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D R Kearns

Publications and source records attributed to D R Kearns.

At least 73 records · Page 4Linked to original sources
PubMed1980

A 300 MHz and 600 MHz proton NMR study of a 12 base pair restriction fragment: investigation of structure by relaxation measurements.

The 1H NMR spectrum of a 12 base pair DNA restriction fragment has been measured at 300 and 600 MHz and resonances from over 70 protons are individually resolved. Relaxation rate measurements have been carried out at 300 MHz and compared with the theoretical predictions obtained using an isotropic rigid rotor model with coordinates derived from a Dreiding model of DNA. The model gives results that are in excellent agreement with experiment for most protons when a 7 nsec rotational correlation time is used, although agreement is improved for certain base protons by using a shorter correlation time for the sugar group, or by increasing the sugar-base interproton distances. A comparison of non-selective and selective spin-lattice relaxation rates for carbon bound protons indicates that there is extensive spin diffusion even in this short DNA fragment. Examination of the spin-spin relaxation rates for the same type of proton on different base pairs reveals little sequence effect on conformation.

Base Composition↗
PubMed1979

1H nuclear magnetic resonance investigation of flexibility in DNA.

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 less than 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 molecues, especially in the backbone, than is indicated by classic hydrodynamic studies of DNA.

Animals↗
PubMed1979

1H NMR investigation of the conformational states of DNA in nucleosome core particles.

In this study 1H NMR has been used to investigate the conformational state of DNA in nucleosome core particles. The nucleosome core particles exhibit partially resolved low field (10-15 ppm) spectra due to imino protons in Watson-Crick base pairs (one resonance per GC or AT base pair). To a first approximation, the spectrum is virtually identical with that of protein-free 140 base pair DNA, and from this observation we draw two important conclusions: (i) Since the low field spectra of DNA are known to be sensitive to conformation, the conformation of DNA in the core particles is essentially the same as that of free DNA (presumably B-form), (ii) since kinks occurring at a frequency at 1 in 10 or 1 in 20 base pairs would result in a core particle spectrum different from that of free DNA we find no NMR evidence supporting either the Crick-Klug or the Sobell models for kinking DNA around the core histones. Linewidth considerations indicate that the rotational correlation time for the core particles is approximately 1.5 X 10(-7) sec, whereas the end-over-end tumbling time of the free 140 base pair DNA is 3 X 10(-7) sec.

Animals↗
PubMed1978

Spectroscopic properties of ethidium monoazide: a fluorescent photoaffinity label for nucleic acids.

The non-covalent binding of ethidium monoazide to nucleic acids is entirely analogous to that of ethidium (binding constant approximately 2-3 X 10(5) M). The ethidium monoazide can be photochemically covalently linked to nucleic acids in high yield, up to 75%, by long wavelength light. The fluorescence of ethidium monoazide and ethidium crosslinked to nucleic acids show the same environmental sensitivity as does the fluorescence of ethidium. These properties of ethidium monoazide indicate its use as a fluorescent photoaffinity label for nucleic acids. Ethidium diazide can be photochemically linked to nucleic acids but appears to have properties substantially different from those of ethidium.

Affinity Labels↗
PubMed1978

Base pairing structure in the poly d(G-T) double helix: wobble base pairs.

High resolution nuclear magnetic resonance (NMR) and ethidium bromide binding studies are used to demonstrate that poly d(G-T) forms an ordered double helical structure at low temperatures (below 24 degrees C in 0.3 M NaCl) in which G and T are hydrogen bonded together in a wobble base pair hydrogen bonding scheme as proposed earlier by Lezius and Domin. Alternative hydrogen bonding schemes involving the tautomeric form of either T or G, such as have been proposed to account for mutation rates in DNA synthesis, are eliminated.

Chemical Phenomena↗