Design and Characterization of Programmable DNA Nanotubes Supporting Information

1 Methods Design, data-processing and modelling: DNA sequences were designed using our own algorithms based on sequence symmetry minimization implemented in Matlab and C (available at http://www.dna.caltech.edu/DNAdesign/). Curve fits for persistence length data and models for lattice strain energies were calculated in Matlab. Molecular models were constructed and visualized using a combination of NAMOT, RasMol, and PyMol (scripts and coordinates at http://www.dna.caltech.edu/SupplementaryMaterial/). The molecular models are for visualization only and have not been subjected to molecular dynamics calculations. DNA sample preparation: Lyophilized HPLCor PAGEpurified DNA oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA), resuspended in water, quantitated by UV absorbance at 260 nm, and stored at -20◦C. All samples were prepared in a 1X Tris-Acetate-EDTA (TAE) buffer with 12.5 mM magnesium acetate (pH=8.3). An equimolar mixture of strands (5 strands if one tile, 10 strands if two) was annealed from 95◦C to 25◦C at 1◦C/minute in 0.1◦C (AFM) or 5◦C (fluorescence microscopy) steps in a PCR machine (Eppendorf Mastercycler). For AFM, each strand was present at 200 nM, for fluorescence microscopy the total concentration of tiles was kept at 400 nM. For fluorescence microscopy, a single fluorescein-labeled strand was incorporated into each tile; the position of the dye was varied from the 5′ end of the #3 strand to the 5′ end of the #5 strand with no apparent effect. AFM of REp+SEp(3:FAM) was similar to that of REp+SEp. Preparation of PVP coated glass: Adapted from. Microscope slides and coverslips were washed in 1M NaOH for 1 hour, rinsed thoroughly with de-ionized (DI) water and immersed in 1% v/v acetic acid solution for 2 hours. Then, they were rinsed again with DI water and silanized in a 1% v/v 3(trimethoxysilyl)propylmethacrylate (Aldrich) in 1% v/v acetic acid for 36 hours. For polymer coating, 500 mL of a 4% w/v Mw = 360, 000 poly(vinylpyrrolidone) (PVP, USB Corp.) solution with 2.5 mL of 10% w/w ammonium persulfate solution and 250 μl of N,N,N′,N′-tetramethylethylenediamine (TEMED, Acros) was prepared. Slides and coverslips were incubated in the PVP solution at 80◦C for 18 hours. They were then rinsed and stored in DI water. Coating was stable for at least 2 weeks. Preparation for fluorescence microscopy: Samples were left