The results of the search for low-energy conformations of poly(dA).poly(dT) and of the poly(dA).poly(dT) "complex" with the spine of hydration similar to that found by Dickerson and co-workers (Kopka, M.L., Fratini, A.V., Drew, H.R. and Dickerson, R.E. (1983) J. Mol. Biol. 163, 129-146) in the minor groove of the CGCGAATTCGCG crystals are described. It is shown that the existence of such a spine in the minor groove of poly(dA).poly(dT) is energetically favourable. Moreover, the spine of hydration makes the polynucleotide conformation similar to the poly(dA).poly(dT) structure in fibers and to the conformation of the central part of CGCGAATTCGCG in crystals; it also acquires features characteristic of the structure of poly(dA).poly(dT) and DNA oligo(dA)-tracts in solution. It is shown that the existence of the TpA step in conformations characteristic of the poly(dA).poly(dT) complex with the spine of hydration is energetically unfavourable (in contrast to the ApT step) and therefore this step should result in destabilization of the spine of hydration in the DNA minor groove. Thus, it appears that the spine of hydration as described by Dickerson and co-workers is unlikely to exist in the poly d(A-T).poly d(A-T) structure. The data obtained permit us to interpret a large body of experimental facts concerning the unusual structure and properties of poly(dA).poly(dT) and oligo(dA)-tracts in DNA both in fibers and in solution. The results provide evidence of the existence of the minor groove spine of hydration both in fibers and in solution on A/T tracts of DNA which do not contain the TpA step. The spine plays an active role in the formation of the anomalous conformation of these tracts.
Two groups of HMG box proteins are distinguished. Proteins in the first group contain multiple HMG boxes, are non-sequence-specific, and recognize structural features as found in cruciform DNA and cross-over DNA. The abundant chromosomal protein HMG-1 belongs to this subgroup. Proteins in the second group carry a single HMG box with affinity for the minor groove of the heptamer motif AACAAAG or variations thereof. A solution structure for the non-sequence-specific C-terminal HMG box of HMG-1 has recently been proposed. Now, we report the solution structure of the sequence-specific HMG-box of the SRY-related protein ). Helices I and II are positioned in an antiparallel mode and form one arm of the HMG box. Helix III is less rigid, makes an average angle of about 90°with helices I and II, and constitutes the other arm of the molecule. As in HMG1B, the overall structure of the Sox-4 HMG box is L-shaped and is maintained by a cluster of conserved, mainly aromatic residues.The cloning of the RNA polymerase I transcription factor UBF 1 (1) has originally led to the recognition of a novel type of DNA-binding domain, the so-called HMG box. The HMG box was named after its homology with high mobility group (HMG)-1 proteins and is defined by a loose consensus sequence of about 80 amino acids (2). At this moment, more than 60 proteins with one or more HMG boxes have been reported. An evolutionary study of the HMG box family indicated that two major subfamilies can be discriminated (3). One of these subfamilies contains proteins with a single HMG box, which binds with high sequence specificity to variants of the DNA sequence (A/T)(A/T)CAAAG. Members of this subfamily include products of the mammalian sex determinator Sry and related Sox genes (Sry HMG box-containing genes) (4, 5), the Schizosaccharomyces pombe transcription factor Ste11ϩ (6), the lymphoid factors TCF-1 (7, 8) and LEF-1 (9, 10), and the products of several fungal mating type genes such as Mat-Mc of S. pombe (11) and Mt a1 of Neurospora crassa (12).DNA binding occurs in the minor groove, as was shown for TCF-1, LEF-1, Mat-Mc, SRY, and Sox-4 by methylation-and diethyl-pyrocarbonate carboxylation interference footprinting and T(C/A)I nucleotide substitutions (13-16) and is accompanied by the induction of a strong bend in the DNA helix (14, 16 -18). A bend-swap experiment demonstrated that LEF-1 and its specific DNA-binding motif can functionally replace bending induced by the integration host factor at the attP locus in phage integrase reaction (16).The other subfamily includes proteins with multiple HMG boxes and with a rather nonspecific affinity for DNA, such as the HMG-1 and -2 proteins (19), UBF (1) and mtTF1 (20). Characteristic of these HMG boxes is their affinity for the cis-platinated -GG-adduct in DNA (21, 22) and cruciform DNA (23, 24), independent of sequence determinants. This suggested that the non-sequence-specific HMG boxes recognize DNA structure instead of DNA sequence (25).Circular dichroism measurements and secondary structure prediction met...
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