Diffinity Genomics RapidTip2 Instruction Manual

USER HANDBOOK
User Notice:
For optimal purication results, sharply tap
the RapidTip2 package 2–3 times on a at
surface so that the particles drop to the
bottom of the tips.
Version B (March 2012)
For PCR Purication with
Polymerase Removal

Page 2 www.difnitygenomics.com
Table Of Contents
Kit Contents 3
Storage 3
Product Use Limitations 4
Product Warranty and Satisfaction Guarantee 4
Quality Control 5
Technical Assistance 5
Safety Information (Disposal) 5
Product Specifications 6
Introduction 7
Diffinity Technology Principle 8
Equipment to be Supplied by User 9
Guidelines — Pipetting with the RapidTip2 10
Pipetting Examples 11
RapidTip2 PCR Purification Protocols 12
Quantifying DNA Recovery 13
Troubleshooting Guide 14
Ordering Information 15

Difnity RapidTip2 Page 3
Kit Contents
Diffinity RapidTip2s can be used with universal or Rainin LTS
style pipettes. All kits come with a user handbook.
Cat Number Product Description Contents
RR050-008
RR050-008L*
Diffinity RapidTip2 for
PCR Purification with
Polymerase Removal
1 Pack of 8
RapidTip2s
RR050-048
RR050-048L*
Diffinity RapidTip2 for
PCR Purification with
Polymerase Removal
1 Box of 48
RapidTip2s
RR050-096
RR050-096L*
Diffinity RapidTip2 for
PCR Purification with
Polymerase Removal
1 Box of 96
RapidTip2s
* L — denotes Rainin LTS format pipette tips.
Storage
Diffinity RapidTip2s should be stored in low humidity at room
temperature (15–25 degrees Celsius). Under these conditions,
Diffinity RapidTip2s can be stored and used for up to 12
months without reduction in performance or quality. An
expiration date is on the label of the 48 and 96 tip boxes.

Page 4 www.difnitygenomics.com
Product Use Limitations
Diffinity RapidTip2s are intended for research use only. Diffinity
RapidTip2 is designed for purification of 50 μl PCR solutions
prior to dideoxy (BigDye) reaction for Sanger Sequencing,
restriction digestion, or T-A cloning. RapidTip2 is compatible
with most universal and Rainin LTS pipettors. RapidTip2 is not
compatible with detergents, mineral oil, or ready-to-load style
PCR master mixes that contain a density-increasing compound.
Product Warranty and Satisfaction Guarantee
Diffinity Genomics will guarantee the performance of Diffinity
RapidTip2s for the uses and performance as described in
our product literature. If the product fails to perform to your
satisfaction for any reason other than misuse, we will replace
the product free of charge or refund the purchase price —
whichever you choose. Diffinity Genomics maintains the right
to update or modify the product to enhance its performance. A
copy of our terms and conditions can be found on our web site.
If you have questions about the product or its performance,
please contact Diffinity Genomics customer service at
1-877-362-1812.

Difnity RapidTip2 Page 5
Quality Control
Each lot of Diffinity RapidTip2s is tested against predetermined
specifications to ensure consistent quality.
Technical Assistance
Call 1-877-362-1812 between 8am and 4pm Eastern Time
Monday through Friday or visit www.diffinitygenomics.com for
help with common questions.
Safety Information (Disposal)
Diffinity RapidTip2s may be disposed in regular lab trash. For
more information, please consult the material safety data sheet
(MSDS) available on request by calling Customer Service at
1-877-362-1812.

Page 6 www.difnitygenomics.com
Product Specications
Capacity: PCR Sample Size 50 ±5 microliters
dsDNA Recovery up to 90%
(100bp to 10Kb)
Impurity Removal (dNTP,
primers, primer-dimers)
up to 90%
(less than 40–50 bp)
DNA Polymerase removal
(Taq, Hot-Start, High-
Fidelity)
up to 1:1000 dilution with
no measurable amplification
activity
Diffinity RapidTip2 tips are designed to remove dNTPs,
primers, primer-dimers, and DNA polymerase at typical PCR
concentrations.

