Helix Geometry and Hydration in A-DNA, B-DNA, and Z-DNA

Dickerson, R.E.; Drew, Horace R.; Conner, Benjamin N.; Kopka, Mary L.; Pjura, Philip

doi:10.1101/sqb.1983.047.01.004

Cited by 60 publications

(31 citation statements)

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“…A cooperative length of 25 bp was reported for the trifluorethanol-induced B-Z transition in poly(dG-dC) (20). Previous investigators argued that the B-Z transition is entropically driven (7,8,13 [6][7][8] kcal/mol for the Z-B transition of (m5dC-dG)3 in solutions containing 20-40% methanol, and an entropy change of [21][22][23][24][25][26][27] cal/K-mol. These values are both much larger than ours and of opposite sign.…”

Section: Discussionmentioning

confidence: 99%

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Thermodynamics of the B to Z transition in poly(m5dG-dC).

Chaires¹,

Sturtevant²

1986

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

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Differential scanning calorimetry, temperature-dependent absorbance, and circular dichroic spectroscopy were used to study the thermodynamics of the B-Z transition in poly(m5dG-dC). In sodium phosphate buffer (pH 7.0) containing 50 mM NaCl and 1.0 mM MgCl2, the reversible B-Z transition of the polymer is centered at 38.20C and is characterized by AHw = 0.61 -0.07 kcal/(mol-base pair) (1 cal = 4.184 J), AIVH = 68 ± 7 kcal/mol, and a cooperative unit of length 110 ± 20 base pairs. A second transition centered at 53.60C is observed and represents a conformational change of poly(m5dG-dC) from the Z to an alternate left-handed form of unknown structure. This transition does not arise from aggregation to the Ze form, or from the helix-coil transition. The left-handed helix-coil transition is observed at 120.9 ± 0.3OC and is characterized by AHcw = 9.1 -1.0 kcal/(mol-base pair).These results indicate a substantial enthalpic contribution to the B-Z transition, in contrast to previous assertions that the process is entropically driven.The chemistry and biology of left-handed Z DNA are of intense current interest (1, 2). DNA sequences that are in the Z conformation (or that may be induced to adopt the Z conformation) have been identified in vivo (3-6), and a role for Z DNA in the regulation of gene expression has been proposed (1).In spite of a considerable number of fundamental studies on the B-Z transition, the thermodynamics of the process remains incompletely described. In their seminal work on the transition of poly (dG-dC) to what has proven to be the left-handed Z form, Pohl and Jovin (7) reported that the NaCl-induced transition of the polymer was independent of temperature over the range 20-50'C and inferred from their data that the van't Hoff enthalpy of the transition was near zero under their conditions. Roy and Miles (8), however, reported a thermally driven interconversion of poly(m5dG-dC) from the B to the Z form in dilute Na+/Mg2+ solutions. Temperature-dependent conformational transitions to the Z form in poly(dG-dC) and poly(m5dG-dC) under a variety of solution conditions were subsequently reported (9-14).We report here results obtained from differential scanning calorimetry (DSC) that provide a reliable estimate for the enthalpy of the B-Z transition of poly(m5dG-dC). DSC measurements provide a direct and sensitive measure of the transition enthalpy, and thus offer a significant advantage over methods based on the indirect van't Hoff analysis. Complementary absorbance and circular dichroic measurements allow us to identify the conformation of the polymer as a function of temperature. Our results provide evidence for a previously unobserved conformational transition within the left-handed DNA family. MATERIALS AND METHODSPolynucleotides. Poly(m5dG-dC) (lot 782-26 and lot NG517938) was purchased from Pharmacia P-L Biochemicals. Samples were used without further purification and were prepared by dissolving the polymer in 6 mM Na2HPO4/ 2 mM NaH2PO4/50 mM NaCl/1 mM MgCl2, pH 7.0 (henceforth referred...

