Hologic Diagenode Bioruptor Pico User manual

Version 2 I11.2022
Bioruptor® Pico
Sonication System

Guarantee
Limited one year global warranty
Diagenode guarantees all products from any manufacturing defects as we rigorously test all
products to meet strict quality standards. Diagenode warrants that all standard components of
its instruments will be free of defects in materials and workmanship for a period of one (1) year
from the date that the warranty period begins, unless the original quotation or accompanying
documentation states a different warranty period. All warranty periods begin on the date of delivery
and apply only to the rst purchaser of the product. If a manufacturing defect arises and a valid
claim is received within the warranty period, Diagenode, at its discretion, will repair or replace the
product in accordance with the warranty terms and conditions stated herein. In case of repair or
replacement of a product under warranty, Diagenode will cover the expenses to return the repaired
or replacement product.
This warranty covers only manufacturing defects and does not cover any damage caused by misuse,
lack of compliance to recommendations stated in the manual, neglect, accidents, abrasion, or
exposure to extreme temperatures, chemical solvents, or acids. We strongly recommend that
maintenance or repairs of Diagenode’s products are performed by our approved Diagenode service
center. Improper or incorrectly performed maintenance or repairs will void the warranty.
Technical assistance & ordering information
For the rest of the world, please contact Diagenode s.a.
Diagenode s.a. BELGIUM | EUROPE
LIEGE SCIENCE PARK
Rue Bois Saint-Jean, 3
4102 Seraing (Ougrée) - Belgium
Tel: [phone]
Fax: [phone]
[e-mail]
[e-mail]
Diagenode LLC. USA | NORTH AMERICA
400 Morris Avenue, Suite #101
Denville, NJ 07834 - USA
Tel: [phone]
Fax: [phone]
[e-mail]
[e-mail]

3
Contents
BIORUPTOR® PICO
Critical steps for maintenanceand efcient shearing 7
Introduction 8
Technical specications 9
Equipment installation 13
Installation 14
Tube holders & tubes 17
BIORUPTOR® COOLER
Safety 20
Design and functions 23
Operation 33
Maintenance 35
Disposal 40
Technical data 41

4BIORUPTOR®PICO MANUAL

BIORUPTOR®PICO

7
Critical steps for maintenance
and efcient shearing
General warnings
• DO NOT turn on the instrument without water.
• DO NOT tilt the Bioruptor® Pico. To change the water, use either the plastic pump or a beaker (be careful
not to scratch the bottom of the sonicaton bath).
Sonication bath levels
• The sonication bath must be lled with distilled water to the ll line. Fill line replacement stickers can
be obtained by contacting Diagenode.
• At least once per month.
Sonication bath temperature
• Optimal temperature for sonication is 4°C. Sample temperature should not exceed 8°C.
• The Bioruptor® Cooler (Cat. No. B02010010, B02010011, B02010012) has to be used to guarantee the
automatic temperature control of the sonication bath during the entire sonication process.
Validated tubes for the Bioruptor®Pico
• DNA shearing: 0.1 ml (Cat.No. C30010015), 0.2 ml (Cat.No. C30010020) and 0.65 ml (New Cat. No.
C30010011; Old Cat. No. WA-005-0500) Bioruptor® Microtubes for DNA shearing.
• Chromatin shearing: 0.1 ml (Cat. No. C30010015), 0.2 ml (Cat.No. C30010020) and 1.5 ml (Cat.No.
C30010016) Bioruptor® Microtubes and 15 ml (Cat.No. C01020031) Bioruptor®Tubes & sonication beads.
Fitting 0.1, 0.65, 1.5, or 15 ml tubes in the tube holder
• Place the tubes in the corresponding tube holder. Never leave empty spaces in the tube holder. Fill the
empty spaces with tubes containing the same volume of water. Screw the lid on the tube holder without
over-tightening it.
• Carefully place the tube holder on the holding plate.
• During sonication, samples must remain at the bottom of the tube. If needed, briey centrifuge samples
during sonication after pausing the run.

