Abstract
Pyrrole–imidazole polyamides (Py–Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py–Im polyamides.
This chapter is reprinted and modified with permission from “Sequence-specific DNA Binding Pyrrole–Imidazole Polyamides and Their Applications” Kawamoto, Y.; Bando, T.; Sugiyama, H. Bioorg. Med. Chem. 2018, 26, 1393–1411. Copyright 2018 Elsevier.
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References
Watson JD, Crick FHC (1953) Nature 171:737–738
Rhodes D, Lipps HJ (2015) Nucleic Acids Res 43:8627–8637
(a) Finlay AC, Hochstein FA, Sobin BA, Murphy FX (1951) J Am Chem Soc 73:341–343. (b) Arcamone F, Penco P, Orezzi P, Nicolella V, Pirelli A (1964) Nature 203:1064–1065
Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE (1985) Proc Natl Acad Sci U S A 82:1376–1380
(a) Coll M, Frederick CA, Wang AH-J, Rich A (1987) Proc Natl Acad Sci U S A 84:8385–8389. (b) Pelton JG, Wemmer DE (1989) Proc Natl Acad Sci U S A 86:5723–5727
(a) Wade WS, Mrksich M, Dervan PB (1992) J Am Chem Soc 114:8783–8794. (b) Mrksich M, Wade WS, Dwyer TJ, Geierstanger BH, Wemmer DE, Dervan PB (1992) Proc Natl Acad Sci U S A 89:7586–7590. (c) Wade WS, Mrksich M, Dervan PB (1993) Biochemistry 32:11385–11389
Mrksich M, Dervan PB (1993) J Am Chem Soc 115:2572–2576
(a) Mrksich M, Dervan PB (1994) J Am Chem Soc 115:9892–9899. (b) Mrksich M, Dervan PB (1994) J Am Chem Soc 116:3663–3664. (c) Chen YH, Lown JW (1994) J Am Chem Soc 116:6995–7005. (d) Greenberg WA, Baird EE, Dervan PB (1998) Chem Eur J 4:796–805. (e) O’Hare CC, Mack D, Tandon M, Sharma SK, Lown JW, Kopka ML, Dickerson RE, Hartley JA (2002) Proc Natl Acad Sci U S A 99:72–77. f Olenyuk B, Jitianu C, Dervan PB (2003) J Am Chem Soc 125:4741–4751. (g) Fechter EJ, Olenyuk B, Dervan PB (2004) Angew Chem Int Ed 43:3591–3594. (h) O’Hare CC, Uthe P, Mackay H, Blackmon K, Jones J, Brown T, Nguyen B, Wilson WD, Lee M, Hartley JA (2007) Biochemistry 46:11661–11670. (i) Mackay H, Brown T, Uthe PB, Westrate L, Sielaff A, Jones J, Lajiness JP, Kluza J, O’Hare C, Nguyen B, Davis Z, Bruce C, Wilson WD, Hartley JA, Lee M (2008) Bioorg. Med. Chem. 16:9145–9153. (j) Franks A, Tronrud C, Kiakos K, Kluza J, Munde M, Brown T, Mackay H, Wilson WD, Hochhauser D, Hartley JA, Lee M (2010) Bioorg Med Chem 18:5553–5561. (k) Guo C, Asamitsu S, Kashiwazaki G, Sato S, Bando T, Sugiyama H (2017) ChemBioChem 18:166–170
(a) Mrksich M, Parks ME, Dervan PB (1994) J Am Chem Soc 116:7983–7988. (b) Baird EE, Dervan PB (1996) J Am Chem Soc 118:6141–6146. (c) Wurtz NR, Turner JM, Baird EE, Dervan PB (2001) Org Lett 3:1201–1203. (d) Trauger JW, Baird EE, Dervan PB (1996) Nature 382:559–561
For reviews: (a) Dervan PB (2001) Bioorg Med Chem 9:2215–2235. (b) Dervan PB, Edelson BS (2003) Curr Opin Struct Biol 13:284–299. (c) Melander C, Burnett R, Gottesfeld JM (2004) J Biotechnol 112:195–220. (d) Murty MSRC, Sugiyama H (2004) Biol Pharm Bull 27:468–474. (e) Dervan PB, Doss RM, Marques MA (2005) Curr Med Chem: Anti-Cancer Agents 5:373–387. (f) Bando T, Sugiyama H (2006) Acc Chem Res 39, 935–944. (g) Blackledge MS, Melander C (2013) Bioorg Med Chem 21:6101–6114. (h) Pandian GN, Sugiyama H (2016) Bull Chem Soc Jpn 89:843–868. (i) Kawamoto Y, Bando T, Sugiyama H (2018) Bioorg Med Chem 26:1393–1411
Kielkopf CL, Baird EE, Dervan PD, Rees DC (1998) Nat Struct Biol 5:104–109
(a) Chenoweth DM, Dervan PB (2009) Proc Natl Acad Sci U S A 106:13175–13179. (b) Chenoweth DM, Dervan PB (2010) J Am Chem Soc 132:14521–14529
