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BIOPHYSICS
How sequence defines structure: A crystallographic map of DNA structure and conformation

Franklin A. Hays, Amy Teegarden, Zebulon J. R. Jones, Michael Harms, Dustin Raup, Jeffrey Watson, Emily Cavaliere, and P. Shing Ho ^*

Department of Biochemistry and Biophysics, Oregon State University, Agricultural and Life Sciences Building 2011, Corvallis, OR 97331-7305

Edited by Alexander Rich, Massachusetts Institute of Technology, Cambridge, MA, and approved March 31, 2005 (received for review December 17, 2004)

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.

molecular screening

This paper was submitted directly (Track II) to the PNAS office.

Abbreviation: IR, inverted repeat.

Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 1ZEZ, 1ZF4, 1ZF3, 1ZFC, 1ZF2, 1ZF1, 1ZEW, 1ZFM, 1ZFH, 1ZFF, 1ZF5, 1ZFE, 1ZF7, 1ZFG, 1ZF0, 1ZFB, 1ZEX, 1ZEY, 1ZFA, 1ZF9, 1ZF8, and 1ZF6).

^* To whom correspondence should be addressed. E-mail: hops{at}onid.orst.edu.

© 2005 by The National Academy of Sciences of the USA

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