Table A23.3.1.2

Dickerson, R. E.

doi:10.1107/97809553602060000716

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 23.3, pp. 613-619

Table A23.3.1.2

R. E. Dickerson^a ^*

^a Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095–1570, USA
Correspondence e-mail: red@mbi.ucla.edu

Table A23.3.1.2 | top | pdf |
X-ray analyses of B-DNA helices and their complexes with minor-groove-binding drug molecules

See introductory notes to Table A23.3.1.1. Space group $[P2_{1}2_{1}2_{1}]$ unless specified otherwise.

Notes: (triplet) = external triplet formed from overhanging bases. Overhanging, unpaired bases are $[\underline{\underline{\hbox{double underlined}}}]$ . $[{\underline{\hbox{Single underlining}}}]$ calls attention to interesting or relevant sequence aspects. Other notes as in Table A23.3.1.1.

I. DNA duplexes without bound drugs

(a) Dodecamers, space group $[P2_{1}2_{1}2_{1}]$

(1) Oligonucleotides without mismatches

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
CGCGAATTCGCG, 290 K	4	12	1980, UCLA (CIT)	BDL001	(B1–5, B75)
CGCGAATTCGCG, 16 K	4	12	1982, UCLA (CIT)	BDL002	(B6)
CGCGAATTCGCG, re-refinement	4	12	1987, Strasbourg	BDL020	(B23)
CGCGAATTCGCG, anisotropic temperature-factor refinement	4	12	1985, Berkeley	BDL005	(B10)
CGCG $[\underline{\hbox{AATT}}^{\rm 5br}\hbox{CGCG}]$ , 293 K	4	12	1982, UCLA (CIT)	BDLB03	(B7, B8)
CGCG $[\underline{\hbox{AATT}}^{\rm 5br}\hbox{CGCG}]$ , 280 K	4	12	1982, UCLA (CIT)	BDLB04	(B7, B8, B75)
CGCG $[\underline{\hbox{A}}^{\rm 6me}\underline{\hbox{ATT}}\hbox{CGCG}]$	4	12	1988, MIT	BDLB13	(B24)
CGCG $[\underline{\hbox{AA}}^{\rm 6ame}\underline{\hbox{T}}^{\rm 6ame}\underline{\hbox{T}}\hbox{CGCG}]$	4	12	1997, Northwestern	BDLS79	(B111)
CGCG $[\underline{\hbox{AA}}^{\rm 6aOH}\underline{\hbox{T}}^{\rm 6aOH}\underline{\hbox{T}}\hbox{CGCG}]$	4	12	1997, Northwestern	BDLS80	(B111)
CGCGAASSCGCG	4	12	1996, Manchester	BDLS67	(B97)
CGCAIAT^5meCTGCG	4	12	1997, Weizmann	BDLB82	(B113)
CGCAAAAAAGCG	4	12	1987, Cambridge	BDL006	(B20, B75)
CGCAAAAATGCG	4	12	1989, Yale	BDL015	(B31, B75)
CGCAAATTTGCG	4	12	1987, MIT	BDL016	(B17)
CGCAAATTTGCG	4	12	1992, Institute of Cancer Research	BDL038	(B52, B75)
CGCATATATGCG	4	12	1988, UCLA	BDL007	(B27)
CGCGTTAACGCG	4	12	1991, Ohio State	BDL059	(B40, B86)
CGCGATATCGCG	4	12	1997, Weizmann	BDL078	(B113)
CGCAIAT^5meCTGCG	4	12	1997, Weizmann	BDLB76	(B113)
CGTGAATTCACG	4	12	1991, UCLA	BDL029	(B44, B75)
CGTGAATTCACG	4	12	1991, Rutgers	BDL028	(B45)
CGCGAAAACGCG/ CGCGTT/TTCGCG (nicked strand)	4	12	1990, MIT	BDL021,32	(B35)

(2) Mismatch oligonucleotides (mismatches underlined)