8BIORUPTOR®PICO MANUAL
Introduction
Diagenode’s Bioruptor® Pico uses a gentle method of sonication to retain the integrity of
DNA and/or biological complexes, including chromatin, protein-protein binding, protein-
DNA complexes and other biochemical and biological assay systems. The Bioruptor® Pico
sonication system uses a sonication bath to generate indirect sonication waves, which
emanate from an ultrasound element below the water tank. Because the system is gentler
than other sonicators, the Bioruptor® Pico produces better and more consistent results than
with harsher sonication methods. Up to 16 closed tubes can be sonicated in parallel and the
continuous rotation of tubes allows even distribution of the energy for efcient sonication.
The Bioruptor® Pico enables automation of sonication, guaranteeing higher reproducibility
of results.
The effect of ultrasound on biological sample
The Bioruptor® Pico sonication system uses
ultrasound to create focused mechanical stress to
shear chromatin or DNA. Ultrasound waves pass
through the sample expanding and contracting the
liquid. During expansion, negative pressures pull
the molecules away from one another to form a
cavity or bubble. This process is called cavitation.
The bubble continues to absorb energy until it can
no longer sustain itself and implodes. This produces intense focused shearing forces, that
disperse and break biomolecules. The fragmentation of chromatin or DNA takes place as a
consequence of this mechanical stress or shear.
With the Bioruptor® Pico, the entire volume of water present in the sonication bath is exposed
to ultrasound, allowing all the samples to be efciently sonicated in parallel (Figure 1).
Use of Bioruptor®Pico by pregnant women
Exposure to 20-60 kHz sound waves has not been shown to be harmful to human health.
However, we would recommend avoiding unnecessary exposure. Diagenode recommends
that pregnant women should not be exposed to 20-60 kHz wave lengths for a long period of
time.

9
Bioruptor® Pico technical specications
BIORUPTOR®PICO
Power supply 100-230V, 50/60Hz, 2.1A (EU) / 4.2A (US)
Ultrasonic wave frequency 20-60 kHz
Ultrasonic wave output power 25-210 W
Sonication unit dimensions 350 (W) x 245 (D) x 280 (H) mm
Sonication bath volume 750 ml
Timer Digital
Possibility to control water ow via
connector kit for Bioruptor® Cooler Yes
Tube holder Available for 0.1, 0.65, 1.5 or 15 ml tubes
Total weight 7,90 kg
Number of samples to be processed
simultaneously
0.1 ml tubes – 12 samples
0.2 ml tubes – 16 samples
0.65 ml tubes – 12 samples
1.5 ml tubes – 6 samples
15 ml tubes – 6 samples

10 BIORUPTOR®PICO MANUAL
Getting to know your Bioruptor® Pico system
Bioruptor®Pico components overview
Bioruptor®Cooler
Power cable (EU) Power cable (US)
Sonication unit
Sonication bath
Motorized lid
Tube holder

11
Sonication bath
The sonication bath is a critical component of the instrument. The generators below the
tank produce ultrasonic waves which are then transferred through water. The sonication
bath requires special handling and care as described below.
Handling
The sonication unit must remain upright at all times, especially when moved. Tilting the
sonication unit or handling roughly may damage the ultrasound emitter component,
resulting in a substantial drop in sonication efciency. If transportation of the apparatus is
required after initial set-up, it is imperative to keep the sonication unit at a right angle to the
ground during the transport at all times.
Water level and quality
The level of the water has been optimized and should always reach the red line (sticker on
the wall of the tank). Distilled water should be used to ll the tank. Replacement stickers
can be obtained from Diagenode.
Water temperature
The water in the sonication bath must be kept at 4°C. Ultrasonic waves produced by the
Bioruptor® Pico generate heat. Drop off in sonication efciency will occur above 8°C. To
ensure preservation of the samples and to prevent damage to the instrument, it is necessary
to start the sonication process with cold water and to keep it at 4°C during the sonication
process.
Automatic temperature control
The Bioruptor® Cooler (Cat. No. B02010010, B02010011, B02010012) to guarantee the
automatic temperature control of the sonication bath during the entire sonication process
(Figure 2). The cooling system features two pumps and produces a regular water ow to

