Table A23.3.1.1

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

pdf | chapter contents | chapter index | related articles

International Tables for Crystallography (2006). Vol. F. ch. 23.3, pp. 609-613

Table A23.3.1.1

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 References are current as of late 1997; sequences marked `to be published' in 1997 that still are unpublished two years later have been deleted.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)

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

Year	Reference
1981	(A1) 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.
1981	(A2) Z. Shakked, D. Rabinovich, W. B. T. Cruse, E. Egert, O. Kennard, G. Sala, S. A. Salisbury & M. A. Viswamitra (1981). Proc. R. Soc. London Ser. B, 213, 479–487.
1982	(A3) B. N. Conner, T. Takano, S. Tanaka, K. Itakura & R. E. Dickerson (1982). Nature (London), 295, 294–299.
	(A4) S. Fujii, A. H.-J. Wang, J. van Boom & A. Rich (1982). Nucleic Acids Res. Symp. Ser. 11, 109–112.
	(A5) A. H.-J. Wang, S. Fujii, J. H. van Boom & A. Rich (1982). Proc. Natl Acad. Sci. USA, 79, 3968–3972.
	(A6) A. H.-J. Wang, S. Fujii, J. H. van Boom, G. A. van der Marel, S. A. A. van Boeckel & A. Rich (1982). Nature (London), 299, 601–604.
1983	(A7) Z. Shakked, D. Rabinovich, O. Kennard, W. B. T. Cruse, S. A. Salisbury & M. A. Viswamitra (1983). J. Mol. Biol. 166, 183–201.
1984	(A8) B. N. Conner, C. Yoon, J. L. Dickerson & R. E. Dickerson (1984). J. Mol. Biol. 174, 663–695.
1985	(A9) T. Brown, O. Kennard, G. Kneale & D. Rabinovich (1985). Nature (London), 315, 604–606.
	(A10) G. Kneale, T. Brown, O. Kennard & D. Rabinovich (1985). J. Mol. Biol. 186, 805–814.
	(A11) M. McCall, T. Brown & O. Kennard (1985). J. Mol. Biol. 183, 385–396.
1986	(A12) W. N. Hunter, G. Kneale, T. Brown, D. Rabinovich & O. Kennard (1986). J. Mol. Biol. 190, 605–618.
	(A13) O. Kennard, W. B. T. Cruse, J. Nachman, T. Prange, Z. Shakked & D. Rabinovich (1986). J. Biomol. Struct. Dyn. 3, 623–647.
	(A14) M. McCall, T. Brown, W. N. Hunter & O. Kennard (1986). Nature (London), 322, 661–664.
1987	(A15) C. A. Frederick, D. Saal, G. A. van der Marel, J. H. van Boom, A. H.-J. Wang & A. Rich (1987). Biopolymers, 26, S145–S160.
	(A16) T. E. Haran, Z. Shakked, A. H.-J. Wang & A. Rich (1987). J. Biomol. Struct. Dyn. 5, 199–217.
	(A17) U. Heinemann, H. Lauble, R. Frank & H. Bloeker (1987). Nucleic Acids Res. 15, 9531–9550.
	(A18) S. Jain, G. Zon & M. Sundaralingam (1987). J. Mol. Biol. 197, 141–145.
1988	(A19) A. C. Dock-Bregeon, B. Chevrier, A. Podjarny, D. Moras, J. S. de Bear, G. R. Gough, P. T. Gilham & J. E. Johnson (1988). Nature (London), 335, 375–378.
	(A20) M. Eisenstein, H. Hope, T. E. Haran, F. Frolow, Z. Shakked & D. Rabinovich (1988). Acta Cryst. B44, 625–628.
	(A21) H. Lauble, R. Frank, H. Bloecker & U. Heinemann (1988). Nucleic Acids Res. 16, 7799–7816.
	(A22) D. Rabinovich, T. Haran, M. Eisenstein & Z. Shakked (1988). J. Mol. Biol. 200, 151–161.
1989	(A23) C. A. Bingman, S. Jain, D. Jebaratnam & M. Sundaralingam (1989). Sixth Conversation in Biomolecular Stereodynamics, Albany, NY, Abstracts p. 28.
	(A24) W. B. T. Cruse, J. Aymani, O. Kennard, T. Brown, A. G. C. Jack & G. A. Leonard (1989). Nucleic Acids Res. 17, 55–72.
	(A25) A. C. Dock-Bregeon, B. Chevrier, A. Podjarny, J. Johnson, J. S. de Bear, G. R. Gough, P. T. Gilham & D. Moras. (1989). J. Mol. Biol. 209, 459–474.
	(A26) C. A. Frederick, G. J. Quigley, M.-K. Teng, M. Coll, G. A. van der Marel, J. H. van Boom, A. Rich & A. H.-J. Wang (1989). Eur. J. Biochem. 181, 295–307.
	(A27) W. N. Hunter, B. L. D'Estaintot & O. Kennard (1989). Biochemisty, 28, 2444–2451.
	(A28) S. Jain & M. Sundaralingam (1989). J. Biol. Chem. 264, 12780–12784.
	(A29) S. Jain, G. Zon & M. Sundaralingam (1989). Biochemistry, 28, 2360–2364.
	(A30) Z. Shakked, G. Guerstein-Guzikevich, F. Frolow & D. Rabinovich (1989). Nature (London), 342, 456–460.
