Structure of poly d(AI).poly d(CT) in two different packing arrangements

Three-dimensional structure of the sodium salt of iota-carrageenan

The three-dimensional structure of the sodium salt of iota-carrageenan has been determined by using X-ray diffraction data collected from its polycrystalline and oriented fibers. The molecule forms a half-staggered, parallel, threefold, right-handed double helix that is stabilized by interchain hydrogen bonds from 2- and 6-hydroxyl groups in the galactosyl units. Three helices are organized in a trigonal unit cell, of dimensions a=24.02 and c=12.93 A, with a lateral separation of 13.9 A for each pair. Both 2- and 4-sulfate groups are essential in helix-helix interactions that are mediated only by sodium ions and water molecules.

Structure of Poly (U).poly (A).poly (U)

The molecular structure of poly (U).poly (A).poly (U) has been determined and refined using the continuous x-ray intensity data on layer lines in the diffraction pattern obtained from an oriented fiber of the RNA. The final R-value for the preferred structure is 0.24, far lower than that for the plausible alternatives. The polymer forms an 11-fold right-handed triple-helix of pitch 33.5A and each base triplet is stabilized by Crick-Watson-Hoogsteen hydrogen bonds. The ribose rings in the three strands have C3'-endo, C2'-endo and C2'-endo conformations, respectively. The helix derives additional stability through systematic interchain hydrogen bonds involving ribose hydroxyls and uracil bases. The relatively grooveless cylindrical shape of the triple-helix is consistent with the lack of lateral organization.

Structure of poly (I).poly (A).poly (I)

The molecular structure of poly (I).poly (A).poly (I) has been determined and refined using the continuous intensity data on layer lines in the x-ray diffraction pattern obtained from an oriented fiber of this polymorphic RNA complex. The polymer forms a 12-fold right-handed triple-helix of pitch 39.7A and each base-triplet is stabilized by quasi Crick-Watson-Hoogsteen hydrogen bonds. The ribose rings in all the three strands have C3'-endo conformations. The final R-value for this best structure is 0.24 and the x-ray fit is significantly superior to all the alternative structures where the different chains might have different furanose conformations. This all-purine triple-helix, counter-intuitively, has a diameter roughly 3A shorter than that of DNA and RNA triple-helices containing a homopurine and two complementary homopyrimidine strands. Its compact, grooveless cylindrical shape is consistent with the lack of lateral organization.

Structure of poly (dT).poly (dA).poly (dT)

The molecular structure of poly (dT).poly (dA).poly (dT) has been determined and refined using the continuous x-ray intensity data on layer lines in the diffraction pattern obtained from an oriented fiber of the DNA. The final R-value for the preferred structure is 0.29 significantly lower than that for plausible alternatives. The molecule forms a 12-fold right-handed triple-helix of pitch 38.4 A and each base triplet is stabilized by a set of four Crick-Watson-Hoogsteen hydrogen bonds. The deoxyribose rings in all the three strands have C2'-endo conformations. The grooveless cylindrical shape of the triple-helix is consistent with the lack of lateral organization in the fiber.

Developments in fiber diffraction

Improved specimen preparation methods, third generation synchrotron sources, new data processing algorithms and molecular dynamics refinement techniques are, together, allowing the high-resolution structure determination of larger and larger macromolecular complexes by fiber diffraction. New synchrotron sources are also making possible both time-resolved studies and studies of ordered fibers only a few microns in diameter.