(a) Yang X-L, Hubbard RB, Lee M, Tao Z-F, Sugiyama H, Wang AH-J (1999) Nucleic Acids Res 27:4183–4190. (b) Lacy ER, Cox KK, Wilson WD, Lee M (2002) Nucleic Acids Res 30:1834–1841
Swalley SE, Baird EE, Dervan PB (1999) J Am Chem Soc 121:1113–1120
(a) Herman DM, Baird EE, Dervan PB (1998) J Am Chem Soc 120:1382–1391. (b) Rucker VC, Melander C, Dervan PB (2003) Helv. Chim. Acta 86:1839–1851
(a) Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB (2012) J Am Chem Soc 134:17814–17822. (b) Kang JS, Meier JL, Dervan PB (2014) J Am Chem Soc 136:3687–3694
Dose C, Ho D, Gaub HE, Dervan PB, Albrecht CH (2007) Angew Chem Int Ed 46:8384–8387
Dose C, Farkas ME, Chenoweth DM, Dervan PB (2008) J Am Chem Soc 130:6859–6866
Parks ME, Baird EE, Dervan PB (1996) J Am Chem Soc 118:6147–6152
(a) Turner JM, Baird EE, Dervan PB (1997) J Am Chem Soc 119:7636–7644. (b) Turner JM, Swalley SE, Baird EE, Dervan PB (1998) J Am Chem Soc 120:6219–6226
(a) White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB (1998) Nature 391:468–471. (b) Kielkopf CL, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC (1998) Science 282:111–115
(a) Floreancig PE, Swalley SE, Trauger JW, Dervan PB (2000) J Am Chem Soc 122:6342–6350. (b) Woods CR, Ishii T, Wu B, Bair KW, Boger DL (2002) J Am Chem Soc 124:2148–2152. (c) Zhang W, Bando T, Sugiyama H (2006) J Am Chem Soc 128:8766–8776. (d) Zhang W, Jiang S-K, Wu Y-L, Guo C-X, Zhang H-F, Sugiyama H, Chen X-L (2012) ChemBioChem 13:47–50. (e) Zhang W, Minoshima M, Sugiyama H (2006) J Am Chem Soc 128:14905–14912
(a) Zhan Z-YJ, Dervan PB (2000) Bioorg Med Chem 8:2467–2474. (b) Foister S, Marques MA, Doss RM, Dervan PB (2003) Bioorg Med Chem 11:4333–4340. (c) Padroni G, Parkinson JA, Fox KR, Burley GA (2018) Nucleic Acids Res 46:42–53. (d) Anthony NG, Johnston BF, Khalaf AI, MacKay SP, Parkinson JA, Suckling CJ, Waigh RD (2004) J Am Chem Soc 126:11338–11349. (e) James PL, Merkina EE, Khalaf AI, Suckling CJ, Waigh RD, Brown T, Fox KR (2004) Nucleic Acids Res 32:3410–3417. (f) Nguyen DH, Szewczyk JW, Baird EE, Dervan PB (2001) Bioorg Med Chem 9:7–17. (g) Marques MA, Doss RM, Urbach AR, Dervan PB (2002) Helv Chim Acta 85:4485–4517. (h) Muzikar KA, Meier JL, Gubler DA, Raskatov JA, Dervan PB (2011) Org Lett 13:5612–5615
(a) Renneberg D, Dervan PB (2003) J Am Chem Soc 125:5707–5716. (b) Briehn CA, Weyermann P, Dervan PB (2003) Chem Eur J 9:2110–2122. (c) Marques MA, Doss RM, Foister S, Dervan PB (2004) J Am Chem Soc 126:10339–10349. (d) Doss R, Marques MA, Foister S, Chenoweth DM, Dervan PB (2006) J Am Chem Soc 128:9074–9079. (e) Chenoweth DM, Viger A, Dervan PB (2007) J Am Chem Soc 129:2216–2217
(a) Lacy ER, Le NM, Price CA, Lee M, Wilson WD (2002) J Am Chem Soc 124:2153–2163. (b) Buchmueller KL, Staples AM, Uthe PB, Howard CM, Pacheco KA, Cox KK, Henry JA, Bailey SL, Horick SM, Nguyen B, Wilson WD, Lee M (2005) Nucleic Acids Res 33:912– 921. (c) Chavda S, Liu Y, Babu B, Davis R, Sielaff A, Ruprich J, Westrate L, Tronrud C, Ferguson A, Franks A, Tzou S, Adkins C, Rice T, Mackay H, Kluza J, Tahir SA, Lin S, Kiakos K, Bruce CD, Wilson WD, Hartley JA, Lee M (2011) Biochemistry 50:3127–3136. (d) Satam V, Babu B, Patil P, Brien KA, Olson K, Savagian M, Lee M, Mepham A, Jobe LB, Bingham JP, Pett L, Wang S, Ferrara M, Bruce CD, Wilson WD, Lee M, Hartley JA, Kiakos K (2015) Bioorg Med Chem Lett 25:3681–3685
Hawkins CA, Pela´ez de Clairac R, Dominey RN, Baird EE, White S, Dervan PB, Wemmer DE (2000) J Am Chem Soc 122:5235–5243