Difnity RapidTip2 Page 7
Introduction
Diffinity Genomics has developed an innovative new
technology that removes undesirable impurities from PCR
reactions leaving you with nothing but purified DNA!
This revolutionary technology effectively removes dNTPs,
primers, primer-dimers, and DNA polymerase while providing
up to 90% recovery of pure DNA fragments ranging in length
from 100bp to 10Kb. It dramatically reduces the amount of
time to purify and prepare PCR reactions for use in downstream
applications, such as Sanger sequencing, restriction digestion,
and/or T-A cloning.
The RapidTip family of tips for PCR purification require just
one-tip, one-step, and one-minute for PCR purification!

Page 8 www.difnitygenomics.com
Difnity™ Technology Principle
The Diffinity RapidTip2 contains everything you need for PCR
purification. The tip is filled with our proprietary adsorption
technology, which has a differential affinity for PCR reaction
components. The impurities are removed from the solution as
it enters the pipette tip. Dispensing the solution yields purified,
high quality DNA ready to use for downstream applications.
You won’t need additional equipment, reagents, buffers, or
enzymes — only a pipettor!
Difnity RapidTip2 puries PCR
solutions and removes DNA
polymerase comparably to
popular spin column methods.
The positive control (+) con-
tains polymerase and all PCR
reagents but did not undergo
purication and therefore has
a 600bp band. The control
purication (C) and RapidTip2
purication (R) do not have
bands showing that polymerase
was removed during purica-
tion.
Difnity RapidTip2 effectively
removes dNTPs (not visible on
gel), primers (20bp), and primer-
dimers (50bp). The PCR product
was divided and subjected to PCR
purication with either competitor’s
products (C) or RapidTip2 (RT2: 1,
2, 3). RapidTip2 has high yield: the
PCR amplicon (2Kb) shows no loss
of band intensity after purication. 20bp--
50bp--
2Kb--
U C C 1 2 3
---RT2---
+ -C R
Standard
Hot Start
Proofreading

Difnity RapidTip2 Page 9
Diffinity RapidTip2
purification
improves sequence
quality. Sequence
chromatograms
show improved
peak quality and
lower background in
Diffinity RapidTip2
purified samples
as compared to
unpurified samples.
Equipment to be Supplied by User
• PCR Sample (50 μl ±5 μl)
• Tubes to store purified DNA
• Pipettor — manual or programmable
• Standard pipette tips for liquid transfer
(if necessary)
RapidTip2
unpuried

Page 10 www.difnitygenomics.com
Guidelines — Pipetting with the RapidTip2
Careful pipetting is important to achieve effective purification
with the RapidTip2. The following pipetting guidelines will help
ensure optimal results:
1. Pre-wet the particles
On the first aspirate step, aspirate approximately the first
half of the sample and pause 5 seconds to ensure complete
wetting of the particles before mixing. Then aspirate the rest
of the sample and dispense.
2. Mix effectively
For effective mixing, it is important that the particles
remain in contact with the sample during each aspirate and
dispense cycle.
Aspirate slowly for the first several cycles until the particles
are completely dispersed into the PCR sample.
Avoid long delays between successive aspirate and dispense
cycles that allow the particles to settle out of solution for
more than 1–2 seconds.
3. Maintain tip-to-sample contact
During aspiration, maintain continuous contact between
the end of the pipette tip and your sample to avoid
aspirating air bubbles in the sample.

Difnity RapidTip2 Page 11
4. Maintain tip-to-well clearance
Maintain clearance between the end of the pipette tip and
the bottom of the sample tube or well to avoid plugging the
tip during mixing.
5. Recovering from particle detachment
If particles become detached from the sample, gently “flick”
the pipettor downward to bring them back into contact
with the sample and proceed with mixing.
Pipetting Examples
Please note that typical PCR samples are colorless — for visualization,
yellow dye was used.
To correct B and to improve performance, gently “flick” the
pipettor downward to bring all particles and the sample back
together, then proceed with mixing.
B. Incorrect mixing:
Particles separated by
air bubble.
A. Correct mixing:
Sample and particles
mixing well.

