Silicon Microarray™ Technology
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Silicon Pins, Printhead and Printing Technical Information

On these pages, the technical specifications, performance attributes and test data for the both the micromachined silicon pins and the holder/printhead are discussed. Information is included on both the substantial advantages of the silicon microcontact printing pins over the traditional machine shop steel pins and quantitative data demonstrating the superior performance of the Silicon Microarray™ technology for your microcontact printing applications.

The topics covered in this section are:


The Silicon Microcontact Printing Pins

The Printhead and Micromachined Collimators

Data showing the lack of prespotting phenomenon

Technical Data on Printing Performance

Other Applications


The ultra high precision of the printed patterns made by the micromachined silicon microcontact printing pins is made possible by the great accuracy of the photolithographic and etching processes used to fabricate the pins. In order to print in an ultra high resolution fashion, both the print tips and the pin holder must possess extremely high tolerances. As with all types of contact printing, the silicon pins and commercial steel pins require the application of force on the pin in order to press the print tip surface against the substrate to print satisfactorily. This pressure requirement, combined with the fact that no substrate is perfectly flat, dictate the printing pins must be compliant and be allowed to move in the z direction (perpendicular to the plane of the substrate). However, to accurately print features on a grid pattern (i.e. to pack the spots as densely as possible without touching) there can be essentially no movement of the pin in the x and y directions when it moves up and down in z. This presents the classic collimation dilemma of needing the smallest possible tolerances between the sliding shaft and collimator without binding.

These problems are addressed by micromachining two silicon plates that are placed parallel to one another in a holder and have rectangular slots to guide and collimate the rectangular shafts of the pins. Our devices have tolerances of only ~5 to 10 microns (0.00025") between the pin shaft and the collimator because of the flatness of the silicon pin (derived from the extreme flatness of the wafer from it was etched), the mirror smoothness of the sliding silicon-on-silicon surfaces and the fine tolerances achievable from the micromachining process. It is clear that to print ever denser arrays, the quality and accuracy of the collimation will have to increase concomitantly with the size diminution of the print tip in order to print smaller spots closer together. The micromachining employed for the Silicon Microarray™ technology fabrication will be able to provide spot size and density to match scanner resolution increases into the future. The Silicon Microarray™ technology can adapt and grow with your future needs to print ever denser arrays.

But before beginning a discussion of the detailed technical specifications of the pins and holders, the following pictures provide dramatic illustrations of some unique physical properties of silicon. Don't try any of these experiments with your steel pins!

Fig. 1
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Fig. 6

Please click on the images to enlarge them: (1) an X-acto®; knife blade inserted between the prong of a silicon microarray pin spreading the prongs apart from 25 to 200 microns. Unless stressed beyond the breakage point, the very high elasticity of silicon allows 100% recovery of the original shape; (2) the pins are unaffected by concentrated nitric acid or H2O2/H2SO4 at room temperature; (3) a silicon pin in the flame of a butane torch glowing red hot; (4) after placing a weight on the silicon pin to generate a pressure of ~1600 lbs/in2 (~100 bars) on the print tip, the tip shows no visible wear after 50,000 print cycles on aluminum oxide sandpaper; (5) the pins survive a fall from the bench top to the floor; (6) Pins dipping directly from a 1536 source plate.

The Silicon Microcontact Printing Pins Go To Top

To dip a pointed object into a liquid and transfer the liquid to a smooth surface to make a pattern is a very old human activity. The silicon microarray pins described here possess many similarities between feather quill pens and fountain pins but also have myriad unique and important features and attributes that make them particularly suitable for microcontact printing. The properties of silicon and silicon oxide make them a logical next step in the fabrication of high precision writing and printing tools because of the ability to fabricate extremely small, durable and accurate features in a material that will pick up and release the desired printing fluid.

The silicon pins are manufactured from extremely flat, highly polished single crystal silicon wafers and therefore each pin is a single crystal silicon except for a thin SiO2 coating. This thin, extremely pure SiO2 coating however serves several extremely important roles. From a molecular surface viewpoint the pin surface is pure silica and therefore has the well known properties associated with glass or quartz such as well known wetting behavior, the ability to be chemically derivatized fluid uptake and release and cleaning. The dense, highly conformal SiO2 coating is made by treating the finished pins in steam at T > 900°C. Many pins are formed from the single crystal wafers in parallel. The pins are etched from the wafers by a series of photolithographic and DRIE operations as described in the silicon micromachining section of this website. Since the photomask used to define the structure of the pins and the pins are synthesized at the same time, the pins are essentially identical in structure and behavior.

Several of the features, advantages and benefits of the Silicon Microarray™ technology, as compared to machine shop fabricated steel pins, are shown below in Table 1.