(a) Trauger JW, Baird EE, Mrksich M, Dervan PB (1996) J Am Chem Soc 118:6160–6166. (b) Swalley SE, Baird EE, Dervan PB (1997) Chem Eur J 3:1600–1607. (c) Trauger JW, Baird EE, Dervan PB (1998) J Am Chem Soc 120:3534–3535
(a) Janssen S, Durussel T, Laemmli UK (2000) Mol Cell 6:999–1011. (b) Janssen S, Cuvier O, Müller M, Laemmli UK (2000) Mol Cell 6:1013–1024. (c) Blattes R, Monod C, Susbielle G, Cuvier O, Wu J-H, Hsieh T-S, Laemmli UK, Käs E (2006) EMBO J 25:2397–2408. (d) Urbach AM, Dervan PB (2001) Proc Natl Acad Sci U S A 98:4343–4348. (e) Urbach AM, Love JJ, Ross SA, Dervan PB (2002) J Mol Biol 320:55–71. (f) Burnett R, Melander C, Puckett JW, Son LS, Wells RD, Dervan PB, Gottesfeld JM (2006) Proc Natl Acad Sci U S A 103:11497–11502. (g) Wang RE, Pandita RK, Cai J, Hunt CR, Taylor J-S (2012) ChemBioChem 13:97–104. (h) Du J, Campau E, Soragni E, Ku S, Puckett JW, Dervan PB, Gottesfeld JM (2012) J Biol Chem 287:29861–29872. (i) Gerhardt J, Bhalla AD, Butler JS, Puckett JW, Dervan PB, Rosenwaks Z, Napierala, M. Cell Rep 16:1218–1227
Melander C, Herman DM, Dervan PB (2000) Chem Eur J 6:4487–4497
(a) Cho JY, Parks MP, Dervan PB (1995) Proc Natl Acad Sci U S A 92:10389–10392. (b) Herman DM, Turner JM, Baird EE, Dervan PB (1999) J Am Chem Soc 121:1121–1129. (c) Melander C, Herman DM, Dervan PB (2000) Chem Eur J 6:4487–4497. (d) Zhang Q, Dwyer TJ, Tsui V, Case DA, Cho J, Dervan PB, Wemmer DE (2004) J Am Chem Soc 126:7958–7966. (e) Chenoweth DM, Harki DA, Phillips JW, Dose C, Dervan PB (2009) J Am Chem Soc 131:7182–7188. (f) Li BC, Montgomery DC, Puckett JW, Dervan PB (2013) J Org Chem 78:124–133
(a) Morinaga H, Bando T, Takagaki T, Yamamoto H, Hashiya K, Sugiyama H (2011) J Am Chem Soc 133:18924–18930. (b) Kashiwazaki G, Chandran A, Asamitsu S, Kawase T, Kawamoto Y, Sawatani Y, Hashiya K, Bando T, Sugiyama H (2016) ChemBioChem 17:1752–1758
Yamamoto M, Bando T, Morinaga N, Kawamoto Y, Hashiya K, Sugiyama H (2014) Chem Eur J 20:752–759
Weyermann P, Dervan PB (2002) J Am Chem Soc 124:6872–6878
(a) Edayathumangalam RS, Weyermann P, Gottesfeld J. M, Dervan, P. B, Luger, K. Proc Natl Acad Sci U S A 101:6864–6869. (b) Edayathumangalam RS, Weyermann P, Dervan, PB, Gottesfeld JM, Luger K (2005) J Mol Biol 345:103–114. (c) Obata S, Asamitsu S, Hashiya K, Bando T, Sugiyama H (2018) Biochemistry 57:498–502
(a) Herman DM, Baird EE, Dervan PB (1999) Chem Eur J 5:975–983. (b) Kers I, Dervan PB (2002) Bioorg Med Chem 10:3339–3349. (c) Schaal TD, Mallet WG, McMinn DL, Nguyen NV, Sopko MM, John S, Parekh BS (2003) Nucleic Acids Res 31:1282–1291. (d) Sasaki S, Bando T, Minoshima M, Shinohara K, Sugiyama H (2008) Chem Eur J 14:864–870. (e) Yamamoto M, Bando T, Kawamoto Y, Taylor RD, Hashiya K, Sugiyama H (2014) Bioconjugate Chem 25:552–559. (f) Taylor RD, Kawamoto Y, Hashiya K, Bando T, Sugiyama H (2014) Chem. Asian J 9:2527–2533
(a) Maeshima K, Janssen S, Laemmli UK (2001) EMBO J 20:3218–3228. (b) Kawamoto Y, Bando T, Kamada F, Li Y, Hashiya K, Maeshima K, Sugiyama H (2013) J Am Chem Soc 135:16468–16477. (c) Hirata A, Nokihara K, Kawamoto Y, Bando T, Sasaki A, Ide S, Maeshima K, Kasama T, Sugiyama H (2014) J Am Chem Soc 136:11546–11554. (d) Kawamoto Y, Sasaki A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H (2015) Chem. Sci. 6:2307–2312. (e) Sasaki A, Ide S, Kawamoto Y, Bando T, Murata Y, Shimura M, Yamada K, Hirata A, Nokihara K, Hirata T, Sugiyama H, Maeshima K (2016) Sci Rep 6:29261. (f) Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H (2016) J Am Chem Soc 138:14100–14107
