PDBsum entry 1zf7

DNA

PDB id: 1zf7

Contents

DNA/RNA

Metals

_NA

_CA ×3

Waters ×21

References listed in PDB file

Key reference

Title

How sequence defines structure: a crystallographic map of DNA structure and conformation.

Authors

F.A.Hays, A.Teegarden, Z.J.Jones, M.Harms, D.Raup, J.Watson, E.Cavaliere, P.S.Ho.

Ref.

Proc Natl Acad Sci U S A, 2005, 102, 7157-7162. [DOI no: 10.1073/pnas.0409455102]

PubMed id

15870206

Abstract

The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects.

Figure 2.
Fig. 2. Map of DNA structure space sampled by crystals of d(CCnnnN[6]N[7]N[8]GG). The map is divided into three specific structural classes (labeled B for B-DNA, A for A-DNA, and J for junctions) and the interfaces between each conformational phase. The sequences in uppercase letters define those that have been uniquely solved or reproduced in the current study, while those in lowercase letters are structures from previous studies, but not reproduced here. The rectangle around GCC indicates that the structure is induced by a change in divalent cations (from Ca^2+ to Mg2+). Similarly, the oval around GGC indicates that the A form is induced by alcohol. Arrows trace paths through the conformational map as the N[6]N[7]N[8] trinucleotide undergoes single-nucleotide transitions or transversions. These are not unique paths, but show one set of consistent single-nucleotide steps through the conformational space.

Figure 3.
Fig. 3. Correlating sequence effects to atomic interactions in junctions. The interactions that are identified as being important for fixing the junction in ACC are shown in the insets. General rules for junction-forming sequences are noted in green, red, and blue for the nucleotides N[6], N[7], and N[8], respectively. The inset for the cytosine C[8] to phosphate of N[7] is rotated relative to the orientation of the overall structure.