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
CGCGAATTGGCG	4	12	1993, Institute of Cancer Research	BDL046	(B72)
CGCGAATTAGCG	4	12	1986, Cambridge	BDL012	(B13, B15)
CGCGAATT $[^{\rm 6et}\underline{\hbox{A}}]$ GCG	4	12	1994, Manchester	BDLB54	(B79)
CGCGAATT $[^{\rm 8oxo}\underline{\hbox{A}}]$ GCG	4	12	1992, Manchester	BDLB33	(B57)
CGCGAATTTGCG	4	12	1985, Cambridge	BDL009	(B19)
CGC $[^{\rm 6me}\underline{\hbox{G}}]$ AATTTGCG	4	12	1990, Edinburgh	BDLB26	(B38)
CGCAATTGGCG	4	12	1989, Manchester	BDL014	(B28, B37)
CGCAAGCTGGCG	4	12	1990, Institute of Cancer Research	BDL022	(B39, B75)
CGCAAATT $[^{\rm 8oxo}\underline{\hbox{G}}]$ GCG	4	12	1994, Edinburgh	BDLB56	(B80)
CGCAAATTCGCG	4	12	1986, Cambridge	BDL011	(B16)
CGCAAATTIGCG	4	12	1992, Edinburgh	BDLB41	(B56)
CGCIAATTAGCG	4	12	1987, Cambridge	BDLB10	(B18)
CGCIAATTCGCG	4	12	1992, Thomas Jefferson	BDLB40	(B61)
CGAGAATTC $[^{\rm 6me}\underline{\hbox{G}}]$ CG	4	12	1994, Rutgers	BDLB53	(B76)
CGTGAATTC $[^{\rm 6me}\underline{\hbox{G}}]$ CG	4	12	1995, Rutgers	BDLB58	(B95)

(b) Dodecamers: other space groups

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCTCTAGAGCG	$[P2_{1}]$	2	24	1996, Barcelona	BDL070	(B102)
CGTAGATCTACG	C 2	4	12	1993, Manchester	BDL042	(B69, B75)
CGCGAAAAAACG	$[P2_{1}2_{1}2]$	4	24	1993, Yale	BDL047	(B64, B75)
ACCGGCGCCACA	R 3	9	12	1989, Strasbourg	BDL018	(B34, B48, B49)
ACCGCCGGCGCC	R 3	9	12	1989, Strasbourg	BDL035	(B48, B49)
ACCGC^5meCGGCGCC	R 3	9	12	1997, Strasbourg	BDLB83	(B109)
ACCGGCGCCACA	R 3	9	12	1991, Strasbourg	BDL034	(B48)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CCAAGATTGG mismatch	C 2	4	5	1987, UCLA	BDJ008	(B22, B25)
CCAACGTTGG, Mg	C 2	4	5	1991, UCLA	BDJ019	(B46, B50)
CCAACITTGG, Ca	C 2	4	5	1992, UCLA	BDJB44	(B70)
CCAGGCCTGG	C 2	4	5	1989, Berlin	BDJ017	(B32)
CCA $[\underline{\hbox{GGC}}^{\rm ara}\underline{\hbox{C}}]$ TGG	C 2	4	5	1991, MIT	BDJS30	(B41)
$[\hbox{CCA}^{\rm 8oxo}\underline{\hbox{GCGC}}]$ TGG	C 2	4	5	1995, MIT	BDJB57	(B91)
CTCTCGAGAG	C 2	4	10	1994, UCLA	BDJ060	(B89)
CGCAATTGCG	C 2	4	10	1997, Institute of Cancer Research	BDJ069	(B114)
CAAAGAAAAG	C 2	4	20	1997, UCLA	BDJ081	(B107)
$[\underline{\underline{\hbox{CG}}}]$ ACGATCGT TGCTAGCA $[\underline{\underline{\hbox{GC}}}]$	$[P2_{1}]$	2	10	1997, NYU	UDJ060	(B112)
$[\underline{\underline{\hbox{GG}}}]$ CCAATTGG GGTTAACC $[\underline{\underline{\hbox{GG}}}]$	$[P2_{1}2_{1}2_{1}]$	4	10	1996, Cambridge	UDJ049	(B103)
CGATCGATCG, Mg	$[P2_{1}2_{1}2_{1}]$	4	10	1991, UCLA	BDJ025	(B42)
CGATTAATCG, Mg	$[P2_{1}2_{1}2_{1}]$	4	10	1992, UCLA	BDJ031	(B58)
CGATATATCG, Mg	$[P2_{1}2_{1}2_{1}]$	4	10	1992, UCLA	BDJ037	(B62)
CGATATATCG, Ca	$[P2_{1}2_{1}2_{1}]$	4	10	1992, UCLA	BDJ036	(B62)
CATGGCCATG, Ca	$[P2_{1}2_{1}2_{1}]$	4	10	1993, UCLA	BDJ051	(B66)
CG $[\underline{\hbox{ATCG}}^{\rm 6me}\underline{\hbox{AT}}]$ CG	$[P3_{2}21]$	6	10	1992, UCLA	BDJB48	(B63)
CCAACITTGG, Mg	$[P3_{2}21]$	6	10	1992, UCLA	BDJB43	(B70)
CCATTAATGG, Mg	$[P3_{2}21]$	6	10	1994, UCLA	BDJ055	(B77)
CCACTAGTGG	$[P3_{2}21]$	6	10	1994, Weizmann	BDJ061	(B82)
$[\hbox{CCA}\hbox{GGC}^{\rm 5me}\underline{ \hbox {C}}\hbox{TGG}]$	P 6	6	10	1992, Berlin	BDJB27	(B43, B54)
$[\hbox{CCA}\underline{\hbox{GGC}}^{\rm 5me}\underline{\hbox{C}}\hbox{TGG}]$	P 6	6	10	1993, Berlin	BDJB49	(B68)
$[\hbox{CCA}\underline{\hbox{GGC}}^{\rm 5me}\underline {\hbox{C}}\hbox{TGG}]$	P 6	6	10	1993, Berlin	BDJB50	(B68)
CCAAGCTTGG	P 6	6	10	1993, UCLA	BDJ052	(B67)
CCGGCGCCGG	R 3	9	10	1992, Berlin	BDJ039	(B55)
CCGCCGGCGG	R 3	9	10	1994, Strasbourg	BD0015	(B85)
CCIIICCCGG	$[P3_{1}]$	3	10	1997, Weizmann	BDJB77	(B113)

