Structure determination by restrained molecular dynamics using NMR pseudocontact
shifts as experimentally determined constraints

[(2R,3R,4R,6R)-2-methyl-4,6-bis(oxidanyl)oxan-3-yl] ethanoate

[(2S,3S,4S,6S)-4,6-dihydroxy-2,4-dimethyl-oxan-3-yl] ethanoate

polydeoxyribonucleotide polysaccharide(D)

Journal of the American Chemical Society
Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints.

The proton NMR spectrum of the ternary complex between the octamer duplex
d(TTGGCCAA)2, two molecules of the drug chromomycin-A3, and a divalent cobalt
ion has been assigned. Assignment procedures used standard two-dimensional
techniques and relied upon the expected NOE contacts observed in the equivalent
diamagnetic complex containing zinc. The magnetic susceptibility tensor for the
cobalt was determined and used to calculate shifts for all nuclei, aiding in
the assignment process and verification. Relaxation, susceptibility,
temperature and field dependence studies of the paramagnetic spectrum enabled
determination of electronic properties of the octahedral cobalt complex. The
electronic relaxation tau(s) was determined to be 2.5 +/- 1.5 ps; the effective
isotropic g value was found to be 2.6 +/- 0.2, indicating strong spin-orbit
coupling. The magnetic susceptibility tensor was determined to be chi(xx) = 8.9
x 10(-3) cm3/mol, chi(yy) = 9.5 x 10(-3) cm3/mol, chi(zz) = 12.8 * 10(-3)
cm3/mol. A tentative rotational correlation time of 8 ns was obtained for the
complex. Both macroscopic and microscopic susceptibility measurements revealed
deviations from Curie behavior over the temperature range accessible in the
study. Non-selective relaxation rates were found to be inaccurate for defining
distances from the metal center. However, pseudocontact shifts could be
calculated with high accuracy using the dipolar shift equation. Isotropic
hyperfine shifts were factored into contact and dipolar terms, revealing that
the dipolar shift predominates and that contact shifts are relatively small.

Gochin M.
Nuclear magnetic resonance characterization of a paramagnetic DNA-drug complex
with high spin cobalt; assignment of the 1H and 31P NMR spectra, and determination of
electronic, spectroscopic and molecular properties.
J Biomol NMR. 1998 Aug;12(2):243-57

Nuclear magnetic resonance characterization of a paramagnetic DNA-drug complex with high spin cobalt; assignment of the 1H and 31P NMR spectra, and determination of electronic, spectroscopic and molecular properties.

BACKGROUND: The drug chromomycin-A(3) binds to the minor groove of DNA and
requires a divalent metal ion for complex formation. (1)H, (31)P and (13)C
pseudocontact shifts occurring in the presence of a tightly bound divalent
cobalt ion in the complex between d(TTGGCCAA)(2) and chromomycin-A(3) have been
used to determine the structure of the complex. The accuracy of the structure
was verified by validation with nuclear Overhauser enhancements (NOEs) and
J-coupling constants not used in the structure calculation. RESULTS: The final
structure was determined to 0.7 A resolution. The structure was compared with a
structure obtained in an earlier study using NOEs, in order to assess the
accuracy of NOEs in giving global structural information for a DNA complex.
Although some basic features of the structures agreed, they differed
substantially in the fine structural details and in the DNA axis curvature
generated by the drug. The distortion of base-pair planarity that was observed
in the NOE structure was not seen in our structure. Differences in drug
orientation and hydrogen bonding also occurred. The curvature and elongation of
the DNA that was obtained previously was not found to occur in our study.
CONCLUSIONS: The use of pseudocontact shifts has enabled us to obtain a
high-precision global structure of the chromomycin-DNA complex, which provides
an accurate template on which to consider targeting minor groove binding drugs.
The effect of such binding is not propagated far along the helix but is
restricted to a local kink in the axis that reverts to its original direction
within four base pairs.

Gochin M.
Structure with Folding & Design., 2000 Apr 15, 8(4):441-52

A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.

update DNA residue label to two-letter code