [审校]

Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, P.R.China;

Corresponding author：

LIU Zhengchun, Email: liuzhengchunseu@126.com

Keywords：

hairpin oligopolyamide; recognition of dsDNA; gene diagnosis; gene therapy; gene editing

DOI：

10.7507/1001-5515.201603004

Video：

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Selective recognition of double strands DNA (dsDNA) has been a research hot spot in molecular biology and biomedicine for a couple decades. Based on the selective interaction between natural nucleic acid/synthetic molecular ligands and dsDNA, gene diagnosis, gene therapy and gene editing would be realized. Hairpin oligopolyamide is a molecular ligand with excellent cellular permeability and nucleases-resistance which can target dsDNA sequence with high affinity and specificity at minor groove. This paper reviews the binding properties and biomedical applications of hairpin oligopolyamide targeting dsDNA, which provide references for further design and application of hairpin oligopolyamide.

Citation： LIWenjia, SHIHuanhuan, DONGBo, LIUZhengchun. Recognition study of double strand DNA with hairpin oligopolyamide. Journal of Biomedical Engineering, 2017, 34(1): 134-139. doi: 10.7507/1001-5515.201603004 Copy

1.	Igarashi J, Fukuda N, Inoue T, et al. Preclinical study of novel gene silencer Pyrrole-Imidazole polyamide targeting human TGF-β1 promoter for hypertrophic scars in a common marmoset primate model. PLoS One, 2015, 10(5): e0125295.
2.	Gottesfeld J M, Neely L, Trauger J W, et al. Regulation of gene expression by small molecules. Nature, 1997, 387(6629): 202-205.
3.	Yano T, Takeuchi-Tomita N, Ueda T, et al. Pyrrole-imidazole polyamide, a synthetic DNA-binding compound, is effective at increasing levels of wild-type mtDNA in both cybrid cells and MELAS patient-derived fibroblast cells with the MELAS A3243G mutation by a selective promotion of wild-type replic. Mitochondrion, 2013, 13(6): 924-925.
4.	Sato A, Nagase H, Obinata D, et al. Inhibition of MMP-9 using a pyrrole-imidazole polyamide reduces cell invasion in renal cell carcinoma. Int J Oncol, 2013, 43(5): 1441-1446.
5.	Erwin G S, Bhimsaria D, Eguchi A, et al. Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angew Chem Int Ed Engl, 2014, 53(38): 10124-10128.
6.	Mrksich M, Wade W S, Dwyer T J, et al. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc Natl Acad Sci U S A, 1992, 89(16): 7586-7590.
7.	Mrksich M, Parks M E, Dervan P B. Hairpin peptide motif——a new class of oligopeptides for sequence-specific recognition in the minor-groove of double-helical DNA. J Am Chem Soc, 1994, 116(18): 7983-7988.
8.	Dervan P B, Burli R W. Sequence-specific DNA recognition by polyamides. Curr Opin Chem Biol, 1999, 3(6): 688-693.
9.	White S, Szewczyk J W, Turner J M, et al. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature, 1998, 391(6666): 468-471.