(a) Best TP, Edelson BS, Nickols NG, Dervan PB (2003) Proc Natl Acad Sci U S A 100:12063–12068. (b) Edelson BS, Best TP, Olenyuk B, Nickols NG, Doss RM, Foister S, Heckel A, Dervan PB (2004) Nucleic Acids Res 32:2802–2818
Gottesfeld JM, Neely L, Trauger JW, Baird EE, Dervan PB (1997) Nature 391:468–471
Dickinson LA, Gulizia RJ, Trauger JW, Baird EE, Mosier DE, Gottesfeld JM, Dervan PB (1998) Proc Natl Acad Sci U S A 95:12890–12895
(a) Olenyuk BZ, Zhang GJ, Klco JM, Nickols NG, Kaelin WG Jr, Dervan PB (2004) Proc Natl Acad Sci U S A 101:16768–16773. (b) Nickols NG, Jacobs CS, Farkas ME, Dervan PB (2007) Nucleic Acids Res 35:363–370. (c) Nickols NG, Jacobs CS, Farkas ME, Dervan PB (2007) ACS Chem Biol 2:561–571. (d) Szablowski JO, Raskatov JA, Dervan PB (2016) Mol Cancer Ther 15:608–617. (e) Mysore VS, Szablowski JO, Dervan PB, Frost PJ (2016) Mol Cancer Res 14:253–266
(a) Nickols NG, Dervan PB (2007) Proc Natl Acad Sci U S A 104:10418–10423. (b) Hargrove AE, Martinez TF, Hare AA, Kurmis AA, Phillips JW, Sud S, Pienta KJ, Dervan PB (2015) PLoS ONE 10:143161. (c) Yang F, Nickols NG, Li BC, Marinov G, Said JW, Dervan PB (2013) Proc Natl Acad Sci U S A 110:1863–1868. (d) Muzikar KA, Nickols NG, Dervan PB (2009) Proc Natl Acad Sci U S A 106:16598–16603 (e) Kurmis AA, Yang F, Welch TR, Nickols NG, Dervan PB (2017) Cancer Res 77:2207–2212. (f) Martínez TF, Phillips JW, Karanja KK, Polaczek P, Wang CM, Li BC, Campbell JL, Dervan PB (2014) Nucleic Acids Res 42:11546–11559
(a) Lai Y-M, Fukuda N, Ueno T, Kishioka H, Matsuda H, Saito S, Matsumoto K, Ayame H, Bando T, Sugiyama H, Mugishima H, Serie K (2005) J Pharmacol Exp Ther 315:571–575. (b) Matsuda H, Fukuda N, Ueno T, Tahira Y, Ayame H, Zhang W, Bando T, Sugiyama H, Saito S, Matsumoto K, Mugishima H, Serie K (2006) J Am Soc Nephrol 17:422–432. (c) MatsudaH, Fukuda N, Ueno T, Katakawa M, Wang X, Watanabe T, Matsui S, Aoyama T, Saito K, Bando T, Matsumoto Y, Nagase H, Matsumoto K, Sugiyama H (2011) Kidney Int 79:46–56. (d) Yao E-H, Fukuda N, Ueno T, Matsuda H, Nagase H, Matsumoto Y, Sugiyama H, Matsumoto K (2009) Cardiovasc Res 81:797–804. (e) Chen M, Matsuda H, Wang L, Watanabe T, Kimura MT, Igarashi J, Wang X, Sakimoto T, Fukuda N, Sawa M, Nagase H (2010) Mol Ther 18:519–527. (f) Washio H, Fukuda N, Matsuda H, Nagase H, Watanabe T, Matsumoto Y, Terui T (2011) J Invest Dermatol 131:1987–1995. (g) Igarashi J, Fukuda N, Inoue T, Nakai S, Saito K, Fujiwara K, Matsuda H, Ueno T, Matsumoto Y, Watanabe T, Nagase H, Bando T, Sugiyama H, Itoh T, Soma M (2015) PLoS ONE 10:125295
(a) Hochhauser D, Kotecha M, O’hare C, Morris PJ, Hartley JA, Taherbhai Z, Harris D, Forni C, Mantovani R, Lee M, Hartley JA (2007) Mol Cancer Ther 6:346–354. (b) Kiakos K, Pett L, Satam V, Patil P, Hochhauser D, Lee M, Hartley JA (2015) Chem Biol 22:862–875
Taniguchi J, Pandian GN, Hidaka T, Hashiya K, Bando T, Kim KK, Sugiyama H (2017) Nucleic Acids Res 45:9219–9228
Hidaka T, Pandian G, Taniguchi J, Nobeyama T, Hashiya K, Bando T, Sugiyama H (2017) J Am Chem Soc 139:8444–8447
(a) Edwards TG, Koeller KJ, Slomczynska U, Fok K, Helmus M, Bashkin JK, Fisher C (2011) Antivir Res 91:177–186. (b) Castaneda CH, Scuderi MJ, Edwards TG, Harris Jr GD, Dupureur CM, Koeller KJ, Fisher C, Bashkin JK (2016) Med Chem Commun 7:2076–2082
