Prediction of a Crystallization Pathway for Z-DNA Hexanucleotides

Ho, P Shing; Kagawa, TF; Tseng, KH; Schroth, G.P.; Zhou, GW

doi:10.1126/science.1948069

Cited by 32 publications

(14 citation statements)

References 9 publications

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“…Therefore, the distortion of a part of one strand into the ZII conformation and subsequent loss of 2-fold symmetry between the strands facilitate a unique packing of Z-DNA molecules into the crystal structure. The proposed mechanism of crystallization could help to rationalize experimental conditions of Z-DNA crystallization discussed by Ho et al (1991).…”

Section: Resultsmentioning

confidence: 94%

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

Schneider¹,

Ginell²,

Jones³

et al. 1992

Biochemistry

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The crystal and molecular structure of d(CGUA'CG)2 (where A' is 2-aminoadenine) has been determined and refined to an R factor of 13.8% for data 8.0-1.3 A. The structure is very similar to the original Z-DNA structures with the sequence d(CGCGCG)2 [Gessner, R. V., Frederick, C. A., Quigley, G. J., Rich, A., & Wang, A. H.-J. (1989) J. Biol. Chem. 264, 7921] and shows that the substitution of 2-aminoadenine-uracil base pairs in the two central steps is consistent with Z-DNA formation. In addition, we show how waters mediating intermolecular interactions may help to explain the ZI-ZII conformational pattern found in many Z-DNA structures.

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Section: Resultsmentioning

confidence: 94%

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

Schneider¹,

Ginell²,

Jones³

et al. 1992

Biochemistry

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“…The present results indicate that the crystal double helix type of (G + C)-rich oligonucleotides of DNA can be predicted, taking advantage of the CD spectral changes induced by TFE. This relatively straightforward approach could be used to choose sequences that are likely to crystallize in a predetermined type of double helix, before the time-consuming hit-or-miss oligonucleotide crystallization process is started (Ho et al, 1991). Further tests of this possibility are in progress in our laboratory.…”

Section: Discussionmentioning

confidence: 99%

Comparison of the solution and crystal conformations of (G + C)-rich fragments of DNA

Vorlı́čková

Subirana

Chládková

et al. 1996

Biophysical Journal

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DNA fragments crystallize in an unpredictable manner, and relationships between their crystal and solution conformations still are not known. We have studied, using circular dichroism spectroscopy, solution conformations of (G + C)-rich DNA fragments, the crystal structures of which were solved in the laboratory of one of the present authors. In aqueous trifluorethanol (TFE) solutions, all of the examined oligonucleotides adopted the same type of double helix as in the crystal. Specifically, the dodecamer d(CCCCCGCGGGGG) crystalized as A-DNA and isomerized into A-DNA at high TFE concentrations. On the other hand, the hexamer d(CCGCGG) crystallized in Z-form containing tilted base pairs, and high TFE concentrations cooperatively transformed it into the same Z-form as adopted by the RNA hexamer r(CGCGCG), although d(CCGCGG) could isomerize into Z-DNA in the NaCl + NiCl2) aqueous solution. The fragments crystallizing as B-DNA remained B-DNA, regardless of the solution conditions, unless they denatured or aggregated. Effects on the oligonucleotide conformation of 2-methyl-2,4-pentanediol and other crystallization agents were also studied. 2-Methyl-2,4-pentanediol induced the same conformational transitions as TFE but, in addition, caused an oligonucleotide condensation that was also promoted by the other crystallization agents. The present results indicate that the crystal double helices of DNA are stable in aqueous TFE rather than aqueous solution.

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“…A comparison of the predicted AGT(B-Z) values in Table II suggests that the dinucleotide must be considered as the minimum unique repeat unit for Z-DNA in terms of the thermodynamic stability. We have previously observed a correlation between the cation strengths (CS) required to crystallize a series of isomorphous hexamer duplex structures as Z-DNA and AGT(B-Z) calculated for these sequences (12). Our spectroscopic studies on Z-DNA formation under solutions for crystallization showed that the conditions for crystallization of hexanucleotides as Z-DNA were also conditions that stabilize the left-handed conformation in solution (12).…”

Section: Resultsmentioning

confidence: 82%

“…We had previously shown that the ion concentrations in solutions that yield Z-DNA crystals of hexanucleotide duplexes are related to the ability of these sequence to adopt the Zconformation in solution. This relationship thus allows us to systematically test predictions for how sequence modifications affect the ability of hexanucleotides to form Z-DNA, and, in fact, has been useful in this laboratory to predict how to crystallize a particular sequence as Z-DNA (12). The self-complimentary hexamer sequence d(m5CGUAm5CG) was crystallized as Z-DNA under significantly lower cation concentrations than the analogous d(TA)-containing sequence.…”

Section: Introductionmentioning

confidence: 99%

Effects of base substituents on the hydration of B- and ZDNA: correlations to the B- to Z-DNA transition

et al. 1993

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We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization of cytosines as Z-DNA is primarily a hydrophobic effect. The hydration free energies of various alternating pyrimidine-purine sequences in the two DNA conformations were calculated as solvent free energies from solvent accessible surfaces. Our analysis focused on the N2 amino group of purine bases that sits in the minor groove of the double helix. Removing this amino group from guanine to form inosine (I) destabilizes Z-DNA, while adding this group to adenines to form 2-aminoadenine (A') stabilizes Z-DNA. These predictions were tested by comparing the salt concentrations required to crystallize hexanucleotide sequences that incorporate d(CG), d(CI), d(TA) and d(TA') base pairs as Z-DNA. Combining the current results with our previous analysis of major groove substituents, we derived a thermodynamic cycle that relates the systematic addition, deletion, or substitution of each base substituent to the B- to Z-DNA transition free energy.

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Prediction of a Crystallization Pathway for Z-DNA Hexanucleotides

Cited by 32 publications

References 9 publications

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

Comparison of the solution and crystal conformations of (G + C)-rich fragments of DNA

Effects of base substituents on the hydration of B- and ZDNA: correlations to the B- to Z-DNA transition

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