10.	Swalley S E, Baird E E, Dervan P B. Effects of gamma-turn and beta-tail amino acids on sequence-specific recognition of DNA by hairpin polyamides. J Am Chem Soc, 1999, 121(6): 1113-1120.
11.	Herman D M, Baird E E, Dervan P B. Stereochemical control of the DNA binding affinity, sequence specificity, and orientation preference of chiral hairpin polyamides in the minor groove. J Am Chem Soc, 1998, 120(7): 1382-1391.
12.	Meier J L, Montgomery D C, Dervan P B. Enhancing the cellular uptake of Py-Im polyamides through next-generation aryl turns. Nucleic Acids Res, 2012, 40(5): 2345-2356.
13.	Yang F, Nickols N G, Li B C, et al. Animal toxicity of hairpin pyrrole-imidazole polyamides varies with the turn unit. J Med Chem, 2013, 56(18): 7449-7457.
14.	Synold T W, Xi B, Wu J, et al. Single-dose pharmacokinetic and toxicity analysis of pyrrole-imidazole polyamides in mice. Cancer Chemother Pharmacol, 2012, 70(4): 617-625.
15.	Li B C, Montgomery D C, Puckett J W, et al. Synthesis of cyclic Py-Im polyamide libraries. J Org Chem, 2013, 78(1): 124-133.
16.	Turner J M, Swalley S E, Baird E E, et al. Aliphatic/aromatic amino acid pairings for polyamide recognition in the minor groove of DNA. J Am Chem Soc, 1998, 120(25): 6219-6226.
17.	Anandhakumar C, Li Yue, Kizaki S, et al. Next-generation sequencing studies guide the design of pyrrole-imidazole polyamides with improved binding specificity by the addition of β-alanine. Chembiochem, 2014, 15(18): 2647-2651.
18.	Kawamoto Y, Bando T, Kamada F, et al. Development of a new method for synthesis of tandem hairpin pyrrole-imidazole polyamide probes targeting human telomeres. J Am Chem Soc, 2013, 135(44): 16468-16477.
19.	Kawamoto Y, Sasaki A, Hashiya K, et al. Tandem trimer pyrrole-imidazole polyamide probes targeting 18 base pairs in human telomere sequences. Chem Sci, 2015, 6(4): 2307-2312.
20.	Bashkin J K, Aston K, Ramos J P, et al. Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine. Biochimie, 2013, 95(2): 271-279.
21.	Marques M A, Doss R M, Urbach A R, et al. Toward an understanding of the chemical etiology for DNA minor-groove recognition by polyamides. Helv Chim Acta, 2002, 85(12): 4485-4517.
22.	Han Y W, Matsumoto T, Yokota H, et al. Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants. Nucleic Acids Res, 2012, 40(22): 11510-11517.
23.	Wang S, Chai Y, Babu B, et al. Conformational modulation of DNA by polyamide binding: structural effects of f-Im-Py-Im based derivatives on 5'-ACGCGT-3'. J Mol Recognit, 2013, 26(8): 331-340.
24.	Hargrove A E, Martinez T F, Hare A A, et al. Tumor repression of VCaP xenografts by a pyrrole-imidazole polyamide. PLoS One, 2015, 10(11): e0143161.
25.	Tsunemi A, Ueno T, Fukuda N, et al. A novel gene regulator, pyrrole-imidazole polyamide targeting ABCA1 gene increases cholesterol efflux from macrophages and plasma HDL concentration. J Mol Med, 2014, 92(5): 509-521.
26.	Kummer N T, Yang F, Dervan P, et al. Radiosensitization by DNA, binding pyrrole, imidazole polyamides. Int J Radiat Oncol Biol Phys, 2015, 93(3, S): E537-E538.
