Schematic illustration of the procedure for forming a chip-integrated nanowire: a DNA and microstructured chip as building blocks, b various stretch- ing methods, c DNA positioned in an
Trang 1Fig 1 Schematic illustration of the procedure for forming a chip-integrated nanowire: (a) DNA and microstructured chip as building blocks, (b) various stretch- ing methods, (c) DNA positioned in an electrode gap, (d) binding of metal ions or
particles and subsequent enhancement lead to a metallized nanowire
are used in our workgroup The work on the optimization of the parameters,for example, DNA concentration, buffer conditions, and conditions for the sur-face modification steps, is very important but often tedious Our experimentshave shown that droplet sizes between 0.5 and 1 μl and DNA concentrationsbetween 0.6 and 6 ng μl−1 are practicable Also, surface modification with asimple PDMS (polydimethylsiloxane) vapor treatment in a petri dish offers
a possibility to obtain suitable surfaces for the stretching and positioning ofDNA strands
2.1 Immobilization on Mica
A simple method for stretching DNA on mica has been described by Li et
al [46] and Cherny et al [15] The DNA solution is incubated on one side
of the piece of mica for some minutes and then blown off slowly at an angle
of 45◦ The functionalization of the surface is provided by cleavage of themica Subsequently applied magnesium ions are then able to bridge the netnegatively charged surface and the negative backbone of the DNA However,mica is not suitable for further technological applications because there is noeasy possibility to contact the immobilized molecules and it is not very stable
Trang 2Table 1 Overview of methods for stretching DNA
Magnetic Magnetic tweezers Smith et al [86]
Optical Laser tweezers Perkins et al [75, 76]
Moving interface Drying droplet Bensimon et al [7, 8], Jing et al [39]
Controlled meniscus motion Otobe and Ohtani [69]
Moving meniscus Michalet et al [60]
Sliding of a coverslip edge Yokota et al [107]
Gas flow-driven droplet Li et al [46]
Spin stretching Yokota et al [108]
Dielectric Washizu et al [97], Holzel et al [36]
for handling For this reason, there is a need for methods using substratessuch as glass or silicon, which are important technological materials
2.2 Immobilization on Glass
One of the most important impulses for stretching DNA molecules was thesearch for new methods for obtaining obtaining restriction maps of isolatedchromatin and DNA molecules [35] Optical methods for mapping individualDNA molecules have been described for yeast artificial chromosomes (YACs)[13, 14], restriction fragments and cosmid probes [72], and λ-DNA [98, 107],for example The idea has been extended to human genomic DNA One ap-plication was the mapping of microdeletions in the tuberous sclerosis 2 gene[60] Fluorescence-stained stretched DNA can be determined optically with anaccuracy of better than one micron The literature describes many methodsand variations for the immobilization of DNA in solution on planar substrates.There are many applications which use the interface between air and liquid.The DNA strands can be aligned on a surfaces either by the receding menis-cus of a drying droplet or by simply pulling the substrate out of the solution
in a controlled way In the first case, the molecules are positioned radiallywith a large concentration of DNA in the center of the drop and few ex-tended fibers/bundles in the peripheral region The second approach leads tostretched strands in the direction in which the substrate is moved out of thesolution As mentioned above, all surfaces need a suitable functionalizationfor binding the DNA Functionalizations usually provide a positive charge toattract and bind the DNA The chemicals commonly used are APTES (3-aminopropyltriethoxysilane) [24], ODTS (octadecyltrichlorosilane) [92], andPMMA (polymethylmethacrylate) [30]
Trang 32.3 Immobilization on Microstructured Chips
The next step is the integration of DNA strands into technological ments such as microstructured chips with electrodes or defined electrode gaps.Bridging such gaps with molecules followed by a metallization step leads tonanowires with ohmic behavior Such a process has to be practicable, gener-ally applicable and reproducible The binding of the DNA to the electrodes
environ-is typically done by interaction of complementary sequences [11] but can also
be achieved by electrostatic interaction between negatively charged moleculeends and a positively charged surface on the electrode [52] Ideally, one DNAmolecule or bundle is immobilized in one gap Thereby, bundles are made morestable for further imaging or metallization steps In a highly parallel process,using the receding-meniscus method, precise positioning of DNA in severalelectrode gaps could be achieved [53] Here the DNA follows the electrodestructure, and also span the gaps
Fig 2 Left: atomic force microscope picture of an immobilized DNA strand in
an electrode gap Right: Electron-scanning microscope picture of a
nanoparticle-labeled DNA strand, spanning an electrode gap
3 Nanoparticle Binding on DNA
Owing to their interesting and powerful properties, colloidal nanocrystals ornanoparticles find wide use in biology and adjacent fields, such as life sciencesand nanotechnology One main application is use as a label or a stain To-gether with biological molecules [64, 61], they can work as building blocks,enabling the formation of complex patterns and assemblies Molecular recog-nition leads, for example, to two-dimensional crystals and tubes [82, 83, 84].Thereby, DNA can provide a nanoscale scaffold [65, 55], so that it is possi-ble to build up nanowires of metallized DNA [11, 80, 79], as we shall see inSection 4 Bioconjugation between DNA and nanoparticles can be performed
Trang 4via simple adsorption [27] or with the well-known biotin–avidin system [85].