Table 1 Comparison of the features, advantages and benefits between
silicon and stainless steel microspotting pins

Silicon Microarray™
Stainless Steel
Packing density of pins into holder Very High; 96, 384 or 1536 source plates can be directly used, <1mm pin spacing possible Packing density of steel pins limited to 4.5 mm
Highly precise volumetric uptake Smaller (25 - 250 nL per dip) volumetric uptake, reduced oligo waste Larger (~ 1 - 2 µL)
Prespotting phenomenon Essentially no prespotting is observed Prespotting is observed
Cost <25% the cost of the current finest printing technologies Expensive
Complete depletion of printing fluid from pin The pins print to dryness utilizing all sample imbibed Most fluid taken remains in pin
Tip sizes available Tip sizes ranging from 50x50µm to 200x200µm Tip sizes ranging from 75µm to 360µm in diameter
Deposited drop size and uniformity Since tip has smaller, more precise features, smaller more uniform spots result Larger, more irregular spots
Pin-to-pin uniformity as manufactured Pins are identical Much more variability
Hardness of tip material Much harder, no tip deterioration such as bending, blunting or mushrooming Softer, less resistance to tip bending
Ease of mass production Parallel fabrication using semiconductor fabtiction technologies One at a time in a machine shop
Machining tolerances/feature size In micrometers (µm), 25µm =0.001" In thousandths of an inch
Ease of complex feature fabrication All features (large or small) made at once Each feature individually machined
Surface friction sliding against other materials Lower, leading to reduced wear and improved repeatability Higher, requires hand polishing
Weight of pins Si pins weigh 0.5% of steel pins; less tip wear Heavy pins damage tips
Chemical resistance Excellent Good
Methods known to chemically modify surface Extensive surface chemistry of SiO2 known Less well developed

The silicon pins are fabricated by a plasma etching technique known as DRIE (Deep Reactive Ion Etching; see our web page on silicon microfabrication). Employing the so-called "Bosch" process, narrow trenches can be cut into silicon with aspect ratios as high as 1:20 or even 1:30 with nearly vertical sidewall slopes. Using this technique, many pins are simultaneously cut from a double side polished 100mm or 150mm silicon wafers that are either 200µm or 300µm thick. The two large surfaces of the flat silicon pin shaft (200µm thick by 1000µm wide), which are as flat as the extremely flat polished wafers surfaces, provides most of the surface area that contacts the collimators (vide infra).

Please see the ordering page for various pin sizes and styles available.

Fig. 7 A photograph of micromachined silicon pins on a 100mm (4") silicon wafer

The Printhead and Micromachined Collimators Go To Top

In this section, a description of the printhead, how it functions, how the print tip pressure is controlled and how the pins are collimated are covered.

In order to print a spot of sufficient quality, in direct analogy to stamping a pattern with an ink coated rubber stamp, the print tip pressure must be controlled to optimize quality. Too little pressure and the printed deposit could be misshapen or too light, but with too much pressure, the spot can enlarge. In addition to the proper pressure, it is also obvious that high quality printing dictates the pins be very highly collimated and be allowed to move in the z direction (perpendicular to the plane of the substrate) to provide the requisite ideal printing pressure. However there cannot be any motion at all in the x and y directions - the classic collimation problem.

The collimators in the printhead for the Silicon Microarray™ technology are micromachined for maximum precision and the rectangular shaft is fabrciated to have only 5µ of clearance on each of the four sides of the collimating holes. Tolerances of this magnitude are extremely difficult to achieve by traditional machine shop fabrication techniques. Key to the functioning of this high precision collimator are the flatness and straightness of the pins shaft, the accuracy of the cut forming the collimation hole, the hardness of the SiO2 pin and collimator surface and, importantly, the collimator and pin are made of the same material and therefore the pin and the collimator cannot scratch or gouge each other. This latter fact is also important in that the silicon pins can be used to print in a cold room as the collimator and pin expand and contract at the same rate thereby avoiding any seizure of the pins in the printhead upon cooling or warming.

Instead of the single tip pressure available from the currently used metal pin printing protocols (i.e. the weight of the pin), the silicon pins in the printhead are held in place by an elastomeric foam which exerts a controllable linear force at moderate z deflections of 0.05-0.30mm (Fig. 8).

Fig. 8 Tip pressure vs z deflection data for four foams with different stiffness

It is clear that in analogy to any type of contact printing, such as printing press, an ink stamp or the currently used steel pins, that there is an optimum printing pressure which is unlikely to necessarily correspond to the weight of a printing pin. By judicious choice of the "stiffness" and thickness of the elastomeric foam, and the amount of z deflection, a wide range of tip pressures are obtainable. Since the elastomeric foam exerts force to return the pins to their original rest position after deflection, users will never again experience a pin that sticks in the printhead and fails to fall back to its original position on the subsequent print cycle.
The very accurate collimation to print spots on a very fine pitch is again provided by silicon micromachining. As shown in Fig. 9, the collimator is wet etched on the top side to facilitate loading of the pin and the bottom side is shaped by DRIE to provide the 5µ tolerances required between the pin shaft and the collimator.

