How Sequence Defines Structure: A Crystallographic Map of DNA Structure and Conformation

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...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2005-05, Vol.102 (20), p.7157-7162
Main Authors: Hays, Franklin A., Teegarden, Amy, Zebulon J. R. Jones, Harms, Michael, Raup, Dustin, Watson, Jeffrey, Cavaliere, Emily, Ho, P. Shing, Rich, Alexander
Format: Article
Language:English
Subjects:
A form DNA
Base Sequence - genetics
Biological Sciences
Crystal lattices
Crystal structure
Crystallization
Crystallography
Crystals
Datasets
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA mapping
Genetic screening
Genomics
Models, Molecular
Molecular structure
Nucleic Acid Conformation
Nucleotides
Oligonucleotides - genetics
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Summary: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 N8are 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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0409455102