Alabama A&M University

School of Engineering and Technology

Department of Mechanical Engineering


ME 470: Senior Design


Automated Washing Process for Microarray Plates


Submitted by:
Jose Long
EzbanMorissette
Darneshia Williams
Cameron Alexander (Team Leader)


Date Submitted: March 25, 2014



Instructor:
Dr. Mohamed Seif
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Automated Washing Process for Microarray Plates

Abstract

The purpose of the following research is to build an automated system that will be used in
facilitating the washing process of microarray plates. The current process of manually washing
microarray plates, developed for the immobilization of DNA molecules, can become a tedious and
time-consuming task. The critical issue is that with the current automated methods plates can only
process a small number of plates. This is a very costly and time consuming problem considering
there are anywhere from 100-300 plates processed in a week. The project will concentrate on
developing several conceptual designs with the plan to implement a program in order to automate
the process. The process will concentrate on using LabView, a visual programming language. We
chose to use this simply for the fact it is what our corporate sponsor uses and it is now an industry
standard. After a comparison of several design concepts, one design was deemed feasible and
suitable for the needed applications, pending further investigation. This is helpful because a
starting point has been provided in regards to how this device will be constructed and a building
block is set in place for future research.


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Table of Contents
Cover Page..i
Table of Contents..ii
Abstract ............................................................................................................................................. 2
I. Introduction ................................................................................................................................... 4
II. Project Description ....................................................................................................................... 5
II.a Design Constraints and Design Variables..7
III. Project Design and Analysis ....................................................................................................... 7
III.a Design Analysis of the Racking System ............................................................................ 8
IIII.b Design Analysis of the Agitator System.............................................................................. 9
III.c Design Analysis of Automation Programming ..................................................................... 9
IV. Results and Discussion ............................................................................................................. 10
V. Conclusion ................................................................................................................................. 10
Acknowledgements ........................................................................................................................ 11


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I. Introduction

The microarray plate we are using to develop an automated washing process is called a
Nexterion Plate E MTP 96 (Figure 1). It was developed for the immobilization of DNA
molecules onto a coated microplate sized glass allowing high sample throughout with
reproducibility and higher sensitivity. The plate is manufactured from high quality glass and laser
cutting technology is used to obtain defect and particle free plate surfaces. They are cleaned and
coated under a strict process to control all the fabrication step endures coating uniformity and
reproducibility from batch to batch.

Currently, the process for washing and drying microarray plates to remove unboundmolecules are
mostly done manually. Because of the time and expenses involved, this process canbecome
problematic to a company. The objective of this project is to automate the process in order to
improve the time and cost efficiency.

The current process is as follows:
1. Arrays are printed and DNA is immobilized being incubated at room temperature for 30
minutes
2. Plates put through following washing process:
a. Rinsing plates once for 5 minutes in
Triton X-100 solution at room
temperature .
b. Rinsing plates twice for 2 minutes in
Hydrochloric acid solution at room temperature .
c. Rinsing once, for 10 min in Potassium chloride solution at room temperature.
Figure 1
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d. Rinsing once, for 1 minute in de-ionized water at room temperature.
e. Rinsing once, for 15 min in ethanolamine solution at room temperature.
f. Rinsing a minimum of four times for 1 minute in de-ionized water at room
temperature.
g. Drying the plates in an oil-free air or nitrogen stream to avoid any water stains on
the plate surface.
3. Entire process conducted by hand, using beakers and an platform shaker.

The Triton X-100 contains 100 micro liters Triton X-100 and 100 milliliters de-ionized
water warmed to 37 C (before adding Triton X-100). The Hydrochloric acid solution
contains10 micro liters in Hydrochloric acid and 100 milliliters de-ionized water at room
temperature. The Potassium chloride solution contains 0.58 grams Potassium chloride and 100
milliliters de-ionized water at room temperature. The ethanolamine solution contains 310 micro
liters ethanolamine: 100 milliliters blocking solution (warmed to 50 C).
II. Project Description
The main objective of this project is to build an automated system that will be used to wash DNA
covered microarray plates. This automated system will include several sub-systems, including, but
not limited to:
1. Racking System
2. The Agitator System
3. The Automation Programming
The process in which we use must first accommodate the Nexterion Plate (110 x 74 x 1.0
mm ( 0.1 thickness and weight: 18 g ( 0.5 g) plate type Schott) and 25 x 75 mm slides as well.
Next we have to incorporate a minimum of four wash buffers at appropriate temperatures. It
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mustalert user when going into block wash then pause the process and require user intervention to
continue. At this step in the process addition of ethanolamine will be required. The materials
cannot interact with reagents. Lastly, it must safely & effectively dry plates. The process will be
ergonomically friendly with weight of handling no more than 20lbs, and about waist high (for a
52 female).
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II.a Design Constraints and Design Variables
The following table summarizes the relationship between the overall constraints and the design
variables:

III. Analysis of Design Constraints

The project will contain three sub-systems. The incorporated systems are that of a racking system,
an agitator system, and an automation sequence. Each system will be essential to certain aspects

The Constraint


The Associated Design Variables
Materials cannot interact with reagents.