A very efficient and strong method is the use of thiol groups to attach DNA,
as first described for thiolated oligonucleotides on planar gold surfaces andlater applied to gold nanoparticles [2, 62, 23, 50, 17] With these techniques,the nanoparticles were attached to a receptor (the oligonucleotide); now it
is possible to bind these constructs to positions where a ligand tary sequence) is present This leads to programmable DNA patterns andopens the way to realizing nanocircuits, possibly using nanocrystals as single-electron transistors [43] or arranging them in a desired pattern on the surface[22] A further simple but smart method is the electrostatic binding of ligand-stabilized nanoparticles to the DNA backbone The result is an extended linearchain-like structure or ribbon-like structure composed of parallel nanoparticles[95] Positively charged gold nanoparticles have been used to bind to a DNAstrand spanning a microstructured gap [54] The arrangement of nanoscalebuilding blocks on biomolecular scaffolds demonstrated in this way is a viableapproach to obtaining closely spaced assemblies and a step towards biomolec-ular nanolithography
(complemen-4 Metallization of DNA
The last step process described above is the metallization of the aligned DNAstrands Conductivity is the main requirement for basic electronic buildingblocks such as wires, resistors, or p–n junctions According to the predominantconventional wisdom, after a long period of dissent among different researchgroups, DNA is a poor conductor over longer distances There are many theo-ries that describe how such electron transport can work Fink and Schneberger[25] reported a direct measurement of electrical current across DNA moleculesthat were 600 nm long They concluded that the inner p-electrons of the baseindicated that the DNA had the properties of good semiconductor On theother hand, photoinduced electron transfer experiments showed a poor macro-scopic electrical conductivity in DNA films [66, 12] Removal of the watermantle around the double helix leads to reduced conductivity along lambdaphage DNA and is strongly temperature-dependent around room tempera-ture [91] Electronic-structure calculations and direct measurements throughλ-DNA molecules adsorbed on mica exhibit values of 106 Ω cm−1 and alsoshow a dramatic effect on the measured conductivity which rises to high valuesafter low-energy electron bombardment [18] The utility of electrostatic forcemicroscopy for probing the conductance of DNA has been demonstrated andhas revealed an insulating behavior, in contrast to conducting single-wall car-bon nanotubes [10] Measurements between nanofabricated gold or platinumelectrodes with different gap sizes (40500 nm) showed likewise that DNA isinsulating over longer distances [88] However, there is a consensus that chargetransport takes place over the base pairs and their p-orbitals [28] There aremany advantages and disadvantages of these different methods but it seems
Trang 5very probable that native DNA has to be discarded for electronic circuits,and replaced by additional materials to provide the desired properties In ad-dition, the additional materials should have a geometry similar to that of thetemplate DNA.
4.1 Metals and How to Obtain Wires from Them
Table 2 shows the metals frequently used in approaches to making nanowire.Interestingly, all elements applied as nanowires are members of either thefirst or the eighth subgroup of the periodic system of elements All of themexhibit a very good conductivity and are noble metals so that they can beeasily reduced The idea is to attach metallic clusters or metal particles tothe DNA and to form so-called “pearl chains” These can be used in thenext step to form a continuous film on the biomolecule in order to achieve aconducting wire The size of such mesoscopic clusters is in the range of thediameter of a DNA strand This is important for homogeneous metal coverageafter the enhancement step that will be discussed below However, a chain
of cationic gold colloids or Cd/S clusters [90] electrostatically bound to theanionic backbone of the DNA will not lead to a conducting wire, because thedistance between the particles is too large Therefore, growth of the clustersuntil they achieve spatial contact is needed So, they are usually used asseeds in a two-step procedure In this way, Cd/S clusters could be used toassemble an array of semiconductor nanoparticles matching the shape of thebiopolymer, to form a nanowire [16] Furthermore, selective localization ofsilver ions along the DNA through Ag+/Na+ion exchange can be used for theseed-binding step The recognition capabilities of DNA was used to construct ametal wire 12 mm long and 100 nm wide, connecting two electrodes [11] DNAmetallization can also be accomplished by deposition of palladium Palladiumactivates the template to form a continuous palladium film after a reducingstep [79, 19] The binding of palladium complexes is very similar to the process
of binding of cis-platin, which is very well understood The use of cis-platin
is very important in cancer therapy The binding of such complexes changesthe tertiary structure of the DNA Additionally, the B-structure of the DNAbecomes changed dramatically in the binding region, and base pairs are broken[47, 67]
4.2 The Final Step Towards Nanowires
