Crystal structure of a continuous three-dimensional DNA lattice.

DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. Here we report the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer. The structure consists of stacked layers of parallel helices with adjacent layers linked through parallel-stranded base pairing. The hexagonal lattice geometry contains solvent channels that appear large enough to allow 3'-linked guest molecules into the crystal. We have successfully used these parallel base pairs to design and produce crystals with greatly enlarged solvent channels. This lattice may have applications as a molecular scaffold for structure determination of guest molecules, as a molecular sieve, or in the assembly of molecular electronics. Predictable non-Watson-Crick base pairs, like those described here, may present a new tool in structural DNA nanotechnology.

[1]  E. Westhof,et al.  RNA folding: beyond Watson-Crick pairs. , 2000, Structure.

[2]  F. Azorín,et al.  Structural polymorphism of homopurine DNA sequences. d(GGA)n and d(GGGA)n repeats form intramolecular hairpins stabilized by different base-pairing interactions. , 1996, Biochemistry.

[3]  E. Westhof,et al.  TectoRNA: modular assembly units for the construction of RNA nano-objects. , 2001, Nucleic acids research.

[4]  N. Seeman,et al.  A nanomechanical device based on the B–Z transition of DNA , 1999, Nature.

[5]  J. Rebek,et al.  Reversible encapsulation by self-assembling resorcinarene subunits , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[6]  D. Patel,et al.  Interlocked mismatch-aligned arrowhead DNA motifs. , 1999, Structure.

[7]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[8]  N. Seeman.  DNA in a material world , 2003, Nature.

[9]  Batey,et al.  Tertiary Motifs in RNA Structure and Folding. , 1999, Angewandte Chemie.

[10]  S. Chou,et al.  The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs. , 1994, Journal of molecular biology.

[11]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[12]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[13]  M. Caruthers,et al.  Gene synthesis machines: DNA chemistry and its uses. , 1985, Science.

[14]  E Westhof,et al.  Non-Watson-Crick base pairs in RNA-protein recognition. , 1999, Chemistry & biology.

[15]  Philip S Lukeman,et al.  Nylon/DNA: Single-stranded DNA with a covalently stitched nylon lining. , 2003, Journal of the American Chemical Society.

[16]  J G Stowell,et al.  Helical rosette nanotubes: design, self-assembly, and characterization. , 2001, Journal of the American Chemical Society.

[17]  B H Robinson,et al.  The design of a biochip: a self-assembling molecular-scale memory device. , 1987, Protein engineering.

[18]  C. Henriques,et al.  Structure-activity relationship in zeolites , 1995 .

[19]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[20]  Aaron Klug,et al.  Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops , 1989, Nature.

[21]  W. Olson,et al.  3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. , 2003, Nucleic acids research.

[22]  Weihong Tan,et al.  A Single DNA Molecule Nanomotor , 2002 .

[23]  D. McRee,et al.  A visual protein crystallographic software system for X11/Xview , 1992 .

[24]  Jean-Louis Mergny,et al.  DNA duplex–quadruplex exchange as the basis for a nanomolecular machine , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[25]  N C Seeman,et al.  A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT. , 1997, Journal of molecular biology.

[26]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[27]  J. Kondo,et al.  Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs. , 2002, Nucleic acids research.

[28]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[29]  J. Dodge,et al.  Structure/activity relationships , 1998 .

[30]  R. Dickerson,et al.  Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. , 1991, Journal of molecular biology.

[31]  G. A. van der Marel,et al.  Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs. , 1992, Biochemistry.

[32]  P. Hagerman.  Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[33]  N. Brokaw,et al.  Valuation of consumption and sale of forest goods from a Central American rain forest , 2000, Nature.

[34]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[35]  M Reza Ghadiri,et al.  Self-Assembling Cyclic Peptide Cylinders as Nuclei for Crystal Engineering. , 2001, Angewandte Chemie.

[36]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. , 1999, Biochemistry.