Select appropriate material that will not react
to buffers.
Weight of handling no more than 20lbs.

Select appropriate material(s) that will allow
device to be over 20lbs.
Bench top device useable by a for a 52
female.
Design bench top device at appropriate height.
Incorporate a minimum of four wash buffers at
appropriate temperatures.
Use previously designed food grade soda
canisters for wash buffers.
Accommodate the plates dimensions (110 x
74 x 1.0 mm), and thickness ( 0.1 thickness).
Design a rack that will give the plates a safe
fit.
The plates weight can range from 18 g ( 0.5
g) to 21 g ( 0.5 g), depending on supplier
used.
Design a rack with the appropriate material
that can withstand the weight of the plates.
The agitator to move in a to-and-fro motion
for washing or unidirectional spinning for
drying.
Use a pulley system to control the agitator.

Alert user when going into block wash.

Create program using LabView to alert user
after wash sequences.
Pause the process and require user
intervention to continue.

Create program using LabView to run vs.
stop/pause, and abort sequence to safely
terminate the procedure by draining all liquids
and drying plates/slides.

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of the automated washing process and therefore, will have to undergo future analysis in order to
meet design constraints set by MicroArrays, Inc. Further design analysis of these systems are
described in the following sections.
III.a Design Analysis of the Racking System

Over the course of the fall semester, three conceptual designs were presented. The first
was inspired by a conventional washing machine; it included circular racks that could be stacked
in order to maximize washer capacity (Figure 2). A second design was inspired by a dish washer
and included a square rack that would slide horizontally into the device (Figure 3). A third and
final concept was inspired by a shoe box, the bottom half included the shaker table where the
plates would be sterilized (Figure 4a) and the top portion is used as the drying mechanism (Figure
4b).
Upon further deliberation, it was decided that the design that was inspired by a
conventional washing machine would be best for our applications. A further description of this
design includes an agitator to gently wash the microarray plates and possible drying capabilities.
With this design we have the option on sling drying with the agitator or using a gas such as
nitrogen to dry the plates.
The purpose of using the agitator is to gently wash the plates using a specially designed set
of racks that will lock into the agitator. The agitator will encompass a slow spin cycle once the
plates are submerged into each buffer. After the device purges each buffer into the system, the
agitator will slowly spin, washing the plates in a manner that will clean each plate while going as
a speed that will not damage them.






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Further analysis is scheduled for the research of various concepts surrounding our chosen
design. Planned analysis includes a finite element analysis to test maximum durability and
performance and to ensure the agitator concept does not damage any of the microarray plates.
With the washing machine concept we have the option on sling drying with the agitator or using a
gas such as nitrogen to dry the plates. An investigation into what substances will be used in order
to dry the microarray plates will be conducted. Another factor to consider will be what material
would be most efficient for the device itself, something sturdy but not too heavy and still within
design constraints.
IIII.b Design Analysis of the Agitator System

The design chosen to control the speed of the washing machine system design is a pulley
agitation system. The pulley agitation system will increase and decrease the speed of the rack
according to what stage of the cleaning process the slides are in. The system will be capable of
moving in a to-and-fro motion for washing and will move unidirectional for sling drying. The
prototype system we plan on using is still in the works, as we seek guidance from our professors.
III.c Design Analysis of Automation Programming

For our design we will implement LabView since it is the program our corporate sponsors
Microarrays use. The program created will be programmable to process using alternate times
and/or iterations, log temperature & humidity readings during the processing event(s), LED
indicator running vs. stopped/paused, and abort sequence to safely terminate the procedure by
draining all liquids and drying plates/slides.
1. Program#1: Purge/Prime sequences if necessary
2. Program#2: Full processing event
3. Program#3: Partial processing event
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IV. Results and Discussion

Thus far, our project has been following the timeline we set in order last semester. We researched
current process and brainstorm design considerations, conducted trade studies on project
alternatives, did conceptual development of project, and drafted CAD designs of the project with
two alternatives. As of late, we came upon an issue. When trying to test the drafted CAD model
with ANSYS we discovered our schools license was expired. Hopefully this will be resolved in a
very timely manner, but it is out of our control.
V. Conclusion

After a comparison of several design concepts, one design was deemed feasible and suitable for
the needed applications. What material would be most efficient for the device itself, and the rack
inside the device is still to be determined. We will work on the design details and analysis of the
rack system. Moreover, the agitator system will be designed and analyzed. In the meantime, we
will be conducting trade studies on the automation process that will be best implemented in our
system.



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Acknowledgements

Jerry C. Collins, Ph.D.
Fellow, BMES; Chair, Ethics Committee.
Fellow, AIMBE; CURM Committee.
Board of Directors, AEMB.
Adjunct Faculty, Alabama A & M University.
Adjunct Faculty, Lipscomb University.

Maria del Carmen Brown
Micro Arrays, Operations Manager.

Joel Peek, Ph.D.
Micro Arrays, CEO