27.	He G, Bashkin J K. What is the antiviral potential of pyrrole-imidazole polyamides?. Future Med Chem, 2015, 7(15): 1953-1955.
28.	Edwards T G, Vidmar T J, Koeller K, et al. DNA damage repair genes controlling human papillomavirus (HPV) episome levels under conditions of stability and extreme instability. PLoS One, 2013, 8(10): e75406.
29.	Martínez T F, Phillips J W, Karanja K K, et al. Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res, 2014, 42(18): 11546-11559.
30.	Taylor R D, Asamitsu S, Takenaka T, et al. Sequence-specific DNA alkylation targeting for Kras codon 13 mutation by pyrrole-imidazole polyamide seco-CBI conjugates. Chemistry, 2014, 20(5): 1310-1317.
31.	Hiraoka K, Inoue T, Taylor R D, et al. Inhibition of KRAS codon 12 mutants using a novel DNA-alkylating pyrrole-imidazole polyamide conjugate. Nat Commun, 2015, 6: 6706.
32.	Yamamoto M, Bando T, Kawamoto Y, et al. Specific alkylation of human telomere repeat sequences by a tandem-hairpin motif of pyrrole-imidazole polyamides with indole-seco-CBI. Bioconjug Chem, 2014, 25(3): 552-559.
33.	Park S, Bando T, Shinohara K I, et al. Photocontrollable sequence-specific DNA alkylation by a pyrrole-imidazole polyamide seco-CBI conjugate. Bioconjug Chem, 2011, 22(2): 120-124.
34.	Pandian G N, Sugiyama H. Programmable genetic switches to control transcriptional machinery of pluripotency. Biotechnol J, 2012, 7(6): 798-809.
35.	Pandian G N, Shinohara K, Ohtsuki A, et al. Synthetic small molecules for epigenetic activation of pluripotency genes in mouse embryonic fibroblasts. Chembiochem, 2011, 12(18): 2822-2828.
36.	Li Chao, Du Chao, Tian Hua, et al. Artificial transcription factors which mediate double-strand DNA cleavage. Chemistry, 2010, 16(43): 12935-12940.
37.	Vaijayanthi T, Bando T, Pandian G N, et al. Progress and prospects of pyrrole-imidazole polyamide-fluorophore conjugates as sequence-selective DNA probes. Chembiochem, 2012, 13(15): 2170-2185.
38.	Vaijayanthi T, Bando T, Hashiya K, et al. Design of a new fluorescent probe: pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn. Bioorg Med Chem, 2013, 21(4): 852-855.
39.	Obinata Daisuke, Ito A, Fujiwara K, et al. Pyrrole-imidazole polyamide targeted to break fusion sites in TMPRSS2 and ERG gene fusion represses prostate tumor growth. Cancer Sci, 2014, 105(10): 1272-1278.
40.	Mishra R, Watanabe T, Kimura M T, et al. Identification of a novel E-box binding pyrrole-imidazole polyamide inhibiting MYC-driven cell proliferation. Cancer Sci, 2015, 106(4): 421-429.
41.	Yoshizawa S, Fujiwara K, Sugito K, et al. Pyrrole-imidazole polyamide-mediated silencing of KCNQ1OT1 expression induces cell death in Wilms' tumor cells. Int J Oncol, 2015, 47(1): 115-121.
42.	Raskatov J A, Szablowski J O, Dervan P B. Tumor xenograft uptake of a pyrrole-imidazole (Py-Im) polyamide varies as a function of cell line grafted. J Med Chem, 2014, 57(20): 8471-8476.

