DNA double helical fragment at atomic resolution

Viswamitra, M. A.; Kennard, Olga; Jones, Peter G.; Sheldrick, George M.; Salisbury, Stephen A.; Falvello, Larry R.; Shakked, Zippora

doi:10.1038/273687a0

Cited by 191 publications

(69 citation statements)

References 15 publications

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“…For example, the structure of d(ApTpApT) was determined several years ago (34,35) and showed Watson-Crick base pairs in a nonstandard conformation. Hoogsteen base pairs were suggested (36) An important question is whether Hoogsteen DNA has sequence specificity.…”

Section: Discussionmentioning

confidence: 99%

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Abrescia

Thompson

Huynh‐Dinh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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Section: Discussionmentioning

confidence: 99%

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Abrescia

Thompson

Huynh‐Dinh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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“…[19]), while steric effects are considered to be more important [20]. Therefore, it seems likely that the observed splitting for the duplex is attributed to two distinct conformations of the sugar ring deoxyribose as a C2'-endo conformation while the sugar of adenosine is in a c3'-~izdo puckered conformation [21]. Based on this result, Klug et al [22] suggested that poly(dA-dT) .…”

Section: Con Formmion Of' Poly(da-dt)mentioning

confidence: 99%

13C NMR Study of Conformation and Mobility of 145-Base-Pair Poly(dA-dT) . poly(dA-dT) in Solution

Shindo

1981

Eur J Biochem

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Natural abundance of 13C NMR spectra were obtained for 145-base-pair poly(dA-dT) . poly(d.4-dT) in solution. Two conformers of deoxyribose are present in poly(dA-dT) . poly(dA-dT) in equal amounts, suggesting that the alternating conformation of the phosphodiester backbone previously demonstrated by 3 1 P NMR extends to the deoxyribose residues. The local mobilities of bases and sugars are different for thymidine and adenosine residues.Conformational flexibility of DNA has recently become of interest in regard to the structure and function of the nucleic acid. Fluorescence [I] and theoretical hydrodynamic evaluations [2] have demonstrated that local bending and twisting movements of DNA may take place in a time frame of the oder of tens of nanoseconds. Subsequently, several N M R studies have used this notion, a flexible rather than stiff DNA molecule, in interpretation of the data [3-121. A particular problem in data analysis arises from the fact that, in most of these studies, more or less polydisperse native DNA, of random sequence, has been used. Due to the strong dependence of dynamic properties of macromolecules on size as well as conformation, the analyses of molecular mobility of such DNA would yield qualitative information at the best. Further, we found in 31P NMR investigations of native DNA that chemical shift distribution contributes significkntly to the N M R linewidth [3,8,13]. Similar results have been reported on 'H and i3C N M R of native DNA [9,10].In order to circumvent these problems, it is desirable to obtain a very defined length of DNA with a repeating base sequence and to use simpler probes for analyzing data. In this regard, I3C NMR will give greater advantages in resolution and analysis of NMR relaxation data than 'H and 3iP NMR, although this method suffers from low sensitivity due to low natural abundance of I3C. Recently, the formation of core particles containing synthetic polydeoxyribonucleotides has allowed preparation of homogeneous, alternating sequence DNA of defined length (145 base pairs) 114-161. Here, using 13C NMR, we present an analysis of conformation and mobility at individual carbon atoms in 145-base-pair poly(dA-dT) . poly(dA-dT) in solution. MATERIALS A N D METHODSSemi-synthetic nucleosome core particles containing poly-(dA-dT) were prepared as before [14]. Briefly, chicken erythrocyte inner histones were associated with poly(dA-dT) (P. L. Biochemicals) by salt gradient dialysis. Histone-free poly(dA-dT) . poly(dA-dT) was isolated from the core particles by proteinase K digestion in 1 % sodium dodecyl sulfate, sequential extraction with phenol and chloroform/isoamyl alcohol (27 : I), and double ethanol precipitation. The material as the same length (about 145 base pairs) and the same melting point, 60°C a t a 0.1 M ionic strength, as that previously prepared [13]. Vacuum-dried DNA (ZZ 12 mg) was dissolved in a buffer of 1 mM sodium cacodylate, pH 7.2, 1 mM EDTA, 98 mM NaCl for 13C N M R measurements.Proton-decoupled I3C NMR spectra (67.9 MHz) were recorded on a home...

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“…However, the structural information available at high resolution on AT-rich oligonucleotides, alternating or not, is very limited. Only a single`naked' DNA sequence with only adenine and thymine base pairs has been crystallized so far (Viswamitra et al, 1978). On the other hand, AT-rich sequences are strongly polymorphic (Arnott et al, 1974), so that their study offers a particular interest.…”

Section: Introductionmentioning

confidence: 99%

When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

Abrescia¹,

Subirana²

2002

Acta Crystallogr D Biol Cryst

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The d(ApTpApTpApT) deoxyhexanucleotide packs in two different lattice systems: monoclinic and hexagonal. In this study, it is shown that in the hexagonal crystals twinning and pseudosymmetry coexist. The presence of both components resulted in a puzzling space‐group determination. Only when a correct model became available [Hoogsteen‐DNA; Abrescia et al. (2002), Proc. Natl Acad. Sci. USA, 99, 2806–2811] was it possible to discriminate between twinning and pseudosymmetry. Here, the steps that led to a correct space‐group assignment and to the solution of the oligonucleotide structure in the hexagonal lattice by molecular replacement are described.

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DNA double helical fragment at atomic resolution

Cited by 191 publications

References 15 publications

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

13C NMR Study of Conformation and Mobility of 145-Base-Pair Poly(dA-dT) . poly(dA-dT) in Solution

When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

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