Nucleic acids

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. 609-622 | 1 | 2 |
https://doi.org/10.1107/97809553602060000716

Appendix A23.3.1. X-ray analyses of A, B and Z helices

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 A23.3.1.1 | top | pdf |
X-ray analyses of A helices, DNA and RNA

This table and the two that follow are intended as a historical background and a focus on the geometry of the intact double helix. References are current as of late 1997; sequences marked `to be published' in 1997 that still are unpublished two years later have been deleted. Also omitted are sequences with fewer than four base pairs in the asymmetric unit, complexes with intercalating drugs, helices with bulges or looped-out bases, unusual structures such as quadruplexes, hammerhead ribozymes and tRNA. For information on these and for more recent results, consult the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/ . An NDB number in parentheses indicates that the authors have never made coordinates available to the public. These structures are of little scientific value, but have been included for historical reasons.

Notes: Overhanging, unpaired bases are $[\underline{\underline{\hbox{double underlined}}}]$ . $[\underline{{\hbox{Single underlining}}}]$ calls attention to mismatched bases or other interesting or relevant sequence aspects. Z = number of asymmetric units per cell. Ubp = number of base pairs per asymmetric unit. NDB No. = Nucleic Acid Database serial number. Abbreviations: 2am = 2-amino; 5br = 5-bromo; 6ame = 6′-α-methyl; 4mo = 4-methoxy; 5me = 5-methyl; 6aOH = 6′-α-hydroxyl; 6mo = 6-methoxy; 8oxo = 8-oxo; 6et = 6-ethyl; ara = arabinosyl; ps = phosphorothioate; (P) = leading phosphate; A, T, G, C = DNA; a, u, g, c = RNA; Py = pyrrole; Im = imidazole.

(a) Dodecamers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CCCCCGCGGGGG	$[P3_{2}21]$	6	12	1991, Barcelona	ADL025	(A38)
CCGTACGTACGG	$[P6_{1}22]$	12	6	1992, Ohio State	ADL045	(A41)
GCGTACGTACGC	$[P6_{1}22]$	12	6	1992, Ohio State	ADL046	(A39)

(b) Decamers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
GCGGGCCCGC	$[P6_{1}22]$	12	5	1993, Ohio State	ADJ051	(A46)
GCACGCGTGC	$[P6_{1}22]$	12	5	1996, Ohio State	ADJ075	(A60)
ACCGGCCGGT	$[P6_{1}22]$	12	5	1989, MIT	ADJ022	(A26)
ACCGGCCGGT	$[P6_{1}22]$	12	5	1995, MIT	ADJ065	(A55)
ACCCGCGGGT	$[P6_{1}22]$	12	5	1995, MIT	ADJ066	(A55)
CCCGGCCGGG	$[P2_{1}2_{1}2_{1}]$	4	10	1993, Ohio State	ADJ049	(A47)
CCIGGCC^5meCGG	$[P2_{1}2_{1}2_{1}]$	4	10	1995, Ohio State	ADJB61	(A58)
GCGGGCCCGC	$[P2_{1}2_{1}2_{1}]$	4	10	1993, Ohio State	ADJ050	(A46)
ACCGGCCGGT	$[P2_{1}2_{1}2_{1}]$	4	10	1995, MIT	ADJ067	(A55)
CCGGGCCGCG	$[P2_{1}2_{1}2_{1}]$	4	10	1997, Ohio State	ADJ081,2	(A71)
C^5meCGGGCCCGG	$[P2_{1}2_{1}2_{1}]$	4	10	1997, Ohio State	ADJB87	(A71)
CCGGG^5brCCCGG	$[P2_{1}2_{1}2_{1}]$	4	10	1997, Ohio State	ADJB80	(A71)
CCGGGCC^5meCGG	$[P2_{1}2_{1}2_{1}]$	4	10	1997, Ohio State	ADJB84,5	(A71)
C^5meCGGGCCCGG	$[P6_{1}]$	6	10	1997, Ohio State	ADJB86	(A71)
CCGGGCC^5brCGG	$[P6_{1}]$	6	10	1997, Ohio State	ADJB79	(A71)
CCGGGCC^5meCGG	$[P6_{1}]$	6	10	1997, Ohio State	ADJB83	(A71)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
GGATGGGAG	$[P4_{3}]$	4	9	1986, Cambridge	ADI009	(A14)