1. Igarashi J, Fukuda N, Inoue T, et al. Preclinical study of novel gene silencer Pyrrole-Imidazole polyamide targeting human TGF-β1 promoter for hypertrophic scars in a common marmoset primate model. PLoS One, 2015, 10(5): e0125295.
2. Gottesfeld J M, Neely L, Trauger J W, et al. Regulation of gene expression by small molecules. Nature, 1997, 387(6629): 202-205.
3. Yano T, Takeuchi-Tomita N, Ueda T, et al. Pyrrole-imidazole polyamide, a synthetic DNA-binding compound, is effective at increasing levels of wild-type mtDNA in both cybrid cells and MELAS patient-derived fibroblast cells with the MELAS A3243G mutation by a selective promotion of wild-type replic. Mitochondrion, 2013, 13(6): 924-925.
4. Sato A, Nagase H, Obinata D, et al. Inhibition of MMP-9 using a pyrrole-imidazole polyamide reduces cell invasion in renal cell carcinoma. Int J Oncol, 2013, 43(5): 1441-1446.
5. Erwin G S, Bhimsaria D, Eguchi A, et al. Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angew Chem Int Ed Engl, 2014, 53(38): 10124-10128.
6. Mrksich M, Wade W S, Dwyer T J, et al. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc Natl Acad Sci U S A, 1992, 89(16): 7586-7590.
7. Mrksich M, Parks M E, Dervan P B. Hairpin peptide motif——a new class of oligopeptides for sequence-specific recognition in the minor-groove of double-helical DNA. J Am Chem Soc, 1994, 116(18): 7983-7988.
8. Dervan P B, Burli R W. Sequence-specific DNA recognition by polyamides. Curr Opin Chem Biol, 1999, 3(6): 688-693.
9. White S, Szewczyk J W, Turner J M, et al. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature, 1998, 391(6666): 468-471.
10. Swalley S E, Baird E E, Dervan P B. Effects of gamma-turn and beta-tail amino acids on sequence-specific recognition of DNA by hairpin polyamides. J Am Chem Soc, 1999, 121(6): 1113-1120.
11. Herman D M, Baird E E, Dervan P B. Stereochemical control of the DNA binding affinity, sequence specificity, and orientation preference of chiral hairpin polyamides in the minor groove. J Am Chem Soc, 1998, 120(7): 1382-1391.
12. Meier J L, Montgomery D C, Dervan P B. Enhancing the cellular uptake of Py-Im polyamides through next-generation aryl turns. Nucleic Acids Res, 2012, 40(5): 2345-2356.
13. Yang F, Nickols N G, Li B C, et al. Animal toxicity of hairpin pyrrole-imidazole polyamides varies with the turn unit. J Med Chem, 2013, 56(18): 7449-7457.
14. Synold T W, Xi B, Wu J, et al. Single-dose pharmacokinetic and toxicity analysis of pyrrole-imidazole polyamides in mice. Cancer Chemother Pharmacol, 2012, 70(4): 617-625.
15. Li B C, Montgomery D C, Puckett J W, et al. Synthesis of cyclic Py-Im polyamide libraries. J Org Chem, 2013, 78(1): 124-133.
16. Turner J M, Swalley S E, Baird E E, et al. Aliphatic/aromatic amino acid pairings for polyamide recognition in the minor groove of DNA. J Am Chem Soc, 1998, 120(25): 6219-6226.
17. Anandhakumar C, Li Yue, Kizaki S, et al. Next-generation sequencing studies guide the design of pyrrole-imidazole polyamides with improved binding specificity by the addition of β-alanine. Chembiochem, 2014, 15(18): 2647-2651.
18. Kawamoto Y, Bando T, Kamada F, et al. Development of a new method for synthesis of tandem hairpin pyrrole-imidazole polyamide probes targeting human telomeres. J Am Chem Soc, 2013, 135(44): 16468-16477.
19. Kawamoto Y, Sasaki A, Hashiya K, et al. Tandem trimer pyrrole-imidazole polyamide probes targeting 18 base pairs in human telomere sequences. Chem Sci, 2015, 6(4): 2307-2312.
20. Bashkin J K, Aston K, Ramos J P, et al. Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine. Biochimie, 2013, 95(2): 271-279.
21. Marques M A, Doss R M, Urbach A R, et al. Toward an understanding of the chemical etiology for DNA minor-groove recognition by polyamides. Helv Chim Acta, 2002, 85(12): 4485-4517.