1990	(A31) G. R. Clark, D. G. Brown, M. R. Sanderson, T. Chwalinski, S. Neidle, J. M. Veal, R. L. Jones, W. D. Wilson, G. Zon, E. Garman & D. I. Stuart (1990). Nucleic Acids Res. 18, 5521–5528.
	(A32) C. Courseille, A. Dautant, M. Hospital, B. Langlois d'Estaintot, G. Precigoux, D. Molko & R. Teoule (1990). Acta Cryst. A46, FC9–FC12.
	(A33) M. Eisenstein, F. Frolow, Z. Shakked & D. Rabinovich (1990). Nucleic Acids Res. 18, 3185–3194.
	(A34) Z. Shakked, G. Guerstein-Guzikevich, A. Zaytzev, M. Eisenstein, F. Frolow & D. Rabinovich (1990). In Structure and methods, Vol. 3. DNA and RNA, edited by R. H. Sarma & M. H. Sarma, pp. 55–72. Schenectady, NY: Adenine Press.
	(A35) F. Takusagawa (1990). J. Biomol. Struct. Dyn. 7, 795–809.
1991	(A36) U. Heinemann, L.-N. Rudolph, C. Alings, M. Morr, W. Heikens, R. Frank & H. Bloecker (1991). Nucleic Acids Res. 19, 427–433.
	(A37) S. R. Holbrook, C. Cheong, I. Tinoco Jr & S.-H. Kim (1991). Nature (London), 353, 579–581.
	(A38) N. Verdaguer, J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen & J. A. Subirana (1991). J. Mol. Biol. 221, 623–635.
1992	(A39) C. Bingman, S. Jain, G. Zon & M. Sundaralingam (1992). Nucleic Acids Res. 20, 6637–6647.
	(A40) C. A. Bingman, X. Li, G. Zon & M. Sundaralingam (1992). Biochemistry, 31, 12803–12812.
	(A41) C. A. Bingman, G. Zon & M. Sundaralingam (1992). J. Mol. Biol. 227, 738–756.
	(A42) A. R. Cervi, B. Langlois d'Estaintot & W. N. Hunter (1992). Acta Cryst. B48, 714–719.
	(A43) M. Egli, N. Usman, S. Zhang & A. Rich (1992). Proc. Natl Acad. Sci. USA, 89, 534–538.
1993	(A44) B. Langlois D'Estaintot, A. Dautant, C. Courseille & G. Precigoux (1993). Eur. J. Biochem. 213, 673–682.
	(A45) M. Egli, N. Usman & A. Rich (1993). Biochemistry, 32, 3221–3237.
	(A46) B. Ramakrishnan & M. Sundaralingam (1993). Biochemistry, 32, 11458–11468.
	(A47) B. Ramakrishnan & M. Sundaralingam (1993). J. Mol. Biol. 231, 431–444.
	(A48) N. Thota, X. H. Li, C. Bingman & M. Sundaralingam (1993). Acta Cryst. D49, 282–291.
1994	(A49) C. Ban, B. Ramakrishnan & M. Sundaralingam (1994). J. Mol. Biol. 236, 275–285.
	(A50) C. Ban, B. Ramakrishnan & M. Sundaralingam (1994). Nucleic Acids Res. 22, 5466–5476.
	(A51) W. Cruse, P. Saludjian, E. Biala, P. Strazewski, T. Prange & O. Kennard (1994). Proc. Natl Acad. Sci. USA, 91, 4160–4164.
	(A52) G. A. Leonard, K. E. McAuley-Hecht, S. Ebel, D. M. Lough, T. Brown & W. N. Hunter (1994). Structure, 2, 483–494.
	(A53) P. Lubini, W. Zuercher & M. Egli (1994). Chem. Biol. 1, 39–45.
1995	(A54) M. Eisenstein & Z. Shakked (1995). J. Mol. Biol. 248, 662–678.
	(A55) Y.-G. Gao, H. Robinson, J. H. van Boom & A. H.-J. Wang (1995). Biophys. J. 69, 559–568.
	(A56) B. H. Mooers, G. P. Schroth, W. W. Baxter & P. S. Ho (1995). J. Mol. Biol. 249, 772–784.
	(A57) S. Portmann, N. Usman & M. Egli (1995). Biochemistry, 34, 7569–7575.
	(A58) B. Ramakrishnan & M. Sundaralingam (1995). Biophys. J. 69, 553–558.
	(A59) H. Schindelin, M. Zhang, R. Bald, J.-P. Fuerste, V. A. Erdmann & U. Heinemann (1995). J. Mol. Biol. 249, 595–603.
1996	(A60) C. Ban & M. Sundaralingam (1996). Biophys. J. 71, 1222–1227.
	(A61) M. Egli, S. Portmann & N. Usman (1996). Biochemistry, 35, 8489–8494.
	(A62) N. C. Horton & B. C. Finzel (1996). J. Mol. Biol. 264, 521–533.
	(A63) S. E. Lietzke, C. L. Barnes & C. E. Kundrot (1996). Structure, 4, 917–930.
	(A64) D. B. Tippin & M. Sundaralingam (1996). Acta Cryst. D52, 997–1003.
	(A65) M. C. Wahl, C. Ban, C. Sekharudu, B. Ramakrishnan & M. Sundaralingam (1996). Acta Cryst. D52, 655–667.
	(A66) D. J. Wilcock, A. Adams, C. J. Cardin & L. P. G. Wakelin (1996). Acta Cryst. D52, 481–485.
1997	(A67) R. Biswas & M. Sundaralingam (1997). J. Mol. Biol. 270, 511–519.
	(A68) R. Biswas, M. C. Wahl, C. Ban & M. Sundaralingam (1997). J. Mol. Biol. 267, 1149–1156.
	(A69) L. G. Fernandez, J. A. Subirana, N. Verdagauer, D. Pyshni, L. Campos & L. Malinina (1997). J. Biomol. Struct. Dyn. 15, 151–163.
	(A70) C. M. Nunn & S. Neidle (1997). Acta Cryst. D53, 269–273.
	(A71) D. B. Tippin & M. Sundaralingam (1997). J. Mol. Biol. 267, 1171–1185.