(d) Octamers, space group $[P4_{3}2_{1}2]$

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
CCCCGGGG	8	4	1987, Weizmann/MIT	ADH012	(A16)
CCCCGGGG, 298 K	8	4	1995, Weizmann	ADH056	(A54)
CCCGCGGG	8	4	1997, Moscow	ADH0106	(A69)
CCCTAGGG	8	4	1996, Ohio State	ADH078	(A64)
GCCCGGGC	8	4	1987, Berlin	ADH008	(A17)
GCCCGGGC (methylenephosphonate)	8	4	1991, Berlin	ADHP36	(A36)
GGCCGGCC	8	4	1982, MIT	ADH013,098	(A4,5)
GGCCGGCC, 288 K	8	4	1995, Weizmann	ADH058	(A54)
GG^5meCCGGCC	8	4	1987, MIT	(ADHB21)	(A15)
GGGCGCCC, 293 K	8	4	1988, Weizmann	ADH026	(A22, A34)
GGGCGCCC, 115 K	8	4	1988, Weizmann	ADH027	(A20, A34)
GGGCGCCC, 115 K, re-refinement	8	4	1995, Weizmann	ADH057	(A54)
GTGCGCAC	8	4	1992, Ohio State	ADH047	(A40)
GTGTACAC/spermine	8	4	1987, Wisconsin	ADH014	(A18, A29)
CTCTAGAG	8	4	1989, Cambridge	ADH020	(A27)
GTACGTAC	8	4	1990, Kansas	ADH024	(A35)
GTACGTAC	8	4	1990, Bordeaux	ADH023	(A32)
GTCTAGAC	8	4	1992, Manchester	ADH041	(A42)
ATGCGCAT	8	4	1990, Institute of Cancer Research	(ADH032)	(A31)
ATGCGCAT/spermine	8	4	1990, Institute of Cancer Research	ADH033	(A31)
ACGTACGT	8	4	1996, Trinity, Dublin	ADH070	(A66)

(e) Octamers, space group $[P2_{1}2_{1}2_{1}]$

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
CCCGCGGG	4	8	1997, Moscow	ADH0102–5	(A69)

(f) Octamers, space group $[P6_{1}]$

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
GGGGCCCC	6	8	1985, Cambridge	ADH006	(A11)
GGGATCCC	6	8	1988, Berlin	ADH007	(A21)
GGGCGCCC, 293 K	6	8	1989, Weizmann	(ADH028)	(A30, A34)
GGGCGCCC, 100 K	6	8	1989, Weizmann	ADH029	(A30, A34)
GGGTACCC, 293 K	6	8	1990, Weizmann	ADH030	(A33)
GGGTACCC, 100 K	6	8	1990, Weizmann	ADH031	(A33)
GGGTGCCC	6	8	1988, Weizmann	ADH016	(A22)
GGTATACC	6	8	1981, Weizmann/Cambridge	ADH010	(A2, A7)
GG^5brUA^5brUACC	6	8	1981, Weizmann/Cambridge	ADHB11	(A2, A7, A13)
GGCATGCC	6	8	1997, Institute of Cancer Research	ADH076	(A70)
GGIGCTCC	6	8	1989, Cambridge	ADHB17	(A24)
GGGGCTCC mismatch	6	8	1985, Cambridge/Weizmann	ADH019	(A9, A12)
GGGGTCCC mismatch	6	8	1985, Cambridge/Weizmann	ADH018	(A10)
GGGTGCCC mismatch	6	8	1988, Weizmann	ADH016	(A22)

(g) Octamers, space group $[P6_{1}22]$

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
GTGTACAC	12	4	1989, Wisconsin	ADH034	(A28)
GTGTACAC/spermine	12	4	1993, Ohio State	ADH038	(A48)
GTGTACAC/spermidine	12	4	1993, Ohio State	ADH039	(A48)

(h) Octamers, space group $[P2_{1}2_{1}2]$

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
GTACGTAC	4	8	1993, Bordeaux	ADH059	(A44)

(i) Hexamers, space group $[C222_{1}]$

Sequence	Z	Ubp	Date, institution	NDB No.	Reference
GCCGGC	8	6	1995, Oregon State	ADF073	(A56)
G^5meCG^5meCGC	8	6	1995, Oregon State	ADFB62	(A56)
G^5meCCGGC	8	6	1995, Oregon State	ADFB63	(A56)
G^5meCGCGC	8	6	1995, Oregon State	ADFB72	(A56)

