User:Pranav Rathi/Notebook/OT/2012/05/21/pH-rocker for DNA-sequencing experiments: Difference between revisions
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<div align="center"><html><iframe src="http://www.slideshare.net/pranavrathi/slideshelf" width="615px" height="470px" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:none;" allowfullscreen webkitallowfullscreen mozallowfullscreen></iframe></html></div> | |||
==Introduction== | ==Introduction== | ||
It was seen during DNA-sequencing experiments; sensor moving in circles give consistent results in comparison to sensor kept stable. pH-sensor is designed to simulate the hand movement of stirring in circle. It uses very simple mechanical-planetary gear motor and an ordinary variable power supply. All the components can be easily found in any optics/physics lab. | |||
==Motivation== | ==Motivation== | ||
During DNA Sequencing reactions based on quantification of pH measurements for analyzing sequencing reactions, various factors made it difficult to get consistent data. Few of them were changes in pH in stationary reaction mixture and continuously reaction mixture and speed of stirring (done manually). To overcome this, pH rocker was designed to help keep a steady speed for sensor and also to keep a continuous stirring and get a consistent data. | |||
To analyze the difference there was (between starting the reaction and 1 hour later). | |||
Control – difference of .18 pH | |||
Sample -.94 pH | |||
==Design and Construction== | ==Design and Construction== | ||
Design and construction of the rocker is easy. It is one of the easiest things I made. I have completed all the work within 5 hours. | Design and construction of the rocker is easy. It is one of the easiest things I made. I have completed all the work within 5 hours. | ||
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===Design=== | ===Design=== | ||
The design is very simple. It is required for good stable results that pH sensor is moved in circular motion in the well as what used to be done by hand. So basically I am simulating the circular motion of hand by using a high-torque motor. The sensor wire is pretty stiff so high-torque motor is useful to get smooth circular motion. | |||
The motion-speed of the sensor inside the well is the most important factor. If the sensor is moving too fast than it can mix air into the buffer which can change the pH value. So it is very important to figure out the right speed before deciding the motor and power supply. In this case 15 RPM is a good speed to start. The rocker takes 15 revolutions in 1 minute at 3V. The maximum is 60 RMP at 12V which is more than enough and may be not good for the experiments. The power supply can go from 3 to 12V. | |||
Another important factor is the range of sensor movement which depends on the radius of the hole on which sensor is attached. I have 3 options for that; 3 holes gives range from 1.5cm to 3.5 cm. The most appropriate is 1.5 and 2.5cm. The data is not too sensitive to it but for stability the inner holes are better. | |||
For 96 well plate it is important that the arm can be adjusted to cover the whole well plate; this is achieved by adjusting the angle, height and length of the arm by 90<sup>o</sup> clamp. The rocker can be used with any DC-variable power supply (I bought the power supply from Amazon for $15), which can also let choose different speeds. | |||
I designed the rocker such that most of the tools and hardware are available in my lab with least machining. | |||
===Construction=== | ===Construction=== | ||
For construction please follow the steps in the slide show. The construction is really easy; one of the easiest things i have ever made. | |||
====pH-rocker stand==== | |||
Arrange everything as shown in the slide 5. | |||
====Motor arm==== | |||
Find a disk or wheel (the size is important because it will decide the freedom of circular motion); I choose it to be 3 inches in diameter. I salvaged the disk from an AM/FM radio. Make it fit to the motor shaft. Make 3 4/40 holes from the edge or at some desired distance from the center (this distance will decide how much the sensor will move around the disk). In the well the motion of the sensor should not be too small or too big so I drill 3 holes a centimeter away from each other from the edge, so i can choose any range of motion in the well; slide 6. The holes will hold the rod. | |||
The rod will hold the wire holders. I use 2 wire holders back to back to hold the pH sensor wire. The top wire holder has 4/40 screw to hold it to the rod. I use rubber cushions to apply pressure on the wire holder so it does not move too freely; slide 6. | |||
Now arrange and mount everything like in slide 7 and 8. Your pH rocker is complete and ready for the test. | |||
==Demonstration== | ==Demonstration== | ||
{{#widget:YouTube|id=co6i7E2RtXU}} | |||
==Testimony== | ==Testimony== | ||
Latest revision as of 16:01, 1 February 2013
Introduction
It was seen during DNA-sequencing experiments; sensor moving in circles give consistent results in comparison to sensor kept stable. pH-sensor is designed to simulate the hand movement of stirring in circle. It uses very simple mechanical-planetary gear motor and an ordinary variable power supply. All the components can be easily found in any optics/physics lab.