(a) Oyoshi T, Kawakami W, Narita A, Bando T, Sugiyama HJ (2003) Am Chem Soc 125:4752–4754. (b) Asamitsu S, Kawamoto Y, Hashiya F, Hashiya K, Yamamoto M, Kizaki S, Bando T, Sugiyama H (2014) Bioorg Med Chem 22:4646–4657
(a) Wurtz NR, Dervan PB (2000) Chem Biol 7:153–161. (b) Wang YD, Dziegielewski J, Wurtz NR, Dziegielewska B, Dervan PB, Beerman TA (2003) Nucleic Acids Res 31:1208–1215. (c) Dickinson LA, Burnett R, Melander C, Edelson BS, Arora PS, Dervan PB, Gottesfeld JM (2004) Chem Biol 11:1583–1594. (d) Alvarez D, Chou CJ, Latella L, Zeitlin SG, Ku S, Puri PL, Dervan PB, Gottesfeld JM (2006) Cell Cycle 5:1537–1548. (e) Tsai SM, Farkas ME, Chou CJ, Gottesfeld JM, Dervan PB (2007) Nucleic Acids Res 35:307–316. (f) Chou CJ, Farkas ME, Tsai SM, Alvarez D, Dervan PB, Gottesfeld JM (2008) Mol Cancer Ther 7:769–778. (g) Chou CJ, O’Hare T, Lefebvre S, Alvarez D, Tyner JW, Eide CA, Druker BJ, Gottesfeld JM (2008) PLoS ONE 3:3593. (h) Jespersen C, Soragni E, James Chou C, Arora PS, Dervan PB, Gottesfeld JM (2012) Bioorg Med Chem Lett 22:4068–4071. (i) Morita K, Suzuki K, Maeda S, Matsuo A, Mitsuda Y, Tokushige C, Kashiwazaki G, Taniguchi J, Maeda R, Noura M, Hirata M, Kataoka T, Yano A, Yamada Y, Kiyose H, Tokumasu M, Matsuo H, Tanaka S, Okuno Y, Muto M, Naka K, Ito K, Kitamura T, Kaneda Y, Liu PP, Bando T, Adachi S, Sugiyama H, Kamikubo Y (2017) J Clin Invest 127:2815–2828
(a) Chang AY, Dervan PB (2000) J Am Chem Soc 122:4856–4864. (b) Wang Y-D, Dziegielewski J, Chang AY, Dervan PB, Beerman TA (2002) J Biol Chem 277:42431–42437. (c) Philips BJ, Chang AY, Dervan PB, Beerman TA (2005) Mol Pharmacol 67:877–882
(a) Bando T, Sasaki S, Minoshima M, Dohno C, Shinohara K, Narita A, Sugiyama H (2006) Bioconjugate Chem 17:715–720. (b) Shinohara K, Sasaki S, Minoshima M, Bando T, Sugiyama H (2006) Nucleic Acids Res 34:1189–1195. (c) Shinohara K, Bando T, Sasaki S, Sakakibara Y, Minoshima M, Sugiyama H (2006) Cancer Sci 97:219–225. (d) Sasaki S, Bando T, Minoshima M, Shimizu T, Shinohara K, Takaoka T, Sugiyama H (2006) J Am Chem Soc 128:12162–12168. (e) Kashiwazaki G, Bando T, Yoshidome T, Masui S, Takagaki T, Hashiya K, Pandian GN, Yasuoka J, Akiyoshi K, Sugiyama H (2012) J Med Chem 55:2057–2066. (f) Hiraoka K, Inoue T, Taylor RD, Watanabe T, Koshikawa N, Yoda H, Shinohara K, Takatori A, Sugimoto H, Maru Y, Denda T, Fujiwara K, Balmain A, Ozaki T, Bando T, Sugiyama H, Nagase H (2015) Nat Commun 6:6706. (g) Taylor RD, Chandran A, Kashiwazaki G, Hashiya K, Bando T, Nagase H, Sugiyama H (2015) Chem Eur J 21:14996–15003. (h) Lin J, Hiraoka K, Watanabe T, Kuo T, Shinozuka Y, Takatori A, Koshikawa N, Chandran A, Otsuki J, Sugiyama H, Horton P, Nagase H (2016) PLoS ONE 11:165581
(a) Tao Z-F, Saito I, Sugiyama H (2000) J Am Chem Soc 122:1602–1608. (b) Bando T, Narita A, Saito I, Sugiyama H (2002) Chem Eur J 8:4781–4790. (c) Bando T, Narita A, Iwai A, Kihara K, Sugiyama H (2004) J Am Chem Soc 126:3406–3407. (d) Shinohara K, Narita A, Oyoshi T, Bando T, Teraoka H, Sugiyama H (2004) J Am Chem Soc 126:5113–5118
