1. Top-Down Meets Bottom-Up: Dip-Pen Nanolithography and DNA-Directed Assembly of Nanoscale Electrical Circuits Student: Xu Zhang Chad A. Mirkin et al. Small 2005, 1, No. 1, 64 –69

2. Introduction Interfacing bottom-up chemical and biological assembly schemes with top-down lithography to fabricate complex devices is presently a major goal in nanoscience and technology. Bridging the gap between self-assembly techniques and modern top-down lithography offers a way to incorporate additional functionality (for example, in the form of chemical or biological recognition and sensing capabilities) into conventional electronic and optical devices, and provides a rapid means to test the potential viability of multiple chemically synthesized device components and self-assembly strategies. This paper presents a method that allows multiple, independent chemical recognition events to be incorporated in close proximity in a single electrical junction device by using DNA-directed assembly of specific metal nanoparticles.

3. Strategy: DNA-directed assembly of Au NPs at the gap between electrodes Two different DNA systems used to fabricate the devices: capture (a,d),target (b,e),and probe (c,f) DNA strands. DNA-directed assembly of Au nanoparticles modified with oligonucleotides at the gap between metallic electrodes selectively patterned with DNA via DPN

4. Experimental procedure 1 st : Fabricating the electrodes First, contact pads of thermally evaporated layers of Au and Cr were patterned using photolithography onto a SiO2 substrate Next, electron- beam lithography (EBL) was utilized to define an inner electrode pattern and the inner junction “nanogap” regions (an example is circled in the Figure), which comprises two Au electrode leads separated by a gap of 20–100 nm.

5. Experimental procedure 2 nd : Testing the process of DNA- directed nanoparticle capture into the gaps DNA functionalization of the electrodes by immersing the chips in solutions of hexylthiol- modified DNA strands 1a or 2d. Or by DPN, which results devices with different DNA sequences on neighboring junctions on the same chip. (An APTMS modified Si 3 N 4 AFM tip coated with 5’ HS-DNA ink like 1a, is brought to write on the specific electrode junctions of gold electrode surfaces in a controlled humidity chamber. A new tip coated with a second DNA sequence 2d was used to pattern a second set of nearby junctions. Then passivate the surface with octadecanethiol (ODT). Then apply a droplet of the solution containing both Au nanoparticle-linker conjugates (Au- oligo 1c or 2f – linker oligo 1b or 2e conjugate) to the chip surface and hybridize 3–4 h, then rinse the chip to remove nonspecifically bound NPs.

6. Experimental procedure 3 th : Using Field emission scanning electron microscopy (FESEM) to v erify the DNA deposition on a test pattern A) A low-resolution FESEM image of the entire device; B) dark-field optical microscopy image of the test patterns on the Au bonding pads; C) FESEM image of the assembly of complimentary oligonucleotide- modified 20-nm-diameter Au nanoparticles on the selected area of the test-dot arrays. The dark square visible in the image is an area that has previously been scanned by the FESEM beam.

7. Experimental procedure 4 th : Using (FESEM) to v erify the process of DNA-directed nanoparticle capture into the nanogaps FESEM image of single 20- and 30-nm-diameter Au nanoparticles assembled from solution and bridging the two adjacent nanoelectrode junctions.

8. Experimental procedure 5 th : Electrical characterization Current–voltage (I–V) characteristics of solution-modified, DPN-generated nanogap devices assembled with oligonucleotide-modified Au nanoparticle devices: A) I–V curves of the devices assembled with 30-nm- diameter Au NPs at various temperatures; B,C) I–V curves of the devices assembled with 20-nm (B) and 30-nm (C) diameter Au NPs at T=4.2 K showing the experimental data and the fit to the orthodox Coulomb blockade model (c); D) I–V and the corresponding conductance (numerical dI/dV) plot of the device assembled with 30-nm-diameter Au nanoparticles at T=4.2 K. The inset picture shows a model circuit of the system with a double-barrier junction used for fitting the experimental data.

9. Conclusions The authors have demonstrated that DNA hybridization can be used to direct the assembly of single DNA-functionalized nanoparticles into single-electrode junctions; DPN can be used to interface DNA-directed nanoparticle assembly with conventional microfabrication techniques to produce primitive tunnel junction circuits. And these junctions provide the opportunity to measure electrical transport through well-defined biochemical tunnel junctions, as well the opportunity to develop simple biosensors based on basic on/off- type recognition events.

10. Learn from the paper How to develop the scientific thinking: Top-Down Or Bottom-Up? This paper gave me an example for develop the scientific story using Bottom-Up method. And also a good example for compose the paper using Top-Down method.