Fig. 9 Cross sectional view of the holes in the collimation plates and a silicon pin


Data showing the lack of prespotting phenomenon Go To Top

Fig. 10 shows spots of cy3 labeled random 9-mers in 3X SSC printed onto Superamine slides at 60-65% RH. We obtained 625 spots per dip, with a spot size variation as shown in Fig. 11 which displays a %CV of only 5.4% with no prespotting at all.


Fig. 10 Microarrays of Cy3 labeled 9-mers in 3x SSC printed at PSTI using 75X75Ám silicon pins spaced on 4.5mm centers with a spot spacing of 170Ám (above). The above image shows all the spots (including prespotting) printed from a single uptake volume of 100nL. Arrays printed with a spot spacing of 145Ám (below) using 75x75Ám tips. Please click on the images to see an enlarged view of the arrays.

Fig. 11 Spot size variation of all the spots printed from a single uptake volume (including prespotting) at RH 65%.
Total spots obtained per dip: 625
Avg spot dia.: 97µ
CV: 5.4%
Max. spot dia: 110µ

Min. spot dia: 90µ

Technical Data on Printing Performance Go To Top

In this section, the printing behavior of the pins is illustrated including how the 3-D sculpting of the printing tip has essentially eliminated the prespotting phenomena. Features such as spot morphology, number of spots per dip, volume deposited as a function of tip pressure, humidity and the spot uniformity are discussed. In Fig. 10, spots of Cy3 labeled random 9-mers in 3X SSC printed with 75x75 um tips are shown. Note the very high uniformity of the spots and the conspicuous absence of the "donuts" so often seen when the printed spots dry out.

With representative pin dimensions, such as 100µ x 100µ tips, a ~100nL reservoir and a 15µ metering channel width at the tip, the pin will deliver approximately 400 spots per dip at a relative humidity level of 65%. Note that this is ~10% of the uptake of typical metal pins. The silicon pins can print nearly 100% of the solution it imbibes, and since the amount taken up into the pin is relatively small, the waste of precious DNA solution is substantially abrogated. However, it should be kept in mind that this small uptake is more susceptible to evaporation than the very large amounts of liquid taken up into the metal pins. In addition to wasting DNA, poorly controlled humidity is extremely deleterious to the print quality primarily due to the fact that the solution concentration and viscosity would change rapidly upon evaporation. As shown in Fig. 12, which show two identical print runs except that the humidity was 35% and 65% RH, the spots printed at the higher relative humidity are more numerous and are of obviously of much higher quality.

Fig. 12 Arrays printed with silicon pins at two different humidity levels 35% and 65% RH

In a first for microcontact printing, a tip has been designed and built that has virtually eliminated the prespotting phenomena. The prespotting phenomena refers to those effects associated with the deposition of much larger spots at the beginning of print run (right after dipping into the source well), presumably due to the printing solution sheeting off of the outside surface of the pin instead of issuing from the print tip and reservoir/channel itself (Fig. 13). The elimination of the prespotting can be easily understood with the aid of Fig. 13 and the Quicktime® movies available for download at In the thinned region of the print tip, the tip is machined to provide a 100µ step that is perpendicular to the plane of the pin shaft.

The attractive forces between the solution and the surface, when a surface is well wetted as is the case here with the aqueous DNA printing solution on glass, are perpendicular to the surface (Fig. 13). As can be seen in the above mentioned movies, when the pin is removed from the source plate and the printing fluid begins to sheet down the external surface of the pin shaft, it is retained by the step and does not proceed to the tip and onto the printing surface. In fact, the movies clearly show that while the pin is printing from the tip, the fluid on the shaft is actually traveling up the shaft away form the tip and is attracted into the step and reservoir and never reaches the print surface. In other words, only fluid passing through the metering channel connecting the reservoir and print tip is deposited onto the print surface.

Fig. 13 Schematic representation of the printing solution sticking to the surface of a non thinned pin and a thinned pin

Table 2 summarizes the physical parameters and spot specifications for three different pin tip sizes

Table 2 Statistical analysis of arrays printed with Si Pins
(Arrays are printed on one slide in test print mode)
Tip Size
100 x 100µm
Tip Size
75 x 75µm
Tip Size
50 x 50µm
Average spot diameter
% CV
Total number of spots per one dip
Volumetric uptake
~ 0.1µL


Other Applications Go To Top

In addition to the spotting of DNA microarrays, a wide variety of other materials have been printed, such as:

    • Many types of proteins
    • Glycoproteins and glycolipids
    • Lipids (using hydrophobic pins)
    • Glues and adhesives
    • Solder
Since it is easy to chemically modify the surface of the silicon pins, many materials can be imbibed and released from the pins.

Please contact us for additional information.





Microarray pin, microarray pin, microarray spotting pin, microarray spotting pins

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