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Using DNA to purify different chiral forms of SWNTs

Using DNA to purify different chiral forms of SWNTs Tu, Manohar, Jagota and Zheng, DNA seq. motifs for structure-specific recognition and separation of CNT Nature 460:250 (2009) Problem: CNTs N are exciting nanomaterial with extraordinary strength, conductivity and other

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Using DNA to purify different chiral forms of SWNTs

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  1. Using DNA to purify different chiral forms of SWNTs Tu, Manohar, Jagota and Zheng, DNA seq. motifs for structure-specific recognition and separation of CNT Nature 460:250 (2009) Problem: CNTsN are exciting nanomaterial with extraordinary strength, conductivity and other properties that promise many applications. CNTs with different structures (diameters, wrapping angles) have different properties (metallic, semiconducting); CNTs are made as mixtures; hard to disperse in water (aggregate due hydrophobicity, van der Waals interactions); hard to purify individual species

  2. CNT structure, nomenclature Wildoer et al, Electronic structure of atomically resolved carbon nanotubes Nature 391:59 (1993) Cut sheet along H = line that goes thru (0,0) and upper left vertex of successive hexagons, and line // to H a distance C away;wrap into cylinder joining 0,0 and C; C forms circumference of tube; T = line per- pendicular to C going thru C is // totube axis; H wraps around tube

  3. Different geometry (n, m, diameter) -> different conditionsfor standing waves in electron distribution, big differences in conductivity: metallic when n-m = multiple of 3; semiconducting otherwise different optical absorption/emission spectra for semiconducting CNTs, major absorption at E22 and band gap -> fluorescence peak at E11

  4. ssDNA has been used to solubilize CNTs Acts like soap – bases bind hydrophobically, sugar and charged phosphates interact w/water Bases may “stack” against carbon rings on CNT Various groups have tried to take advantage of sequence variability among ssDNA species to screen for sequence-specific binding to different CNT species, but no big sequence effects on binding. However, sequence does affect ion exchange elution

  5. Variant idea: solubilize CNTs with DNA -> bind to ion-exchange (IEX) column elute with increasing conc. of salt ions (shields bound charges) + + + + + + + + + + + + + + + + + + + + + + - - + - - + - - - - - - - - - - - - increasing conc. of salt - Will different DNAs pack differently on various CNT species -> varying surface charge density and elution profile?

  6. Some oligo sequences -> peaks of specific chiralities eluting from IEX column

  7. How do they identify IEX peaks as different species of CNT? Semiconductor CNTs fluoresce Science 298:2361 (2002)

  8. Fluorescence absorption-emission spectra of their starting material with assigned CNT chiralities Why no species with n-m=3? (Do metallic CNTs fluoresce?) Note big differences in amount of various species

  9. They measured absorption spectra of starting material and that of eluted species. Expect large abs. peaks at E11, E22, … Other peaks in eluted material could be from contaminating species (incl. metallic CNTs); their combined areas used to est. purity E22 E11

  10. How well do summed eluted peaks reproduce absorbance of starting material? What could explain the differences?

  11. Concentration of each eluted species estimated from conc = 10 mg/ml x Abs(E11) -> est. of yield Why are yields low? What happens to the rest of each species? Does binding have to be very regular for elution as (narrow) peak? 4.2/100

  12. hypothesizedstructure of (ATTT)nDNAs bound to graphene based on minimum energy molecular dynamics calculation Note: novel alternating position of bases along backbone novel hydrogen bonds between T-T and A-A in adjacent, anti-parallel strands T A T A T T T T T T T T T A T T A T

  13. “Energy-minimized” anti-parallel array on graphene has base-stacking on graphene and atyp. base pairing betw. strands Note # bases << # rings in graphene If you cut sheet and roll it up to make cylindrical CNT, will DNA strands match to base pair across “seam”?

  14. Major idea: dna strands will be properly aligned to base pair across “seam” only for certainn,m combinations; only these CNT species bind dna uniformly over their surface and hence elute over narrow salt conc. in IEX -> purification Nice hypothesis, but not clear if their calculations support it. Do they predict which sequences bind which n,m species “seamlessly”?

  15. Putative example of pair of anti- parallel (AT3)n oligosthat are said to base-pair “seamlessly” when wrapped around (8,4) CNTs; yellow = sugar-phos backbone; white = vector analogous to “C” in CNT diagram

  16. Will it turn out that Nature uses this kind of planar NA structure, or is it purely a man-made phenomenon? There are lots of short repetitive sequences in human DNA and RNA, with no known function at present… DNA may interfere with (or facilitate) subsequent use of purified CNTS (e.g. due to its neg. charge); can it be removed by exonucleases/heat? Could longer DNA species be used that leave “free” ends available for standard base-pair-mediated control of subsequent assembly steps?

  17. Comparison with other methods that use DNA sequence variability for purification – e.g. to identify ssDNAs that bind particular targets (“aptamers”): For aptamers – make large “library” of oligos (~1014) with variable seq. in middle but invariant seq at ends, select species that bind to target on solid phase, elute, pcr amplify using invariant end seq, repeat selection. Here – need 100s of copies of same species to bind target (because CNTs so long), test only tiny sets of all possible DNA sequences (100’s vs 1014)

  18. They say their method is likely too expensive in DNA cost to be practical. DNA oligos cost ~ $10/mmol of 16-mer, ? enough to purify ~ 1012 (1mg) 1mm-long CNTs (at 0.1% yield, 2 oligos/10nm of CNT). How cheap do individual CNT species have to be for practical applications? CNT “cloning” idea: purified CNT species might serve as seeds and be extended in new synthesis reactions Compare CNTs and DNA as polymer systems: CNTs denser, stiffer, heterogeneous backbone structures; DNA has homogeneous backbone but combinatorially huge variability in monomer order (sequence); engineerable length; potentially engineerable lateral connections

  19. Summary Empirically, they are able to separate many CNT species using short ssDNAs with different alternating purine- pyrimidine motifs They propose novel DNA structures form in complex with CNTs; mostly this is conjecture, but note how rich DNA structure is! Not just B-form double helix. They propose novel mechanism by which these DNA com- plexes lead to purification via IEX. Limited theoretical support.

  20. Next class – how DNA responds to pulling forces Basic idea – Force-displacement relation is of basic interest from biophysics-polymer science point of view; DNA acts like “entropic” chain (Brownian motion randomizes configurations, p(x) ~ # configs with length x ~ e-energy (x)/kT,work required to stretch) Of several models, “worm-like chain” fits data best Technology developed to evaluate force-displacement (laser traps, magnetic traps, single-molecule mechanics) has led to spectacular advances in understanding how certain molecules work as nanomachines ….? more N’s x(F) F

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