A re-examination of the crystal structure of A-DNA using fiber diffraction data.

Classical A-DNA helices with h = 0.25 nm may represent the greatest mass per unit length attainable by polynucleotide duplexes. The X-ray diffraction pattern from polycrystalline and well-oriented fibers of calf thymus DNA in its A-form has been carefully re-examined. Indexing on the basis of a C-face-centered monoclinic unit cell of dimensions a = 2.170 nm, b = 3.990 nm, c = 2.803 nm and beta = 96.82 degrees is superior to alternatives that have been proposed. Two right-handed. Watson-Crick base-paired, helical DNA chains with 2 X 11 nucleotides per 2.803 nm pitch, each carrying C3'-endo furanose rings, pass through the unit cell. The crystallography requires the two chains in the duplex to be antiparallel and conformationally identical but the 11 nucleotides in each pitch may be distinct. However, a secondary structure with a mononucleotide asymmetric unit provides as good an X-ray agreement as one with 11 distinct nucleotides. This relative lack of variability is quite different from what is observed in fibrous B-DNAs.

The synthetic DNA duplex of poly d(Abr5U).poly d(Abr5U) adopts an A-DNA-like structure.

An X-ray fiber diffraction study of the synthetic DNA duplex poly d(Abr5U).poly d(Abr5U) shows that its sodium salt adopts an unexceptional A-DNA-like structure. Similar to A-DNA, two molecules are packed in a monoclinic unit cell (a = 2.23 nm, b = 4.14 nm, c = 5.61 nm and alpha = beta = gamma = 90 degrees) of space group C2. Because of its dinucleotide chemical motif, the c-repeat is twice that in A-DNA but, notably, corresponding backbone conformation angles of adjacent nucleotides are almost identical. This is in marked contrast to many B-like conformations of polydinucleotides.

Modelling and refinement of the crystal structure of nucleoprotamine from Gibbula divaricata.

The molecular structure of nucleoprotamine from Gibbula divaricata and its packing in oriented fibers has been modelled both to fit the X-ray diffraction pattern and to avoid steric compression. The representative model consists of 51 poly (dinucleotide) B-DNA helices with 51 poly(hexapeptide) chains associated with the major grooves. The prevailing peptide conformation is beta. The four arginine residues present are hydrogen-bonded to DNA phosphates while neutral peptides protrude into the minor grooves of neighboring nucleoprotamine molecules which are packed 2.61 nm apart in a screw-disordered, quasi-hexagonal lattice. This model reconciles a number of earlier, apparently conflicting experimental results and explains the remarkable stability of nucleoprotamines.

X-ray diffraction study of DNA complexes with arginine peptides and their relation to nucleoprotamine structure.

It is shown that the formation of complexes with several arginine peptides stabilizes the B-form of DNA with 10 (+/- 0.15) base-pairs per turn at all relative humidities, even upon complete dehydration. From an analysis of the packing arrangement and from the calculated diffraction patterns, it is concluded that arginine is associated with DNA in its major groove. It is also shown that the diffraction pattern of nucleoprotamine can be interpreted by placing the protamine on the major groove of DNA. The strong intensity on the first layer-line is due to the influence of neutral residues on the diffraction pattern. Thus, we conclude that protamine is bound to the major groove of DNA.

Heteronomous DNA.

A fibrous form of poly d(A):poly d(T) has a heteronomous secondary structure which is the first to be confirmed for a polynucleotide duplex: although both chains are 10(1) helices, mutually hydrogen-bonded in the standard (Watson-Crick) fashion, each has a quite different conformation. One chain -- probably poly d(A) -- has C3'-endo-puckered furanose rings characteristic of the A family of polynucleotide secondary structures while the other -- probably poly d(T) -- has the C2'-endo-puckered rings of the B family. Since analogous heteronomous structures could be assumed by DNA-DNA or DNA-RNA duplexes containing more general base sequences the polymorphic range of polynucleotide double-helices may be even greater than we have come to suppose.

Wrinkled DNA.

The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detected in other poly d(PuPy):poly d(PuPy) DNAs such as poly d(IC):poly d(IC) and poly d(AT):poly d(AT) in their D forms which have tetragonal crystal environments. This suggests that such perturbations are intrinsic to all stretches of duplex DNA where purines and pyrimidines alternate and may play a role in the detection and exploitation of such sequences by regulatory proteins.

X-ray diffraction studies of nucleohistone: a polyhelical model of chromosome organization.

The possibility that nucleohistone is constituted by a helical arrangement of DNA molecules is analyzed in this paper. A polyhelical model of nucleohistone in plectanemic double coils of variable dimensions is found to be compatible with the x-ray diffraction results obtained in this and other laboratories. The radius of the coils varies between 35 and 45 A, whereas the pitch varies between 200 and 120 A. Another part of nucleohistone is much less coiled and contributes to the "background" scattering of the sample. This model is compatible with a lampbrush organization of the chromosome.