(d) Other oligonucleotide lengths

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
$[\underline{\underline{\hbox{G}}}]$ CGAATTCG (triplet)	$[P2_{1}2_{1}2_{1}]$	4	8	1996, Cambridge	UDI030	(B94)
GCTTAAGC $[\underline{\underline{\hbox{G}}}]$
CGCTAGCG	$[P2_{1}2_{1}2_{1}]$	4	16	1996, Barcelona	BDH071	(B102)
$[\underline{\underline{\hbox{C}}}]$ GGTGG	$[P6_{1}22]$	12	6	1995, Manitoba	BDF062	(B93)
CCACC $[\underline{\underline{\hbox{G}}}]$
CTCGAG	$[P6_{2}22]$	12	3	1996, Ohio State	BDF068	(B104)
GpsCGpsCGpsC	$[P2_{1}2_{1}2_{1}]$	4	6	1987, Cambridge	BDFP24	(B14)

II. DNA complexes with minor-groove-binding drugs

(a) Netropsin family of polyamides

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
Netropsin: ⁺Py-Py⁺
CGCG $[\underline{\hbox{AATT}}^{\rm 5br}]$ CGCG/N		4	12	1985, UCLA	GDLB05	(B11, B12)
CGCG $[\underline{\hbox{AATT}}^{\rm 5br}]$ CGCG/N		4	12	1995, UCLA	GDLB31	(B88)
CGCGAATTCGCG/N		4	12	1992, Illinois	GDL018	(B59)
CGC $[^{\rm 6et}\hbox{G}\underline{\hbox{AATT}}]$ CGCG/N		4	12	1992, Illinois	GDLB17	(B59)
CGCAAATTTGCG/N		4	12	1993, MIT	GDL014	(B73)
CGCGATATCGCG/N		4	12	1989, MIT	GDL001,4	(B30)
CGCGTTAACGCG/N		4	12	1995, Ohio State	GDL030	(B86)
CGCAATTGCG/N		4	12	1997, Institute of Cancer Research	GDJ046	(B110)

Lexitropsin: ⁺Im-Py⁺
CGCGAATTCGCG/1L		4	12	1995, UCLA	GDL037,8	(B90)

2:1 Di-imidazole Lexitropsin: ⁰Im-Im⁺
CATGGCCATG/2D		4	10	1997, UCLA	GDJ054	(B108)

Distamycin: ⁰Py-Py-Py⁺
CGCAAATTTGCG/1D		4	12	1987, MIT	GDL003	(B17)
ICICICIC/2D	$[P4_{1}22]$	8	4	1994, Ohio State	GDHB25	(B74)
$[\hbox{I}\underline{\hbox{c}}\hbox{ICICIC/2D}]$	$[P4_{1}22]$	8	4	1995, Ohio State	GHHB34	(B87)
$[\hbox{I}\underline{\hbox{c}}\hbox{I}\underline{\hbox{c}}\hbox{ICIC/2D}]$	$[P4_{1}22]$	8	4	1995, Ohio State	GHHB35	(B87)
ICATATIC	$[P4_{1}22]$	8	4	1997, Ohio State	GHHB50	(B105)
ICITACIC	$[P4_{1}22]$	8	4	1997, Ohio State	GHHB51	(B105)
ICATATIC		4	4	1997, Ohio State	GDLB49	(B105)