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Section: Discussionmentioning

confidence: 99%

“…Structural studies show that a family of left-handed Z structures exist in the crystalline state (26,27), and a variety of left-handed forms have been identified in solution (9,19).…”

Section: Discussionmentioning

confidence: 99%

Thermodynamics of the B to Z transition in poly(m5dG-dC).

Chaires¹,

Sturtevant²

1986

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

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“…2 (13,(21)(22)(23)(24). Crossed spheres in the major groove ofc are platinum, and large spheres in the major groove of d and e are bromines.…”

Section: Helices With Various Degrees Of Bendingmentioning

confidence: 99%

A random-walk model for helix bending in B-DNA.

Dickerson¹,

Kopka²,

Pjura³

1983

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

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The double-helical B-DNA dodecamer of sequence d(C-G-C-G-A-A-T-T-C-G-C-G) has been refined independently from x-ray crystal structure analyses in five different variants: d(C-G-C-G-A-A-T-T-C-G-C-G) at 16 K, at room temperature, and with bound cis-diamminedichloroplatinum(II), and d(C-G-C-G-A-A-T-T-brC-G-C-G) in 60% 2-methyl-2,4-pentanediol at 20 degrees C and 7 degrees C. These helices display overall axial bends of 22 degrees, 18 degrees, 17 degrees, 14 degrees, and 3 degrees, respectively, providing an opportunity to investigate the nature of the bending process in B-DNA. Bending from one base pair to the next is best described as a stochastic or random-walk process, having forward, retrograde, and sidewise individual steps, but with an overall sense of bending. Individual steps almost always involve rolling of adjacent base pairs over one another along their long axes, not a tilting or wedge displacement that lifts neighboring base pairs apart at one end. A slight preference is observed for bending the double helix in a direction that compresses the major groove rather than the minor, and this is intuitively reasonable in view of the narrowness of the minor groove and its occupation by the spine of hydration that stabilizes the B form of DNA. This model predicts that, when DNA is wound around the nucleosome core, it should not be smoothly curved but should exhibit discrete bends every five base pairs as proposed by Zhurkin et al. [Zhurkin, V.B., Lysov, Y. P. & Ivanov, V. I. (1979) Nucleic Acids Res. 6, 1081-1096)]. Sharper bends may occur at alternate positions, where the major groove faces the nucleosome core.

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“…It is only recently with the advent of fast and efficient methods of large-scale chemical synthesis of DNA and RNA fragments [l] that the crystal structures of a number of short oligonucleotides comprising examples of the A, B and 2 families of DNA have been solved (see [2,3] for reviews). These studies have revealed the detailed arrangement of individual base pairs in the DNA helix at a resolution heretofore unavailable since fibre diffraction studies can only yield the averaged structure of a nucleic acid polymer [4].…”

Section: Introductionmentioning

confidence: 99%

Probing the three‐dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements

Clore

Gronenborn

1985

FEBS Letters

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DNA and RNA oligonucleotides are ideally suited for high-resolution X-ray crystallographic and 'H-NMR studies. The solution structures of such oligonucleotides can potentially be solved using proton-proton nuclear Overhauser enhancement measurements to demonstrate the proximity of protons in space and to determine their separation, thereby enabling a comparison of the structure in the crystalline and solution states to be made. In this review we describe (i) the general strategy for the sequential resonance assignments of oligonucleotide 'H-NMR spectra, the essential prerequisite for further structural work, (ii) the approach to obtaining interproton distances from pre-steady state nuclear Overhauser enhancement measurements, and (iii) the use of interproton distances in structure determination. This is illustrated by several examples including double-and single-stranded DNA oligonucleotides as well as RNA stem and loop structures.Oligonucleotide NMR NOE

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Helix Geometry and Hydration in A-DNA, B-DNA, and Z-DNA

Cited by 60 publications

References 0 publications

Thermodynamics of the B to Z transition in poly(m5dG-dC).

Thermodynamics of the B to Z transition in poly(m5dG-dC).

A random-walk model for helix bending in B-DNA.

Probing the three‐dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements

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