Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs

Coll, Miquel; Fita, Ignacio; Lloverás, Joaquim; Subirana, Juan A.; Bardella, Francese; Huynh‐Dinh, Tam; Igolen, J.

doi:10.1093/nar/16.17.8695

Cited by 31 publications

(25 citation statements)

References 21 publications

(22 reference statements)

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“…The question therefore remains unanswered. If a higher The single crystal structure of the sequence d(CACGTG) has been solved to Ç 2.5 Å resoluresolution structure of d(CA)rd(TG) dinucleotide does indeed show the same type of pyrimidinetion, 61 which is one of the lowest resolution structures of Z-DNA, and certainly the lowest for this water-water-phosphoribose bridge as was observed with the d(UA), then we can start to underspace group. The structure shows two features that …”

Section: Cytosine Methylationmentioning

confidence: 89%

“…61 The suggestion here was that the adenine [as in a d(UD) dinucleotide] would be predicted to greatly enhance the stability of Z-DNA N2 amino group that is missing from the adenine base contributes to the disruption of the spine of relative to the standard d(TA) dinucleotide to the point where it should behave more like a d(CG) hydration. As with the d(TA) dinucleotide, the bridge from the purine base to the phosphoribose base pair.…”

Section: Cytosine Methylationmentioning

confidence: 96%

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Z-DNA crystallography

Mooers

1997

Biopolymers

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Section: Cytosine Methylationmentioning

confidence: 89%

Section: Cytosine Methylationmentioning

confidence: 96%

Z-DNA crystallography

Mooers

1997

Biopolymers

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“…Several examples of such per-turbations in equilibrium are known for oligomeric DNA. [31][32][33][34][35] Initial ir studies of oriented gels of poly(dAd T ) -N a gave clear evidence of the B structure (above 94% r h ) , the A structure ( a t 75% r h ) , and the disordered state (below 65% r h ) but no evidence for the D structure was r e p~r t e d . '~ This agrees with our results for nonoriented gels.…”

Section: Discussionmentioning

confidence: 99%

Conditions for the stability of the alternative structures of duplex poly(dA‐dT)

Loprete

Hartman

1990

Biopolymers

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SYNOPSISThe alternative structures of the lithium, sodium, potassium, and rubidium salts of poly(dAd T ) were studied using ir spectra of hydrated, nonoriented gels. Poly (dA-dT) Na existed as the B structure a t high hydration and as the A structure a t moderate hydration. A disordered state occurred a t low hydration. No hint of the C, D, or other structures was observed a t any hydration for nonoriented gels containing NaCl up to 0.56 moles NaC1/ mole of nucleotide residue. Poly (dA-dT) -Li existed as the B structure a t high hydration, made a gradual transition to the C structure a t moderate hydration, and became disordered at low hydration. Poly (dA-dT) K and poly( dA-dT) -Rb existed as the B structure a t high hydration and as the presumptive D structure at lower hydration. The addition of Zn ( 11) to poly(dA-dT)-Na produced a gradual transition from the B to the C structure upon dehydration. The addition of NaN03 to poly (dA-dT) * Na gave only the A and B structures, and not the C or Z structures that are promoted by NO, in other base sequences. The D N A secondary structure stabilized by a given ion is determined by a specific base sequence and not simply by the properties of the ion INTRODUCTIONThe nature of the alternative structures of poly (dAdr) and the conditions for the stability of these structures have received much study (reviewed in Ref'. 1 ) . Crystallographic studies of oriented gels of poly ( dA-dT) have demonstrated the existence of the A, B, C, and D structures depending on the counterion to the polymer, the salt content of the gel, and the hydration (or water activity) of the Raman studies have confirmed the existence of the B structure in ~o l u t i o n s~~~~ and the A structure in partially oriented and unoriented gels.' Nuclear magnetic resonance spectra of solutions of poly (dA- Biopolymers, Vol. 30, 753-761 (1990) ('CC OOOS-:~525/90/7-80753-09 $04.00* To whom correspondence should be addressed.nonoriented 16*17 gels, have been assigned to the A, B, C, and D structures of poly (dA-dT) . Although the existence of the A, B, C, and D structures of poly (dA-dT ) has been broadly supported, the stabilizing conditions for these structures are less certain. We have therefore made a systematic survey of the structures that exist and the conditions for stability for the Li, Na, K, and Rb salts of poly(dA-dT) using nonoriented gels in which shifts in equilibrium due to crystal-lattice forces should be minimized.A brief review of the salient results for the conditions of stability of alternative structures of poly (dA-dT) follows.Davies and Baldwin first observed the diffraction patterns of the sodium, lithium, and ammonium salts of poly (dA-dT) using hydrated oriented gels.' They found the A and B structures for the Na and Li salts of poly(dA-dT), respectively. A C-like structure and a new structure, which they called D, were observed for poly (dA-dT) * NH4. Samples of poly (dA-dT) -Na containing ca. 0.2 moles of NaCl per mole of nucleotide (hereafter designated r = 0.2) also gave the D s...

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“…Discussion As expected, the present structure is closely similar to previously reported Z-DNA structures obtained from a variety of studies (Wang et al, 1979;Arnott et al, 1980;Gupta et al, 1980;Mitra et al, 1981;Rich et al, 1984;Ho & Mooers, 1997). Unlike the case of A or B forms, Z-DNA has only a couple of examples of sequencedependent microheterogenity (Coll et al, 1988;Sadasivan & Gautham, 1995). Crystals of several different sequences grown in a variety of conditions assume almost identical left-handed double-helical structures (Ho & Mooers, 1997).…”

Section: Number Of Contactsmentioning

confidence: 99%

Structure of d(CACGCG)\cdotd(CGCGTG) in Crystals Grown in the Presence of Ruthenium^IIIHexammine Chloride

Ponnuraj

Gautham

1998

Acta Cryst D

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Hexammine ions are strong inducers of the transition from the B-form to the left-handed Z-form in DNA. Here the structure of d(CACGCG)Ád(CGCGTG) obtained from crystals grown from a drop containing [Ru(NH 3 ) 6 ]Cl 3 is reported. The structure is clearly characterized as Z-DNA. When compared with the structure of d(CACGCG)Ád(CGCGTG)/MgCl 2 and that of d(CGCGCG) 2 , subtle differences are seen, most noticeably in the water structure. Since stable well diffracting crystals grow easily in the presence of [Ru(NH 3 ) 6 ]Cl 3 and since this ion is not visible in the electron density it is concluded that the ion plays a nonspeci®c role in stabilizing Z-DNA.

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Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs

Cited by 31 publications

References 21 publications

Z-DNA crystallography

Z-DNA crystallography

Conditions for the stability of the alternative structures of duplex poly(dA‐dT)

Structure of d(CACGCG)\cdotd(CGCGTG) in Crystals Grown in the Presence of Ruthenium^IIIHexammine Chloride

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Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs

Cited by 31 publications

References 21 publications

Z-DNA crystallography

Z-DNA crystallography

Conditions for the stability of the alternative structures of duplex poly(dA‐dT)

Structure of d(CACGCG)\cdotd(CGCGTG) in Crystals Grown in the Presence of RutheniumIIIHexammine Chloride

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Structure of d(CACGCG)\cdotd(CGCGTG) in Crystals Grown in the Presence of Ruthenium^IIIHexammine Chloride