The surface of the DNA is now activated with metal complexes or ticles which act as seeds and subsequently as catalysts in the subsequent re-ducing step, which leads to a homogeneous metal-covered wire where the gapsbetween the centers of the metal particles are closed In the case of palladium,Richter et al used a mix of sodium citrate, lactid acic, and dimethylamineborane [80, 79] They achieved wires with a diameter of about 50 nm Some
Trang 6nanopar-Table 2 Commonly used metals for nanowires
Copper VIII Monson and Wooley [63] 3
Platinum VIII Mertig et al [57]
Palladium VIII Richter et al [80, 79] 20
other reducing agents are hydroquinone or sodium borohydrate Also known enhancement steps are the reduction of silver nitrate or silver acetate
well-by hydroquinone [32] and the application of tetrachloroauric acid togetherwith ammonium hydroxide [99, 100] So, it is possible to deposit silver metalvectorially along a DNA molecule to obtain electrical functionality The firststep is the selective localization of silver ions along the DNA through sil-ver/sodium exchange This is selective and is restricted to the DNA templateonly [11] The subsequent “development” of these aggregates is done by thestandard photographic procedure, with an acidic solution of hydroquinoneand silver ions under low light conditions [9, 37] Monson and coworkers [63]have shown that copper can also be used to form nanowirelike structures with
a height of 3 nm They deposited copper metal using aqueous copper nitrate
so that the copper(II) was electrostatically associated with the DNA It wasthen reduced by ascorbic acid to form a metallic copper sheath around themolecule It was demonstrated that copper nanowires were valuable as inter-connects in nanoscale integrated circuitry In ongoing experiments [29] cobaltnanoparticles have been assembled in situ on a template of double-strandedDNA to form magnetic nanowires Palladium ions were bound to DNA andselectively reduced to zero-valence nanoclusters by deposition of Co(0) in adimethylamine borane The nanowires so formed were several microns longand 10 to 20 nm thick
4.3 Sequence-Specific Molecular Lithography
A very novel tool for assembling devices into functional circuits is specific molecular lithography on DNA as a substrate, described by Keren et
sequence-al [42] Here RecA protein binds in a sequence-specific manner and protectsthe DNA against metallization This means that the lithographic informa-tion for this accurate and stable pattern is encoded in the DNA itself Themolecular lithography works with high resolution over a broad range of lengthscales from nanometers to many micrometers In another approach, based onrecognition between molecular building blocks, a DNA scaffold is used to lo-calize semiconducting single-wall carbon nanotubes for the realization of aself-assembled carbon nanotube field-effect transistor operating at room tem-perature [41] It has also been shown [40] that DNA can retain its biological
Trang 7functionality during metallization by aldehyde derivatization So, in this casethe RecA protein protects the DNA molecules in a sequence-specific manneragain and allows complex patterning of molecular-scale electronic circuits.
4.4 Sequence-Specific Molecular Lithography with Nanotubes
As we have seen, carbon nanotubes also play an important role in the field ofmolecular nanotechnology Single-walled carbon nanotubes (SWNTs) whichhave been covalently modified with DNA can hybridize selectively with com-plementary strands, with minimal nonspecific interactions with noncomple-mentary sequences [33] These functionalized nanotubes can now act onceagain as molecular building blocks Because of their interesting features andtheir behavior as either a metal or a semiconductor, they have emerged as im-portant materials for nanofabrication, in both electronic devices and sensors.Controlled and selective localization of SWNTs on aligned DNA molecules
on surfaces was also shown by Wooley and coworkers and could represent
a route to the manipulation and positioning of SWNTs on surfaces Thereare approaches to generating masks for photolithographic processes using asmall number of DNA sequences to build up a structure of any size So, it hasbeen possible to assemble carbon nanotube transistors into circuits by usingDNA [20, 21] This provides an important tool in bottom-up biotemplatednanofabrication
5 Concluding Remarks
Since we have been working on the integration of long DNA and cles, we have seen a great potential for these methods in new approaches toelectronics However, we have to point out that there remains a lot of work to
nanoparti-be done All the steps descrinanoparti-bed here are well established as separate dures However, the combination of these steps into standard procedures hasnot yet been established First of all, the problem of the parallelization of theintegration of the molecules, which will be very important for commercial orforward-looking applications, has not been satisfactory solved This is closelyconnected to the problem of suitable surfaces and both their modificationand their functionalization We have been working a lot on the development
proce-of simple, homogeneous surface modifications, especially on microstructuredchips But even the simple method of a drying droplet is not completely un-derstood today So one has in a large number of samples only a few with DNA
in the desired places, leading to problems of reproducibility and throughput,and a series of established steps will not always work with the same precisionand efficiency as does every separate step
“There is plenty of room at the bottom”, but there is also even more workthere
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