Note: Descriptions are shown in the official language in which they were submitted.
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VIAL
CROSS-REFERENCE TO RELATED APPLICATION
This application is a divisional of Canadian Patent application number
2,331,809
filed June 15, 1999 as PCT/US99/13582.
FIELD OF THE INVENTION:
The present invention relates to the field of synthesizers. More particularly,
this
invention relates to synthesizers that utilize multiple banks of vials to
synthesize custom
sequence defined oligonucleotides, polymers. and other organic compounds.
BACKGROUND OF THE INVENTION:
.10 Oligonucleotides are playing an increasingly important role in diagnostic
medicine.
forensic medicine, and molecular biology research. In addition to
oligonucleotides,
polymers such as peptides, polynucleotides. and other organic chains are also
very
important in scientific research.
Accordingly, the use of and demand for synthetic oligonucleotides. polymers.
and
15 organic chains has increased. In turn, this has spawned development of new
synthesis
systems and methods for basic procedures for custom sequence defined
oligonucleotides.
polymers, and other organic chains.
Typically, the present automated systems and methods place a solid support
such as
controlled pore glass beads (CPG) into a plurality of individual vials which
provide a stable
20 anchor to initiate the synthesis process. Using a series of valves, the
selected reagents are
sequentially placed into the appropriate vial in a predetermined sequence.
Contact of the
reagent with the CPG inside each of the vials causes a reaction that results
in sequenced
growth thereon. Sequential deposits of the selected reagents within the vials
build the
predetermined sequence.
25 A flushing procedure is typically utilized after a particular reagent is
placed into one
of the vials for a predetermined amount of time. While the particular reagent
contacts the
CPG a reaction produces a sequenced growth on the CPG. In conventional
synthesis
machines the flushing procedure is performed on all the vials simultaneously.
During a
flushing operation within conventional synthesis machines, all the reagents
within the
30 plurality of individual vials are flushed and expelled through a shared
central orifice within
the synthesis machine. After completion of a flushing operation. the plurality
of vials are
then capable of receiving another reagent.
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In High Throughput DNA Synthesis in a Multichannel Format, L.E. Sindelar and
J.M. Jaklevic teach an approach to high throughput parallel DNA synthesis in
which a
multi-vial format is utilized. The reactions are carried out in open vials.
Each vial
contains CPG to form the substrate for the synthesis and a high density filter
bottom to
retain the CPG within each vial. There is a common vacuum line that is coupled
to all the
vials. This common vacuum line simultaneously flushes the material contained
within all
the vials. The synthesis of a DNA sequence is carried out by directly
dispensing reagents
into individual reaction vials. A computer controls the sequence in which
reagents are
dispensed and timing periodic flushing operations to expel material from the
reaction vials.
U.S. Patent No. 5,529,756, by Brennan, teaches an apparatus and method for
polymer synthesis utilizing arrays. This apparatus includes an array of
nozzles with each
nozzle coupled to a reservoir containing a reagent and a base assembly having
an array of
reaction vials. A transport mechanism aligns the reaction vials and selected
nozzles to
deposit an appropriate reagent to a selected vial. Each of the reaction vials
has an inlet for
receiving a reagent and an outlet for expelling a material. To perform a
flushing operation.
this apparatus creates a pressure differential between the inlet and outlet of
the array of
vials. During the flushing operation, material within each of the array of
vials are
simultaneously expelled.
A retaining device is customarily utilized to ensure that the CPG remains
within the
corresponding vial during the flushing procedure. This retaining device is
located within
each individual vial and is positioned to prevent the CPG from exiting the
orifice during
the flushing procedure.
Conventional automated synthesis systems perform the flushing operation
simultaneously on all vials within the system. Conventional automated
synthesis systems
lack the ability to selectively perform the flushing operation on groups of
vials within the
system.
What is needed is a synthesizer that is configured to selectively perform
depositing
and flushing operations on groups of vials within the system.
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SUMMARY OF THE INVENTION:
In accordance with one aspect of the present invention, there is
provided a vial comprising a bored interior having a precise dimension to hold
a
frit for retaining material within the vial directly above the frit and
maintain a
consistent flow through the bored interior during a flushing procedure by only
forming a pressure differential to expel material from the vial and a solid
support
retained within the vial above the frit after the flushing procedure.
In accordance with a second aspect of the present invention, there is
provided a vial comprising an exterior dimension to fit directly within a
receiving
1o hole of a cartridge thereby providing a pressure-tight seal directly
between the vial
and the cartridge, a bored interior having a precise dimension to maintain a
consistent flow through the bored interior during flushing procedures by only
forming a pressure differential to expel material from the vial and a solid
support
retained within the vial above a frit after flushing procedures.
