<sup>1</sup>H NMR investigation of the conformational states of DNA in nucleosome core particles

Feigon, Juli; Kearns, David R.

doi:10.1093/nar/6.6.2327

Cited by 31 publications

(14 citation statements)

References 37 publications

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“…This possibility is unlikely because integrated intensities correspond to at least 80% of the expected intensity, based on the spectral range (11-15 ppm) examined, the breadth of the lines observed, and the integrated intensities observed with lower molecular weight samples. Furthermore, the spectra of 140-bp DNA from nucleosome core particles fit well with the series of DNA lengths presented here (24).…”

supporting

confidence: 74%

1H nuclear magnetic resonance investigation of flexibility in DNA.

Early¹,

Kearns²

1979

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

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In this paper we report successful observations of proton NMR spectra of native double helical salmon sperm and calf thymus DNA of various lengths. Measurements of the linewidths arising from proton-proton dipolar interactions are used to obtain information about the dynamic behavior of DNA helices in solution. Depending upon which protons are used to monitor the local internal motions of the DNA, different results are obtained. The lowfield resonances from hydrogen-bonded imino protons in the base pairs indicate that the correlation time for reorientation of base pairs is less than 3 X 10-7 sec, whereas correlation times for motion of neighboring sugar protons relative to the aromatic protons are <5 X 10-8 sec for DNA that is over 200 base pairs long. These observations indicate that there is considerably more internal flexibility in the DNA molecules, especially in the backbone, than is indicated by classic hydrodynamic studies of DNA.The determination of the conformational state and the flexibility of DNA is of considerable interest in connection with studies of the hydrodynamic properties of DNA (1-4), the structure of DNA in chromosomes (5-8), the folding of DNA in phage particles (9), supercoiling in circular DNA (10, 11) and linear DNA (12), and computations of superhelical structure and energetics of DNA foldings (5-8, 10, 11). Information on conformational fluctuations in DNA is also of interest in connection with the use of spectroscopic tools (circular dichroism, infrared, Raman) to deduce the average conformational state of DNA (13)(14)(15).NMR spectroscopy is an excellent tool for studying flexibility in large molecules. Some preliminary 31P NMR studies of high molecular weight calf thymus DNA and chromatin (16) and nucleosome core particles have been reported (17,18), and these indicate there is considerable flexibility in the backbone (linewidths of 20-50 Hz). Previous attempts to use 1H (19) and '3C (20) NMR on native DNA were unsuccessful. Patel has successfully studied the 'H NMR of simple sequence synthetic DNA (21,22), but these molecules are believed to be unusually flexible due to formation of branched duplex regions and hairpins and therefore may not be good models for studying flexibility in native DNA. In 1977, we demonstrated (23) that it is possible to obtain partially resolved NMR spectra on high molecular weight native double-helical DNA, and in the present paper we have used NMR and the fact that NMR linewidths and relaxation times are sensitive to local internal motions to detect flexibility in the DNA that is not evident when the DNA is studied by other classical techniques.Our results show that it is possible to obtain useful proton NMR spectra on DNA of unexpectedly high molecular weight and make possible a number of applications of NMR to the study of DNA properties in solution. EXPERIMENTAL Salmon sperm (or calf thymus) DNA (Worthington) was dissolved (10 mg/ml) in 100 ml of 0.1 M NaAcO/2 mM ZnCl2 at pH 4.6, and S1 nuclease (1000 international units) was added. This so...

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supporting

confidence: 74%

1H nuclear magnetic resonance investigation of flexibility in DNA.

Early¹,

Kearns²

1979

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

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“…This is an ideal situation since it is much shorter than the spin-lattice relaxation time and the time limit at which spin diffusion should set in. A typical mixing time for a biomolecule of comparable size, say, for instance, a small oligonucleotide 10-mer duplex, is 350 ms (Feignon et al, 1979(Feignon et al, , 1983. The NOE spectrum at 200 ms mixing time ( Figure 5) contained cross peaks corresponding to interactions between H-1 of the distal glucosamine residue and H-4, H-6R, and H-6S of the proximal residue.…”

Section: Resultsmentioning

confidence: 99%

An NMR Spectroscopy and Molecular Mechanics Study of the Molecular Basis for the Supramolecular Structure of Lipopolysaccharides

Wang

Hollingsworth

1996

Biochemistry

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Lipopolysaccharides from Gram-negative bacteria interact with the mammalian immune system to trigger a cascade of physiological events leading to a shock syndrome which results in the death in over 70% of cases of severe shock. It is known that the supramolecular structures of lipopolysaccharide aggregates are critical contributors to their biological activities. Despite this, the molecular basis for the formation if the regular hexagonal plates and arrays observed in lipopolysaccharide films and suspensions is unknown. Since these structures are two dimensional, it is unlikely that X-ray crystallographic methods will shed much light on their detailed structure. Knowing this structure is important since it is becoming increasingly likely that the insertion of the lipopolysaccharide hydrocarbon chains in the target host cell membrane may be involved in triggering host responses. This work describes the three-dimensional structure of the lipopolysaccharide lipid A moiety. The structure was obtained by a combination of molecular mechanics calculations and nuclear magnetic resonance spectroscopy. This involved calculation of the dihedral angle between the two glucosamine residues of the lipid A molecule from coupling constants and measuring critical interresidue NOE values. The study also takes into account information from X-ray powder diffraction and electron microscopy studies.

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“…While spectral studies agree that the conformation of nucleosome DNA is of the "B-genus" (23)(24)(25)(26), there has been considerable discussion of the way in which this DNA may be deformed to permit superhelix formation.…”

Section: Conformation Of the Dnamentioning

confidence: 99%

“…Although it has been suggested that abrupt bends or kinks in the DNA might occur at periodic intervals (27,28), no special class of backbone conformations has been detected by either phosphorus or proton magnetic resonance (25,26,(29)(30)(31). Moreover, one can build continuously deformed duplex structures that violate none of the known restrictions on bond angles or interatomic contacts in polynucleotides (22,32).…”

Section: Conformation Of the Dnamentioning

confidence: 99%