Motivation
During DNA Sequencing reactions based on quantification of pH measurements for analyzing sequencing reactions, various factors made it difficult to get consistent data. Few of them were changes in pH in stationary reaction mixture and continuously reaction mixture and speed of stirring (done manually). To overcome this, pH rocker was designed to help keep a steady speed for sensor and also to keep a continuous stirring and get a consistent data.
To analyze the difference there was (between starting the reaction and 1 hour later). Control – difference of .18 pH Sample -.94 pH
Design and Construction
Design and construction of the rocker is easy. It is one of the easiest things I made. I have completed all the work within 5 hours.
Components
Most of the components were available in my lab. Some i bought. The slide show has all the parts with part number and company.
pH-rocker stand
- 1 X MB6 thorlabs brad board
- 2 X TR12-thorlabs posts
- 1 X PH4 post holder
- 1 X CL6-thorlabs clamp
- Some 1/4 inch screws
Motor arm
- 1 X PK22G21-Hennkwell 12V high-torque planetary gear motor
- 1 X CP0@T-thorlabs cage plate
- 1 X TR6-thorlabs post
- 1 X RA90-thorlabs post clamp
- 1 X black disk (salvaged from a radio)
- 1 X ER1-thorlabs 1 inch cage rod
- 2 plastic wire holders and 2 rubber cushions
- some 8/32 and 4/40 screws
Power supply
- Powerline variable DC-power supply from amazon.com
pH sensor
- PH37-SS Hach company pH sensor
Well plate
- 96 Well plate for DNA-sequencing
Design
The design is very simple. It is required for good stable results that pH sensor is moved in circular motion in the well as what used to be done by hand. So basically I am simulating the circular motion of hand by using a high-torque motor. The sensor wire is pretty stiff so high-torque motor is useful to get smooth circular motion.
The motion-speed of the sensor inside the well is the most important factor. If the sensor is moving too fast than it can mix air into the buffer which can change the pH value. So it is very important to figure out the right speed before deciding the motor and power supply. In this case 15 RPM is a good speed to start. The rocker takes 15 revolutions in 1 minute at 3V. The maximum is 60 RMP at 12V which is more than enough and may be not good for the experiments. The power supply can go from 3 to 12V.
Another important factor is the range of sensor movement which depends on the radius of the hole on which sensor is attached. I have 3 options for that; 3 holes gives range from 1.5cm to 3.5 cm. The most appropriate is 1.5 and 2.5cm. The data is not too sensitive to it but for stability the inner holes are better.
For 96 well plate it is important that the arm can be adjusted to cover the whole well plate; this is achieved by adjusting the angle, height and length of the arm by 90o clamp. The rocker can be used with any DC-variable power supply (I bought the power supply from Amazon for $15), which can also let choose different speeds.
I designed the rocker such that most of the tools and hardware are available in my lab with least machining.
Construction
For construction please follow the steps in the slide show. The construction is really easy; one of the easiest things i have ever made.
pH-rocker stand
Arrange everything as shown in the slide 5.
Motor arm
Find a disk or wheel (the size is important because it will decide the freedom of circular motion); I choose it to be 3 inches in diameter. I salvaged the disk from an AM/FM radio. Make it fit to the motor shaft. Make 3 4/40 holes from the edge or at some desired distance from the center (this distance will decide how much the sensor will move around the disk). In the well the motion of the sensor should not be too small or too big so I drill 3 holes a centimeter away from each other from the edge, so i can choose any range of motion in the well; slide 6. The holes will hold the rod.
The rod will hold the wire holders. I use 2 wire holders back to back to hold the pH sensor wire. The top wire holder has 4/40 screw to hold it to the rod. I use rubber cushions to apply pressure on the wire holder so it does not move too freely; slide 6.
Now arrange and mount everything like in slide 7 and 8. Your pH rocker is complete and ready for the test.
Demonstration
{{#widget:YouTube|id=co6i7E2RtXU}}