Page 12 www.difnitygenomics.com
RapidTip2 PCR Purication Protocols
Prepare Samples:
Diffinity RapidTip2 is optimized for 50 μl reaction volumes but
can effectively purify samples from 45–55 μl.
• For PCR volumes >55 μl, please aliquot 50 μl into a new
tube for purification.
• For PCR volumes <45 μl, please dilute to 50 μl. This works
best with highly concentrated DNA samples (>50ng/μl)
as your sample concentration will be reduced.
Prepare Tips:
Diffinity RapidTip2 for PCR Purification contains proprietary
particles that purify a PCR reaction; these particles can adhere
to the pipette tip walls during shipping. For optimal results,
sharply tap the box 2–3 times on a flat surface so that particles
are at the bottom of the tips (near the nozzle).
Please note that it is normal to see fine dust-like particles on the side of the
tip. After tapping the box, you should expect to see about 3mm of white
particles above the retainer at the small end of the pipette tip.
Purify Samples:
1. Program pipettor to aspirate 50 or 60 μl???.
2. Place Diffinity RapidTip2 on pipettor — single or
multichannel.
Please note that you can use a multi-channel pipettor to mix more than
1 sample at a time for even higher productivity.

Difnity RapidTip2 Page 13
3. Place pipette tip into 50 μl PCR solution.
4. Pre-wet the particles on first aspirate (see page 10).
Aspirate about half the sample and then pause for 5 seconds to ensure
complete wetting of the particles before mixing. Aspirate the rest of the
sample and then dispense.
5. Set timer and mix for 60 seconds (approximately 15
aspirate/dispense cycles).
Please note that pipetting will be slower than normal — wait for liquid
to completely fill the tip to begin the next mix. It is not necessary to
drive liquid completely out of the tip on every dispense. The particles
should mix completely with the solution and make it appear cloudy
while inside the tip.
6. Dispense all solution into a clean tube when mixing
is complete. Use your pipettor’s blowout mode for
maximum liquid recovery.
Your purified PCR Amplicon is now ready for your downstream
application.
Quantifying DNA Recovery
If you wish to confirm purification, run unpurified and purified
sample in adjacent lanes on a gel to confirm the amplicon
band. To estimate percent recovery, analyses of the samples
pre and post-purification are necessary. For this process, we
recommend either a PicoGreen®2 type assay or visualization on
agarose gel.

Page 14 www.difnitygenomics.com
Troubleshooting Guide
Problem Things to try:
Low DNA
recovery
Run some of the untreated and RapidTip2 purified
PCR on a gel to check your amplicon band
intensity.
Note: Purify at least 45 μl of your PCR reaction to
optimize DNA recovery.
Slow or
difficult
aspiration
Check that pipettor volume is 50 or 60 μl??.
Check that tips are firmly attached to the pipettor.
Note: Diffinity RapidTip2 is incompatible with
detergents, mineral oil, and ready-to-load PCR mixes
that contain density increasing compounds.
Fluid
remains
in the
RapidTip2
It’s normal for a small amount of liquid (~10μl) to
remain inside the Diffinity RapidTip2.
Note: Overdispense or blowout all fluid on the last
dispense cycle.
Failure to
remove
impurities
Verify that particles are at the bottom of the
tip prior to sample treatment; the pipettor is
operating at the proper (slow) speed settings;
and that particles are effectively mixing with the
sample during pipetting.
Note: Remove trapped air bubbles by gently “flicking”
the pipettor downward for additional aspirate/dispense
cycles.
Visit www.diffinitygenomics.com/FAQs.asp for additional
information.

Difnity RapidTip2 Page 15
Ordering Information
You can place an order by:
1. Contacting one of our distributors worldwide. For a
complete list, visit our website.
2. Call Diffinity Genomics Customer Service and place the
order by phone: [phone]
3. Visit our website and place an order online via the online
Diffinity store: www.diffinitygenomics.com/order.asp
For more information, please visit our website:
www.diffinitygenomics.com

Difnity Genomics RapidTip2 User Handbook
Version B (March 2012)
Printed in the United States
Difnity Genomics, Inc.
150 Lucius Gordon Drive, West Henrietta, NY 14586
© 2011 Difnity Genomics, Inc. All rights reserved. Difnity
Genomics, Difnity and RapidTip are trademarks of Difnity
Genomics, Inc. All other names may be trademarks or
registered trademarks of their respective owners.