(b) Hoechst family

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
Hoechst 33258 (para -OH on phenyl ring A)
CGCGAATTCGCG/H	4	12	1987, UCLA	GDL006	(B21)
CGCGAATTCGCG/H	4	12	1988, MIT	GDL002	(B26)
CGCGAATTCGCG/H, 273 K	4	12	1991, UCLA	GDL010,11	(B47)
CGCGAATTCGCG/H, 248 K	4	12	1991, UCLA	GDL012	(B47)
CGCGAATTCGCG/H, 173 K	4	12	1991, UCLA	GDL013	(B47)
CGCGATATCGCG/H	4	12	1989, MIT	GDL007	(B29)
CGCAAATTTGCG/H	4	12	1994, Institute of Cancer Research	GDL028	(B83)
CGCAAATTTGCG/H	4	12	1994, MIT	GDL026	(B84)
CGCGAATTCGCG/H	4	12	1992, Illinois	GDL022	(B60)
$[\hbox{CGC}^{\rm 6et}\hbox{G}\underline{\hbox{AATT}}]$ CGCG/H	4	12	1992, Illinois	GDLB19	(B60)

Meta-OH(N) Hoechst 33258 (meta -OH on ring A)
CGCGAATTCGCG/H `in'	4	12	1996, Institute of Cancer Research	GDL047	(B99)
CGCGAATTCGCG/H `out'	4	12	1996, Institute of Cancer Research	GDL048	(B99)
Hoechst 33342 (para -OEt on ring A)
CGCGAATTCGCG/H	4	12	1992, Illinois	GDLB20	(B60)
$[\hbox{CGC}^{\rm 6et}\hbox{G}\underline{\hbox{AATT}}]$ CGCG/H	4	12	1992, Illinois	GDLB20	(B60)

Bis-benzimidazole compound (imidazole for piperazine on Hoechst 33258)
CGCGAATTCGCG/B	4	12	1995, Institute of Cancer Research	GDL033	(B96)

Tribiz or Tris-benzimidazole (extended Hoechst 33258 analogue)
CGCAAATTTGCG/T	4	12	1996, Institute of Cancer Research	GDL039	(B98)

Bis-amidinium derivative of Hoechst 33258
CGCGAATTCGCG	4	12	1997, Institute of Cancer Research	GDL052	(B106)

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
Berenil
CGCGAATTCGCG/B	4	12	1990, Institute of Cancer Research	GDL009	(B36)
CGCGAATTCGCG/B	4	12	1992, Institute of Cancer Research	GDL016	(B51)

2,5-Bis(4-guanylphenyl)furan (berenil analogue)
CGCGAATTCGCG/F	4	12	1996, Institute of Cancer Research	GDL036	(B100)

2,5-Bis{[4-(N-isopropyl)amidino]phenyl}furan (berenil analogue)
CGCGAATTCGCG/F	4	12	1996, Institute of Cancer Research	GDL044	(B101)

2,5-Bis{[4-(N-cyclopropyl)amidino]phenyl}furan (berenil analogue)
CGCGAATTCGCG/F	4	12	1997, Institute of Cancer Research	GDL045	(B101)

(d) Other minor-groove binders

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
DAPI
CGCGAATTCGCG/D		4	12	1989, UCLA	GDL008	(B33)

Pentamidine
CGCGAATTCGCG/P		4	12	1992, Institute of Cancer Research	GDL015	(B53)

γ-Oxapentamidine
CGCGAATTCGCG/P		4	12	1994, Institute of Cancer Research	GDL027	(B81)

Propamidine
CGCGAATTCGCG/P		4	12	1993, Institute of Cancer Research	GDL023	(B71)
CGCGAATTCGCG/P		4	12	1995, Institute of Cancer Research	GDL032	(B92)
SN6999
$[\hbox{CGC}^{\rm 6et}\hbox{G}\underline{\hbox{AATT}}\hbox{CGCG/S}]$		4	12	1993, Illinois	GDLB24	(B65)

Anthramycin
CCAACGTTGG/A	$[P3_{2}21]$	6	5	1993, UCLA	GDJB29	(B78)

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