(j) Tetramers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
⁵ⁱ CCGG	$[P4_{3}2_{1}2]$	8	4	1981, UCLA (CIT)	ADDB01	(A1, A3, A8)

(k) RNA/DNA and RNA/RNA (lower case = RNA)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CCGGC g CCGG	$[P2_{1}2_{1}2_{1}]$	4	10	1994, Ohio State	AHJ052	(A49)
c CGGCGCCGg	$[P2_{1}2_{1}2_{1}]$	4	10	1994, Ohio State	AHJ060	(A50)
g CGTATACGC	$[P2_{1}2_{1}2_{1}]$	4	10	1993, MIT	AHJ043	(A45)
GCGTaTACGC	$[P2_{1}2_{1}2_{1}]$	4	10	1993, MIT	AHJ044	(A45)
GCGT^meaTACGC	$[P2_{1}2_{1}2_{1}]$	4	10	1994, ETH Zürich	AHJS55	(A53)
g c GTATACGC	$[P2_{1}2_{1}2_{1}]$	4	10	1995, MIT	AHJ068	(A55)
g c g TATACGC	$[P2_{1}2_{1}2_{1}]$	4	10	1982, MIT	AHJ015	(A4, A6)
g c g TATACCC\	$[P2_{1}2_{1}2_{1}]$	4	10	1992, MIT	AHJ040	(A43)
\GGGTATACGC
u u c g g g c g c c\	$[P4_{3}22]$	8	10	1996, Upjohn	UHJ055	(A62)
\GGCGCCCGAA
c c c c g g g g	$[P6_{1}22]$	12	4	1995, ETH Zürich	ARH063	(A57)
c c c c g g g g	R 32	18	8	1995, ETH Zürich	ARH064	(A57)
c c c c g g g g	R 32	18	8	1996, Northwestern	ARH074	(A61)
g u a u a u a C	R 3	9	8	1996, Ohio State	AHH071	(A65)
g u a u g u a C	R 3	9	8	1997, Ohio State	AHH077	(A68)
g u g u g u a C	R 3	9	8	1997, Ohio State	AHH089	(A67)
g c u u c g g c ^brU	C 2	4	9	1994, Cambridge	AHIB53	(A51)
(P)g g a c u u c g g u c c	C 2	4	6	1991, Berkeley	ARL037	(A37)
c g c g a a t t a g c g	$[P2_{1}]$	2	12	1994, Manchester	ARL048	(A52)
u a a g g a g g u g a u	P 1	1	24	1995, Berlin	ARL062	(A59)
g g c g c u u g c g u c	P 1	1	24	1996, Colorado	URL050	(A63)
u u a u a u a u a u a u a a	$[P2_{1}2_{1}2_{1}]$	4	4	1988, Strasbourg	ARN035	(A19, A25)

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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)

References (numbered chronologically by year and alphabetically by first author within each year)

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Table A23.3.1.3 | top | pdf |
X-ray analyses of Z helices

See introductory notes to Table A23.3.1.1. odm = 6H,8H-3,4-dihydropyrimido[4,5c][1,2]oxazin-7-one.

(a) Hexadecamers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCGCGTTTTCGCGCG (hairpin)	C 2	4	8	1988, UCLA	UDP011	(Z20, Z25)

(b) Decamers (disordered)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
GCGCGCGCGC	$[P6_{5}]$	6	2	1996, Ohio State	ZDJ050	(Z46)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCICICG	$[P6_{5}]$	6	8	1992, Thomas Jefferson	ZDH030	(Z32)
CGCGCGCG	$[P6_{5}]$	6	8	1985, MIT	(ZDH017)	(Z10)
CGCATGCG	$[P6_{5}]$	6	8	1985, MIT	(ZDH016)	(Z10)

(d) Heptamers (overhanging 5′ bases)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
GCGCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Oregon State	ZDG054	(Z50)
G^5meCGCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Oregon State	ZDG055	(Z50)
GCGCGCG/GCGCGCT	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Oregon State	ZDG056	(Z50)
GCGCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Ohio State	ZDG057	(Z51)