12 BIORUPTOR®PICO MANUAL
maintain a constant water level in the tank. The integrated regulating valve ensures that
water will only be replaced during the off cycle to avoid any interference between the water
ow and the sonication process.
Motorized lid
The motorized lid, along with the gear plate accessory, keeps the sample
tubes in constant rotation and ensures optimal position in the sonication
bath during sonication. When in motion, do not hamper the rotation of the
white gear plate. Avoid the immersion of the motor into the water. Do not
heat the white plastic as it will warp.
Tube holders
Several sizes of tubes can be used with the Bioruptor® Pico.
The minimum and maximum sample volume to be used with each tube is given in the table
below.
TUBE SIZE MINIMUM MAXIMUM
0.1 ml 5 or 10 µl 50 µl
0.2 ml 20 µl 100 µl
0.65 ml 100 µl 100 µl
1.5 ml 100 µl 300 µl
15 ml 500 µl 2 ml
Bioruptor® Cooler Sonication unit

13
Equipment installation
The following pages contain information on installing your particular Bioruptor® Pico model.
This equipment must only be installed by personnel after reading this section. Consider
all hazards even though no particular hazards have been identied during installation.
Before starting installation work, turn the main switch off and secure the unit against being
re-energized. No special tools are required. One square meter is needed to set-up the
Bioruptor® Pico.
Devices are designed to be safe under the following conditions:
Installation overview
• Indoor use
• Altitude up to 2,000 meters
• Operating external temperature 15°C to 25°C
(do not install the Bioruptor in a cold room)
• Maximum relative humidity 80%
• Transient overvoltage typically present on the
MAINS supply
• Degree of protection: IP20
• Power plug must be grounded
• POLLUTION DEGREE 2 (Normally only
non-conductive pollution occurs. However,
occasionally a temporary conductivity caused
by condensation is expected)
• Never install this equipment in a place where
environmental conditions and warnings
mentioned above are infringed
Power cord
Distilled water
Digital timer
Motorized lid
Tube holder
Valve connection cable for Bioruptor® Cooler
Tubing
BIORUPTOR® PICO
BIORUPTOR® COOLER
Fig. Schematic installation overview of the Bioruptor® Pico System in combination with the Bioruptor® Cooler.

14 BIORUPTOR®PICO MANUAL
Installing the Bioruptor® Pico system
Before starting the installation, turn the main switches off and make sure that the unit is not
plugged into an electrical outlet.
1. Open the boxes and unpack all components
2. Place the Bioruptor®on a bench
• Important Note: Please make sure that the Bioruptor® Pico is always placed on a level surface.
3. Place the Bioruptor® Cooler on the bench or below the Bioruptor®
4. Connect the Bioruptor® Pico to the Bioruptor® Cooler with the cooling long red and blue
isolated tubing by inserting them into the connectors as shown in the image. Respect
the red and blue color codes. (Optional: Cut the length you need for the output and input
ow. Make sure there is enough slack.)
5. Plug the Bioruptor® cable into the outlet on the back side of the Single Cycle Valve Box
and on the Bioruptor® Pico.
6. Plug the power cord into the outlet and switch on the power switch on the back side of
the sonication unit.
7. Plug the power cord into the outlet of the Bioruptor® Cooler.
8. Press main switch on the front side of the Bioruptor®
9. Fill the tank of the Bioruptor® Cooler with 3.5 liter and the sonication bath of the
Bioruptor® up to the marh (700 or 730 ml; depending on the model) with distilled or
deionized water.
11. Set the temperature to 4°C.
12. Detailed operating instructions for the Bioruptor® Cooler are available at page XXX.
Bioruptor® CoolerBioruptor® Pico

15
Controlling the sonication
1
Digital Timer:
Allows the user to easily program the sonication of samples (ON/OFF pulse time &
total time). See use of digital timer in next section below.
2Start Button:
Begins sonication
3Stop Button:
Cancels sonication
Switch on power switch (back side of sonication unit)
1
2
3