22. Han Y W, Matsumoto T, Yokota H, et al. Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants. Nucleic Acids Res, 2012, 40(22): 11510-11517.
23. Wang S, Chai Y, Babu B, et al. Conformational modulation of DNA by polyamide binding: structural effects of f-Im-Py-Im based derivatives on 5'-ACGCGT-3'. J Mol Recognit, 2013, 26(8): 331-340.
24. Hargrove A E, Martinez T F, Hare A A, et al. Tumor repression of VCaP xenografts by a pyrrole-imidazole polyamide. PLoS One, 2015, 10(11): e0143161.
25. Tsunemi A, Ueno T, Fukuda N, et al. A novel gene regulator, pyrrole-imidazole polyamide targeting ABCA1 gene increases cholesterol efflux from macrophages and plasma HDL concentration. J Mol Med, 2014, 92(5): 509-521.
26. Kummer N T, Yang F, Dervan P, et al. Radiosensitization by DNA, binding pyrrole, imidazole polyamides. Int J Radiat Oncol Biol Phys, 2015, 93(3, S): E537-E538.
27. He G, Bashkin J K. What is the antiviral potential of pyrrole-imidazole polyamides?. Future Med Chem, 2015, 7(15): 1953-1955.
28. Edwards T G, Vidmar T J, Koeller K, et al. DNA damage repair genes controlling human papillomavirus (HPV) episome levels under conditions of stability and extreme instability. PLoS One, 2013, 8(10): e75406.
29. Martínez T F, Phillips J W, Karanja K K, et al. Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res, 2014, 42(18): 11546-11559.
30. Taylor R D, Asamitsu S, Takenaka T, et al. Sequence-specific DNA alkylation targeting for Kras codon 13 mutation by pyrrole-imidazole polyamide seco-CBI conjugates. Chemistry, 2014, 20(5): 1310-1317.
31. Hiraoka K, Inoue T, Taylor R D, et al. Inhibition of KRAS codon 12 mutants using a novel DNA-alkylating pyrrole-imidazole polyamide conjugate. Nat Commun, 2015, 6: 6706.
32. Yamamoto M, Bando T, Kawamoto Y, et al. Specific alkylation of human telomere repeat sequences by a tandem-hairpin motif of pyrrole-imidazole polyamides with indole-seco-CBI. Bioconjug Chem, 2014, 25(3): 552-559.
33. Park S, Bando T, Shinohara K I, et al. Photocontrollable sequence-specific DNA alkylation by a pyrrole-imidazole polyamide seco-CBI conjugate. Bioconjug Chem, 2011, 22(2): 120-124.
34. Pandian G N, Sugiyama H. Programmable genetic switches to control transcriptional machinery of pluripotency. Biotechnol J, 2012, 7(6): 798-809.
35. Pandian G N, Shinohara K, Ohtsuki A, et al. Synthetic small molecules for epigenetic activation of pluripotency genes in mouse embryonic fibroblasts. Chembiochem, 2011, 12(18): 2822-2828.
36. Li Chao, Du Chao, Tian Hua, et al. Artificial transcription factors which mediate double-strand DNA cleavage. Chemistry, 2010, 16(43): 12935-12940.
37. Vaijayanthi T, Bando T, Pandian G N, et al. Progress and prospects of pyrrole-imidazole polyamide-fluorophore conjugates as sequence-selective DNA probes. Chembiochem, 2012, 13(15): 2170-2185.
38. Vaijayanthi T, Bando T, Hashiya K, et al. Design of a new fluorescent probe: pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn. Bioorg Med Chem, 2013, 21(4): 852-855.
39. Obinata Daisuke, Ito A, Fujiwara K, et al. Pyrrole-imidazole polyamide targeted to break fusion sites in TMPRSS2 and ERG gene fusion represses prostate tumor growth. Cancer Sci, 2014, 105(10): 1272-1278.
40. Mishra R, Watanabe T, Kimura M T, et al. Identification of a novel E-box binding pyrrole-imidazole polyamide inhibiting MYC-driven cell proliferation. Cancer Sci, 2015, 106(4): 421-429.
41. Yoshizawa S, Fujiwara K, Sugito K, et al. Pyrrole-imidazole polyamide-mediated silencing of KCNQ1OT1 expression induces cell death in Wilms' tumor cells. Int J Oncol, 2015, 47(1): 115-121.
42. Raskatov J A, Szablowski J O, Dervan P B. Tumor xenograft uptake of a pyrrole-imidazole (Py-Im) polyamide varies as a function of cell line grafted. J Med Chem, 2014, 57(20): 8471-8476.

Journal of Biomedical Engineering

Recognition study of double strand DNA with hairpin oligopolyamide

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