(e) Hexamers

(1) Alternating CG: Pu-Py alternation retained

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCGCG, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	ZDF002	(Z23)
CGCGCG, DL racemate	$[P\overline{1}]$	2	6	1993, Osaka	ZDF040	(Z36)
CGCGCG/spermine	$[P2_{1}2_{1}2_{1}]$	4	6	1991, MIT	ZDF029	(Z29)
CGCGCG/spermine, 163 K	$[P2_{1}2_{1}2_{1}]$	4	6	1994, MIT	ZDF035	(Z41)
CGCGCG/spermine, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1979, MIT	ZDF001	(Z1, Z23)
CGCGCG/spermidine	$[P2_{1}2_{1}2_{1}]$	4	6	1996, MIT	ZDF052	(Z47)
CGCGCG/thermospermidine	$[P2_{1}2_{1}2_{1}]$	4	6	1996, MIT	ZDF053	(Z48)
CGCGCG, Co, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1985, MIT	(ZDF019)	(Z11)
CGCGCG, Co, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	(ZDF044)	(Z37)
CGCGCG/spermine, Co	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	(ZDF045)	(Z37)
CGCGCG, Ru	$[P2_{1}2_{1}2_{1}]$	4	6	1987, MIT	(ZDF007)	(Z18)
CG c g CG	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	(ZHF026)	(Z24)

(2) Alternating CG: Pu-Py alternation broken

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CCGCGG	$[C222_{1}]$	8	6	1994, Moscow	UDF025	(Z42)

(3) Modified CG bases: Pu-Py alternation retained

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CG^araCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	(ZDFS27)	(Z24)
CGC^6moGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1990, Rutgers	ZDFB21	(Z26)
CGCG^4moCG	$[P2_{1}2_{1}2_{1}]$	4	6	1990, Cambridge	ZDFB25	(Z27)
CGCG^4moCG	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Manchester	ZDFB36	(Z35)
CGCG^5brCG	$[P2_{1}2_{1}2_{1}]$	4	6	1996, Manchester	ZDFB51	(Z49)
CGCG^odmCG	$[P2_{1}2_{1}2_{1}]$	4	6	1995, Cambridge	ZDFB43	(Z43)
^5me CG^5meCG^5meCG	$[P2_{1}2_{1}2_{1}]$	4	6	1982, MIT	ZDFB03	(Z6, Z7)
^5br CG^5brCG^5brCG, 291 K	$[P2_{1}2_{1}2_{1}]$	4	6	1986, Strasbourg	ZDFB04	(Z16, Z19)
^5br CG^5brCG^5brCG, 310 K	$[P2_{1}2_{1}2_{1}]$	4	6	1986, Strasbourg	ZDFB05	(Z16, Z19)
Aminohexyl-CG^5brCGCG	C 2	4	6	1993, Illinois	(ZDFA32)	(Z38)
^ara CG^araCG^araCG (disordered)	$[P6_{5}22]$	12	2	1992, Illinois	ZDFS33	(Z34)

(4) Modified CG bases: Pu-Py alternation broken

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
$[^{\rm 5me}\hbox{CG}\underline{\hbox{G}}\hbox{G}^{\rm 5me}\hbox{CG}]$	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Oregon State	ZDFB37	(Z40)

(5) With A, T, U, I bases: Pu-Py alternation retained

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
^5me CGTA^5meCG	$[P2_{1}2_{1}2_{1}]$	4	6	1984, MIT	ZDFB06	(Z8)
CGT^2amACG	$[P3_{2}21]$	6	3	1995, Rutgers	ZDFB41	(Z44)
CGT^2amACG, Pt	$[P3_{2}21]$	6	3	1995, Rutgers	ZDFB42	(Z44)
CGU^2amACG	$[P2_{1}2_{1}2_{1}]$	4	6	1992, Rutgers	ZDFB31	(Z33)
^5me CGUA^5meCG	$[P2_{1}2_{1}2_{1}]$	4	6	1990, Oregon State	ZDFB24	(Z28)
^5me CGUA^5meCG, Cu	$[P2_{1}2_{1}2_{1}]$	4	5	1991, Oregon State	ZDFB10	(Z30)
CACGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1988, MIT	(ZDF008)	(Z21)
C^2amACGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1986, MIT	ZDFB11	(Z17)
CGCICG	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Thomas Jefferson	(ZDFB34)	(Z39)
CACGCG/CGCGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1995, Madras	ZDF039	(Z45)
CGCACG/CGTGCG	$[P2_{1}]$	2	6	1995, Madras	ZDF038	(Z45)

