Using DNA to purify different chiral forms of SWNTs Tu, Manohar, Jagota and Zheng, DNA seq. motifs for structure-specific recognition and separation of.

Using DNA to purify different chiral forms of SWNTs Tu, Manohar, Jagota and Zheng, DNA seq. motifs forstructure-specific recognition and separation of CNTNature 460:250 (2009)

Problem: CNTsN are exciting nanomaterial withextraordinary strength, conductivity and otherproperties 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

Cut sheet along H = line that goes thru (0,0) and upper left vertexof 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 // to tube axis; H wraps around tube

Wildoer et al, Electronicstructure of atomically resolvedcarbon nanotubesNature 391:59(1993)

CNT structure, nomenclature

Different geometry (n, m, diameter) -> different conditions for standing waves in electron distribution, big differences in conductivity:

metallic when n-m = multiple of 3; semiconducting otherwise

different optical absorption/emission spectrafor semiconducting CNTs,major absorption at E22

and band gap -> fluorescencepeak at E11

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 ofsequence 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

Variant idea: solubilize CNTs with DNA -> bind to ion-exchange (IEX) column elute with increasing conc. of salt ions (shields bound charges)

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increasing conc. of salt

Will different DNAs pack differently on various CNT species -> varying surface charge density and elution profile?

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

How do they identify IEX peaks as different species of CNT?

Semiconductor CNTs fluoresce

Science 298:2361 (2002)

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

They measured absorption spectraof starting materialand that of eluted species.Expect large abs. peaks atE11, E22, …Other peaks in elutedmaterial could befrom contaminatingspecies (incl. metallicCNTs); their combinedareas used to est. purity

E22 E11

How well do summed eluted peaks reproduceabsorbance of starting material?

What could explain the differences?

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 eachspecies? Does binding have to be very regular for elution as (narrow) peak?

4.2/100

Note: novel alternating position of basesalong backbone

novel hydrogenbonds between T-Tand A-A in adjacent,anti-parallel strands

hypothesized structure of (ATTT)n DNAs bound to graphenebased on minimum energy molecular dynamics calculation

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“Energy-minimized”anti-parallel arrayon graphene hasbase-stacking ongraphene 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”?

Major idea: dna strands will be properly alignedto base pair across “seam” only for certain n,mcombinations; only these CNT species bind dnauniformly over their surface and hence elute overnarrow salt conc. in IEX -> purification

Nice hypothesis, but not clear if their calculationssupport it. Do they predict which sequences bindwhich n,m species “seamlessly”?

Putative exampleof pair of anti-parallel (AT3)n oligos that are saidto base-pair“seamlessly” whenwrapped around (8,4) CNTs;yellow = sugar-phosbackbone;white = vectoranalogous to “C”in CNT diagram

Will it turn out that Nature uses this kind of planar NAstructure, or is it purely a man-made phenomenon?

There are lots of short repetitive sequences in humanDNA 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” endsavailable for standard base-pair-mediated control ofsubsequent assembly steps?

Comparison with other methods that use DNA sequence variability for purification – e.g. to identifyssDNAs 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 bindtarget (because CNTs so long), test only tiny sets of all possible DNA sequences (100’s vs 1014)

They say their method is likely too expensive in DNA costto 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 individualCNT 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

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.

Next class – how DNA responds to pulling forces

Basic idea –

Force-displacement relation is of basic interest frombiophysics-polymer science point of view;DNA acts like “entropic” chain (Brownian motionrandomizes configurations, p(x) ~ # configs withlength 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

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