(a) Mapp AK, Ansari AZ, Ptashne M, Dervan PB (2000) Proc Natl Acad Sci U S A 97:3930–3935. (b) Ansari AZ, Mapp AK, Nguyen DH, Dervan PB, Ptashne M (2001) Chem Biol 8:583–592. (c) Arora PS, Ansari AZ, Best TP, Ptashne M, Dervan PB (2002) J Am Chem Soc 124:13067–13071. (d) Kwon Y, Arndt HD, Mao Q, Choi Y, Kawazoe Y, Dervan PB, Uesugi M (2004) J Am Chem Soc 126:15940–15941. (e) Arndt H-D, Hauschild KE, Sullivan DP, Lake K, Dervan PB, Ansari AZ (2003) J Am Chem Soc 125:13322–13323. (f) Hauschild KE, Metzler RE, Arndt H-D, Moretti R, Raffaelle R, Dervan PB, Ansari AZ (2005) Proc Natl Acad Sci U S A 102, 5008–5013. (g) Stafford RL, Arndt H-D, Brezinski ML, Ansari AZ, Dervan PB (2007) J Am Chem Soc 129:2660–2668. (h) Stafford RL, Dervan PB (2007) J Am Chem Soc 129:14026–14033. (i) Moretti R, Donato LJ, Brezinski ML, Stafford RL, Hoff H, Thorson JS, Dervan PB, Ansari AZ (2008) ACS Chem Biol 3:220–229
(a) Xiao XS, Yu P, Lim HS, Sikder D, Kodadek TA (2007) Angew Chem Int Ed 46:2865–2868. (b) Xiao XS, Yu P, Lim HS, Sikder D, Kodadek TA (2007) J Comb Chem 9:592–600
(a) Ohtsuki A, Kimura MT, Minoshima M, Suzuki T, Ikeda M, Bando T, Nagase H, Shinohara KI, Sugiyama H (2009) Tetrahedron Lett 50:7288–7292. (b) Pandian GN, Shinohara K, Ohtsuki A, Nakano Y, Minoshima M, Bando T, Nagase H, Yamada Y, Watanabe A, Terada N, Sato S, Morinaga H, Sugiyama H (2011) ChemBioChem 12:2822–2828. (c) Pandian GN, Ohtsuki A, Bando T, Sato S, Hashiya K, Sugiyama H (2012) Bioorg Med Chem 20:2656–2660. (d) Pandian GN, Nakano Y, Sato S, Morinaga H, Bando T, Nagase H, Sugiyama H (2012) Sci Rep 2:544. (e) Pandian GN, Taniguchi J, Junetha S, Sato S, Han L, Saha A, Anandhkumar C, Bando T, Nagase H, Vaijayanthi T, Taylor RD, Sugiyama H (2014) Sci Rep 4:3843. (f) Han L, Pandian GN, Junetha S, Sato S, Anandahkumar C, Taniguchi J, Saha A, Bando T, Nagase H, Sugiyama H (2013) Angew Chem Int Ed 52:13410–13413. (g) Pandian GN, Sato S, Anandhakumar C, Taniguchi J, Takashima K, Syed J, Han L, Saha A, Bando T, Nagase H, Sugiyama H (2014) ACS Chem Biol 9:2729–2736. (h) Syed J, Chandran A, Pandian GN, Taniguchi J, Sato S, Hashiya K, Kashiwazaki G, Bando T, Sugiyama H (2015) ChemBioChem 16:1497–1501. (i) Wei Y, Pandian GN, Zou T, Taniguchi J, Sato S, Kashiwazaki G, Vaijayanthi T, Hidaka T, Bando T, Sugiyama H (2016) ChemistryOpen 5:517–521
Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H (2015) Angew Chem Int Ed 54:8700–8703
Yu Z, Taniguchi J, Wei Y, Pandian G, Hashiya K, Bando T, Sugiyama H (2017) Eur J Med Chem 138:320–327
Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A, Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ (2017) Science 358:1617–1622
(a) Patel S, Jung D, Yin PT, Carlton P, Yamamoto M, Bando T, Sugiyama H, Lee K-B (2014) ACS Nano 8:8959–8967. (b) Patel S, Yin PT, Sugiyama H, Lee K-B (2015) ACS Nano 9:6909–6917. (c) Patel S, Pongkulapa T, Yin PT, Pandian GN, Rathnam C, Bando T, Vaijayanthi T, Sugiyama H, Lee K-B (2015) J Am Chem Soc 137:4598–4601. (d) Patel S, Chueng S-TD, Yin PT, Dardir K, Song Z, Pasquale N, Kwan K, Sugiyama H, Lee K-B (2015) Angew Chem Int Ed 54:11983–11988
For review: Vaijayanthi T, Bando T, Pandian GN, Sugiyama H (2012) ChemBioChem 13:2170–2185
Gygi MP, Ferguson MD, Mefford HC, Lund KP, O’Day C, Zhou P, Friedman C, van den Engh G, Stolowitz ML, Trask BJ (2002) Nucleic Acids Res 30:2790–2799
Nozeret K, Loll F, Escudé C, Boutorine AS (2015) ChemBioChem 16:549–554
(a) Rucker VC, Foister S, Melander C, Dervan PB (2003) J Am Chem Soc 125:1195–1202. (b) Rucker VC, Dunn AR, Sharma S, Dervan PB, Gray HB (2004) J Phys Chem B 108:7490–7494
Fujimoto J, Bando T, Minoshima M, Kashiwazaki G, Nishijima S, Shinohara K, Sugiyama H (2008) Bioorg Med Chem 16:9741–9744
Fechter EJ, Olenyuk B, Dervan PB (2005) J Am Chem Soc 127:16685–16691