(6) With A, T, U, I bases: Pu-Py alternation broken

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
$[^{\rm 5br}\hbox{CG}\underline{\hbox{AT}}^{\rm 5br}\hbox{CG}]$	$[P2_{1}2_{1}2_{1}]$	4	6	1985, MIT	(ZDFB09)	(Z13)

(7) With mismatches (underlined)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1985, MIT	ZDF013	(Z12)
C $[\underline{\hbox{G}}\hbox{CG}^{\rm 5fl}\underline{\hbox{U}}]$ G	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	ZDFB12	(Z22)
$[^{\rm 5br}\underline{\hbox{U}}]$ GCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1986, Cambridge	ZDFB14	(Z15)
CGCGTG, Co, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	ZDF046	(Z37)
CGCGTG, Cu, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	ZDF047	(Z37)
$[^{\rm 5me}\hbox{C}\underline{\hbox{G}}^{\rm 5me}\hbox{CG}\underline{\hbox{T}}]$ G, Ba	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	(ZDFB48)	(Z37)

(f) Tetramers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCG	$[C222_{1}]$	8	4	1980, UCLA (CIT)	ZDD015	(Z3, Z4, Z5)
CGCG (disordered)	$[P6_{5}]$	6	6	1980, MIT	ZDD023	(Z2)

References (numbered chronologically by year and alphabetically by first author within each year)

Year	Reference
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1980	(Z2) J. L. Crawford, F. J. Kolpak, A. H.-J. Wang, G. J. Quigley, J. H. van Boom, G. van der Marel & A. Rich (1980). Proc. Natl Acad. Sci. USA, 77, 4016–4020.
1980	(Z3) H. R. Drew, T. Takano, S. Tanaka, K. Itakura & R. E. Dickerson (1980). Nature (London), 286, 567–573.
1981	(Z4) R. E. Dickerson, H. R. Drew & B. N. Conner (1981). Biomolecular stereodynamics, Vol. 1, edited by R. H. Sarma, pp. 1–34. New York: Adenine Press.
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1982	(Z7) S. Fujii, A. H.-J. Wang, J. van Boom & A. Rich (1982). Nucleic Acids Res. Symp. Ser. 11, 109–112.
1984	(Z8) A. H.-J. Wang, T. Hakoshima, G. van der Marel, J. H. van Boom & A. Rich (1984). Cell, 37, 321–331.
1985	(Z9) R. G. Brennan & M. Sundaralingam (1985). J. Mol. Biol. 181, 561–563.
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1986	(Z14) R. G. Brennan, E. Westhof & M. Sundaralingam (1986). J. Biomol. Struct. Dyn. 3, 649–665.
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1987	(Z18) P. S. Ho, C. A. Frederick, D. Saal, A. H.-J. Wang & A. Rich (1987). J. Biomol. Struct. Dyn. 4, 521–534.
1987	(Z19) E. Westhof (1987). J. Biomol. Struct. Dyn. 5, 581–600.
1988	(Z20) R. Chattopadhyaya, S. Ikuta, K. Grzeskowiak & R. E. Dickerson (1988). Nature (London), 334, 175–179.
1988	(Z21) M. Coll, I. Fita, J. Lloveras, J. A. Subirana, F. Bardella, T. Huynh-Dinh & J. Igolen (1988). Nucleic Acids Res. 16, 8695–8705.
1989	(Z22) M. Coll, D. Saal, C. A. Frederick, J. Aymami, A. Rich & A. H.-J. Wang (1989). Nucleic Acids Res. 17, 911–923.
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1990	(Z25) R. Chattopadhyaya, K. Grzeskowiak & R. E. Dickerson (1990). J. Mol. Biol. 211, 189–210.
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1991	(Z29) M. Egli, L. D. Williams, Q. Gao & A. Rich (1991). Biochemistry, 30, 11388–11402.
1991	(Z30) B. H. Geierstanger, T. F. Kagawa, S.-L. Chen, G. J. Quigley & P. S. Ho (1991). J. Biol. Chem. 266, 20185–20191.
1992	(Z32) V. D. Kumar, R. W. Harrison, L. C. Andrews & I. T. Weber (1992). Biochemistry, 31, 1541–1550.
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References

International Tables for Crystallography (2006). Vol. F. ch. 23.3, pp. 609-622
https://doi.org/10.1107/97809553602060000716