Base-pair opening and spermine binding—B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition

Abstract

A sequence that is represented frequently in functionally important sites involving protein-DNA interactions is GTG/CAC, suggesting that the trimer may play a role in regulatory processes. The 2.5 A resolution structure of d(CGGTGG)/d(CCACCG), a part of the interior operator (OI, nucleotides +44 to +49) of the gal operon, co-crystallized with spermine, is described herein. The crystal packing arrangement in this structure is unprecedented in a crystal of B-DNA, revealing a close packing of columns of stacked DNA resembling a 5-stranded twisted wire cable. The final structure contains one hexamer duplex, 17 water molecules and 1.5 spermine molecules per crystallographic asymmetric unit. The hexamer exhibits base-pair opening and shearing at T.A resulting in a novel non-Watson-Crick hydrogen-bonding scheme between adenine and thymine in the GTG region. The ability of this sequence to adopt unusual conformations in its GTG region may be a critical factor conferring sequence selectivity on the binding of Gal repressor. In addition, this is the first conclusive example of a crystal structure of spermine with native B-DNA, providing insight into the mechanics of polyamine-DNA binding, as well as possible explanations for the biological action of spermine.

Detection of RAG Protein-V(D)J Recombination Signal Interactions Near the Site of DNA Cleavage by UV Cross-Linking

“…In addition, the purine-pyrimidine alteration of the consensus heptamer might help to stabilize altered DNA structures that have been observed at CACA stretches (48). Indeed, a large number of biophysical and biochemical experiments have established that (CA) n sequences such as the heptamer element are more bendable and less thermally stable than other DNA sequences (6,9,12) and that they are capable of adopting a variety of conformations (40,47,48). This malleability may be an important part of heptamer recognition by RAG proteins (2, 46) because of the considerable distortion of the DNA backbone necessary for hairpin formation.…”

Crystal structures of A‐DNA duplexes

“…On the other hand, spermine has been located in only one strucand several of its methylated and brominated variants, 5 ranging in solvent content from 67 to 40 to ture of a B-DNA hexamer. 84 Whether the A-form is conformationally more adept to interact with 24%, and at the same time exhibiting an increased number of well-ordered spermine molecules (0, 1, spermine or whether the A-type crystal packing, with crisscrossed helices capped by the shallow and 2, respectively) as well as increased bends (10Њ, 16Њ, and 31Њ, respectively). These crystallographic grooves of neighboring molecules, is more prone to trap spermine remains to be determined.…”

Structure of d(TGCGCA)2 and a Comparison to Other DNA Hexamers

“…Out of a total of 96 hexamer structures reported in the Nucleic Acid Database (NDB) , 43 are Z-DNA and 46 are hexamer±anthracycline complexes. Only three different native hexamer sequences crystallize in right-handed DNA forms, one as A-DNA (Mooers et al, 1995) and two as B-DNA (Tari & Secco, 1995;Wahl et al, 1996). There are four different sequences which alone crystallize as Z-DNA but with a drug intercalated form a distorted right-handed B-type helix: CGCGCG , CGTACG (Wang et al, 1984), CGT(NH 2 )ACG±daunorubicin and CGATCG (Moore et al, 1989).…”