(a) Bando T, Fujimoto J, Minoshima M, Shinohara K, Sasaki S, Kashiwazaki G, Mizumura M, Sugiyama H (2007) Bioorg Med Chem 15:6937–6942. (b) Fujimoto J, Bando T, Minoshima M, Uchida S, Iwasaki M, Shinohara K, Sugiyama H (2008) Bioorg Med Chem 16:5899–5907
(a) Belitsky JM, Leslie SJ, Arora PS, Beerman TA, Dervan PB (2002) Bioorg Med Chem 10:3313–3318. (b) Nishijima S, Shinohara K, Bando T, Minoshima M, Kashiwazaki G, Sugiyama H (2010) Bioorg Med Chem 18:978–983
(a) Jacobs CS, Dervan PB (2009) J Med Chem 52:7380–7388. (b) Liu B, Kodadek T (2009) J Med Chem 52:4604–4612. (c) Takagaki T, Bando T, Kitano M, Hashiya K, Kashiwazaki G, Sugiyama H (2011) Bioorg Med Chem 19:5896–5902. (d) Meier JL, Montgomery DC, Dervan PB (2012) Nucleic Acids Res 40:2345–2356. (e) Hargrove AE, Raskatov JA, Meier JL, Montgomery DC, Dervan PB (2012) J Med Chem 55:5425–5432. (f) Saha A, Pandian GN, Sato S, Taniguchi J, Kawamoto Y, Hashiya K, Bando T, Sugiyama H (2014) ChemMedChem 9:2374–2380
(a) Harki DA, Satyamurthy N, Stout DB, Phelps ME, Dervan PB (2008) Proc Natl Acad Sci U S A 105:13039–13044. (b) Raskatov JA, Puckett JW, Dervan PB (2014) Bioorg Med Chem 22:4371–4375. (c) Raskatov JA, Szablowski JO, Dervan PB (2014) J Med Chem 57:8471–8476
(a) Su W, Schuster M, Bagshaw CR, Rant U, Burley GA (2011) Angew Chem Int Ed 50:2712–2715. (b) Su W, Bagshaw CR, Burley GA (2013) Sci Rep 3:1883
Han Y-W, Tsunaka Y, Yokota H, Matsumoto T, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Sugiyama H, Harada Y (2014) Biomater. Sci. 2:297–307
(a) Morinaga H, Takenaka T, Hashiya F, Kizaki S, Hashiya K, Bando T, Sugiyama H (2013) Nucleic Acids Res 41:4724–4728. (b) Saha A, Hashiya F, Kizaki S, Asamitsu S, Hashiya K, Bando T, Sugiyama H (2015) Chem Commun 51:14485–14488
(a) Cohen JD, Sadowski JP, Dervan PB (2007) Angew Chem Int Ed 46:7956–7959. (b) Cohen JD, Sadowski JP, Dervan PBJ (2008) Am Chem Soc 130:402–403. (c) Yoshidome T, Endo M, Kashiwazaki G, Hidaka K, Bando T, Sugiyama H (2012) J Am Chem Soc 134:4654–4660. (d) Schmidt TL, Nandi CK, Rasched G, Parui PP, Brutschy B, Famulok M, Heckel A (2007) Angew Chem Int Ed 46:4382–4384. (e) Schmidt TL, Heckel A (2009) Small 5:1517–1520. (f) Schmidt TL, Heckel A (2011) Nano Lett 11:1739–1742
(a) Schultz PG, Taylor JS, Dervan PB (1982) J Am Chem Soc 104:6861–6863. (b) Schultz PG, Dervan PB (1983) Proc Natl Acad Sci U S A 80:6834–6837. (c) Schultz PG, Dervan PB (1983) J Am Chem Soc 105:7748–7750. (d) Taylor JS, Schultz PG, Dervan PB (1984) Tetrahedron 40:457–465. (e) Youngquist RS, Dervan PB (1985) Proc Natl Acad Sci U S A 82:2565–2569. (f) Youngquist RS, Dervan PB (1985) J Am Chem Soc 107:5528–5529. (g) Dervan PB (1986) Science 232:464–471. (h) Youngquist RS, Dervan PB (1987) J Am Chem Soc 109:7564–7566
(a) Pitié M, Van Horn JD, Brion D, Burrows CJ, Meunier B (2000) Bioconjugate Chem 11:892–900. (b) Pitié M, Burrows CJ, Meunier B (2000) Nucleic Acids Res 28:4856–4864. (c) Liu D, Zhou J, Li H, Zheng B, Yuan G (2006) Bioorg Med Chem Lett 16:5032–5035. (d) Simon P, Cannata F, Perrouault L, Halby L, Concordet J-P, Boutorine A, Ryabinin V, Sinyakov A, Giovannangeli C (2008) Nucleic Acids Res 36:3531–3538. (e) Li C, Qiao R-Z, Wang Y-Q, Zhao Y-F, Zeng R (2008) Bioorg Med Chem Lett 18:5766–5770. (f) Li C, Du C, Tian H, Jiang C, Du M, Liu Y, Qiao R-Z, Jia Y-X, Zhao Y-F (2010) Chem Eur J 16:12935–12940. (g) Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M (2013) Angew Chem Int Ed 52:13681–13684