16 BIORUPTOR®PICO MANUAL
Digital timer
CYCLE NUMBER, TIME ON and TIME OFF are the
parameters controlling sonication. For changing these
parameters press the OK button. First the TIME ON screen
appears with the ashing number. This parameter can
be modied with the up ( ) and down button ( ). Please
respect the range for each value. Press again the OK button
to conrm the setting. To select TIME OFF and Cycle Num
proceed the same way.
Bioruptor® Pico will sonicate as shown.
Once parameters are set press START (Figure 2).
The information: Close the lid to start the run indicates that
the sonication only starts when the acrylic glass cover is
closed. The cover also prevents from any noise disturbance.
Once the run started the RUNNING screen appears. As
shown in Figure 4 the RUNNING screen indicates the
elapsed time ON, time OFF and the number of cycles.
If the acrylic glass cover will be opened during a run the
sonication will automatically pause. Once the cover is again
closed the machine continues with the sonication process.
As shown in Figure 5, the BREAK CYCLE screen shows
the information when the run stopped. In the example the
machine stopped during the second sonication cycle, after
30 sec of TIME ON and 8 sec of TIME OFF.
If the sonication process worked properly (without any
error messages) the RUN OVER screen appears (Figure 6).
Press ESC to get back to the Main screen to start another
sonication round.
Time ON 30sec
Time OFF 30sec
Cycle Num 10
OK = change params
Figure 1. Main Screen
ON
OFF
TIME
ON
TIME
OFF
CYCLE
START
Cycle number reached
(4 cycles in this example)
Time ON 30sec
Time OFF 30sec
Cycle Num 10
Press START to go
Figure 2. Main Screen
Close the lid to
start the run
OR
Press STOP
Figure 3. Close Lid Screen
ON 07s
OFF 00s 01/10
RUNNING
Figure 4. RUNNING Screen
BREAK CYCLE: 02
OFF: 08
Close the Cover to
continue or STOP
ON: 30
Figure 5. BREAK CYCLE Screen
Press ESC to go
back to main menu
RUN OVER
Figure 6. RUN OVER Screen
IMPORTANT NOTE: Machine has to rest for 20
minutes before starting the next sonication run.

17
Tube holders & tubes
For chromatin and DNA shearing we highly recommend to use the below mentioned tube
holders and the corresponding tubes.
To guarantee homogeneity of chromatin or DNA shearing, the tube holders should always
be completely lled with tubes. Never leave empty spaces in the tube holder. Fill the empty
spaces with tubes containing the same volume of distilled water.
1.5 ml tube holder for
Bioruptor®Pico
(Cat. No. B01200040)
15 ml sonication accessories
for Bioruptor
®
Pico
(Cat. No. B01200016 )
15 ml Bioruptor®Tubes
(recommended for Tissue
disruption for protein
extraction)
(Cat. No. C30010017)
0.65 ml tube holder for
Bioruptor®Pico
(Cat. No. B01200043)
0.1 ml tube holder & tube
adaptor for Bioruptor®Pico
(Cat. No. B01200041)
0.65 ml Bioruptor®
Microtubes (recommended
for chromatin & DNA
shearing)
(New Cat. No. C30010011;
Old Cat. No. WA-005-0500)
1.5 ml Bioruptor®
Microtubes (recommended
for chromatin, not
recommended for DNA
shearing)
(Cat. No. C30010016)
0.1 ml Bioruptor®
Microtubes (recommended
for chromatin & DNA
shearing)
(Cat. No. C30010015)
15 ml Bioruptor®Tubes
& sonication beads
(recommended
for chromatin, not
recommended for DNA
shearing)
(Cat. No. C01020031)

BIORUPTOR®COOLER

20 BIORUPTOR®PICO MANUAL
Safety
General safety instructions
• The equipment must only be operated for the intended use under the conditions stated in this operating
manual. Any other type of operation is considered to be not-intended use and can impair the protection
provided by the device.
• The operating manual is part of the device. The information in this operating manual must therefore be
available in close vicinity to the device. Also store this copy of the operating manual carefully.
Any hazards (electrical shock, re, contact with movable parts, etc.) caused by the use of
the device must be eliminated as much as possible by the design in accordance with the
appropriate standards. Residual hazards are reduced using any of the following measures:
• If relevant, there are safety devices for the device. These devices are essential for the safety of the
device. Their functionality must be ensured with appropriate maintenance activities.
• If relevant, there are warning symbols on the device. These symbols must always be observed.
• There are safety instructions in this operating manual. These instructions must always be observed.
• There are additional specic requirements for the personnel and for the personal protective equipment.
Intended use
The present device is exclusively permitted to be used for tempering and delivering non-
ammable heat transfer liquids to the Bioruptor®.
Non-intended use
The following applications are considered to be not-intended:
• in potentially explosive areas
• for tempering foodstuffs
• with a glass reactor without overpressure protection
• medical use.
Foreseeable misuse
Misuse of the device must always be prevented.
Among other things, the following uses are considered to be fore- seeable misuse:
• Operation of the device without heat transfer liquid
• Incorrect connection of tubes