(a) Tanaka H, Tanaka Y, Minoshima M, Yamaguchi S, Fuse S, Doi T, Kawauchi S, Sugiyama H, Takahashi T (2010) Chem Commun 46:5942–5944. (b) Wirth-Hamdoune D, Ullrich S, Scheffer U, Radanović T, Dürner G, Göbel MW (2016) ChemBioChem 17:506–514
(a) Wang CCC, Dervan PB (2001) J Am Chem Soc 123:8657–8661. (b) Arimondo PB, Bailly C, Boutorine AS, Ryabinin VA, Syniakov AN, Sun JS, Garestier T, Hélène C (2001) Angew Chem Int Ed 40:3045–3048
(a) Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D, Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M (2017) J Am Chem Soc 139:7568–7576. (b) Ishiguro T, Amamoto Y, Tanabe K, Liu J, Kajino H, Fujimura A, Aoi Y, Osakabe A, Horikoshi N, Kurumizaka H, Yamatsugu K, Kawashima SA, Kanai M (2017) Chem 2:840–859
(a) Minoshima M, Bando T, Sasaki S, Fujimoto J, Sugiyama H (2008) Nucleic Acids Res 36:2889–2894. (b) Shinohara K, Yoda N, Takane K, Watanabe T, Fukuyo M, Fujiwara K, Kita K, Nagase H, Nemoto T, Kaneda A (2016) ACS Omega 1:1164–1172
(a) Fechter EJ, Dervan PB (2003) J Am Chem Soc 125:8476–8485. (b) Mackay H, Brown T, Sexton JS, Kotecha M, Nguyen B, Wilson WD, Kluza J, Savic B, O’Hare C, Hochhauser D, Lee M, Hartley JA (2008) Bioorg Med Chem 16:2093–2102
Trauger JW, Dervan PB (2001) Methods Enzymol 340:450–466
(a) Sugiyama H, Hosoda H, Saito I, Asai A, Saito H (1990) Tetrahedron Lett 31:7197–7200. (b) Sugiyama H, Ohmori K, Chan KL, Hosoda M, Asai A, Saito H, Saito I (1993) Tetrahedron Lett 34:2179–2182. (c) Sugiyama H, Fujiwara T, Ura A, Tashiro T, Yamamoto K, Kawanishi S, Saito I (1994) Chem Res Toxicol 7:673–683
Pilch DS, Poklar N, Gelfand CA, Law SM, Breslauer KJ, Baird EE, Dervan PB (1996) Proc Natl Acad Sci U S A 93:8306–8311
(a) Vashisht Gopal YN, Van Dyke MW (2003) Biochemistry 42:6891–6903. (b) Sunavala-Dossabhoy G, Van Dyke MW (2005) Biochemistry 44:2510–2522
(a) Warren CL, Kratochvil NC, Hauschild KE, Foister S, Brezinski ML, Dervan PB, Phillips Jr GN, Ansari AZ (2006) Proc Natl Acad Sci U S A 103:867–872. (b) Puckett JW, Muzikar KA, Tietjen J, Warren CL, Ansari AZ, Dervan PB (2007) J Am Chem Soc 129:12310–12319. (c) Carlson CD, Warren CL, Hauschild KE, Ozers MS, Qadir N, Bhimsaria D, Lee Y, Cerrina F, Ansari AZ (2010) Proc Natl Acad Sci U S A 107:4544–4549
(a) Kang JS, Dervan PB (2015) Q Rev Biophys 48:453–464. (b) Anandhakumar C, Li Y, Kizaki S, Pandian GN, Hashiya K, Bando T, Sugiyama H (2014) ChemBioChem 15:2647–2651. (c) Sawatani Y, Kashiwazaki G, Chandran A, Asamitsu S, Guo C, Sato S, Hashiya K, Bando T, Sugiyama H (2016) Bioorg Med Chem 24:3603–3611. (d) Kashiwazaki G, Maeda R, Kawase T, Hashiya K, Bando T, Sugiyama H (2018) Bioorg Med Chem 26:1–7
(a) Erwin GS, Bhimsaria D, Eguchi A, Ansari AZ (2014) Angew Chem Int Ed 53:10124–10128. (b) Erwin GS, Grieshop MP, Bhimsaria D, Do TJ, Rodriguez-Martinez JA, Mehta C, Khanna K, Swanson SA, Stewart R, Thomson JA, Ramanathan P, Ansari AZ (2016) Proc Natl Acad Sci U S A 113:7418–7427
(a) Chandran A, Syed J, Taylor RD, Kashiwazaki G, Sato S, Hashiya K, Bando T, Sugiyama H (2016) Nucleic Acids Res 44:4014–4024. (b) Chandran A, Syed J, Li Y, Sato S, Bando T, Sugiyama H (2016) ChemBioChem 17:1905–1910
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Kawamoto, Y. (2019). Introduction: Sequence-Specific DNA Binding Pyrrole–Imidazole Polyamides and Their Applications. In: Synthesis and Biological Evaluation of Pyrrole–Imidazole Polyamide Probes for Visualization of Telomeres. Springer Theses. Springer, Singapore. https://doi.org/10.1007/978-981-13-6912-4_1
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