In accordance with a third aspect of the present invention, there is
provided a vial comprising: a. a bored interior having a precise dimension to
hold
a frit for retaining material above the frit and maintain a consistent flow
through the
bored interior during a flushing procedure by only forming a pressure
differential to
expel material from the vial; b. a top opening through which material is
dispensed
into the bored interior; c. a bottom opening of a diameter to retain material
within
the bored interior when no pressure differential is applied and through which
material is flushed during the flushing procedure; d. an exterior dimension to
fit
directly within a receiving hole of a cartridge to form a pressure-tight seal
directly
between the vial and the cartridge when the vial is inserted into a receiving
hole of
the cartridge; and e. a solid support retained within the vial above the frit
after the
flushing procedure.
In accordance with a fourth aspect of the present invention, there is
provided a vial comprising: a. a frit; b. a solid support; c. a bored interior
having a
precise dimension to hold the frit for retaining the solid support above the
frit and
maintain a consistent flow through the bored interior during a flushing
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procedure by only forming a pressure differential to expel material from the
vial,
wherein the solid support and material formed on the solid support is retained
above the frit, within the vial, during a flushing procedure; d. a top opening
through
which material is dispensed into the bored interior; e. a bottom opening of a
s diameter to retain material within the bored interior when no pressure
differential is
applied and through which material is flushed during the flushing procedure;
and f.
an exterior dimension to fit directly within a receiving hole of a cartridge
to form a
pressure-tight seal directly between the vial and a cartridge when the vial is
inserted into a receiving hole of the cartridge.
In accordance with a fifth aspect of the present invention, there is
provided a vial including a bored interior having a precise dimension to hold
a frit,
the vial consisting of a single frit for retaining material within the vial
directly
above the single frit and maintain a consistent flow through the bored
interior
during a flushing procedure by only forming a pressure differential to expel
material from the vial and a solid support retained within the vial above the
single
frit after the flushing procedure.
In accordance with a sixth aspect of the present invention, there is
provided a vial including an exterior dimension to fit directly within a
receiving hole
of a cartridge thereby providing a pressure-tight seal directly between the
vial and
the cartridge, a bored interior having a precise dimension to maintain a
consistent
flow through the bored interior during flushing procedures by only forming a
pressure differential to expel material from the vial and a solid support
retained
within the vial directly above a single frit, the vial consisting of the
single frit, after
flushing procedures.
In accordance with a seventh aspect of the present invention, there
is provided a vial comprising: a bored interior having a precise dimension; a
solid
support for growing a polymer chain; and a single frit for retaining the solid
support
within the vial directly above the single frit and maintain a consistent flow
through
the bored interior during a flushing procedure by only forming a pressure
3o differential to expel material from the vial and retain the solid support
within the
vial above the frit after the flushing procedure.
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In accordance with an eighth aspect of the present invention, there is
provided a vial comprising a bored interior having a precise dimension to hold
a
single frit, the vial consisting of the single frit for retaining material
within the vial
directly above the single frit without any additional frits and maintain a
consistent
flow through the bored interior during a flushing procedure by only forming a
pressure differential to expel material from the vial and a solid support
retained
within the vial above the single frit after the flushing procedure.
In accordance with a ninth aspect of the present invention, there is
provided a plurality of vials each comprising a bored interior having a
precise
1o dimension to hold a frit, wherein the precise dimension is consistent for
each of
the plurality of vials, each of the vials consisting of a single frit for
retaining
material within the vial directly above the single frit and maintain a
consistent flow
through the bored interior during a flushing procedure by only forming a
pressure
differential to expel material from the vial and a solid support retained
within the
vial above the single frit after the flushing procedure.
In accordance with a tenth aspect of the present invention, there is
provided a plurality of vials each comprising an exterior dimension to fit
directly
within a receiving hole of a cartridge thereby providing a pressure-tight seal
directly between the vial and the cartridge, wherein the exterior dimension is
consistent for each of the plurality of vials such that any of the vials will
consistently fit within the receiving hole of the cartridge, each of the
plurality of
vials further comprising a bored interior having a precise dimension to
maintain a
consistent flow through the bored interior during flushing procedures by only
forming a pressure differential to expel material from the vial and a solid
support
retained within the vial directly above a frit, the vial consisting of a
single frit, after
flushing procedures.
In accordance with an eleventh aspect of the present invention,
there is provided a plurality of vials, each of the plurality of vials
comprising: a. a
bored interior having a precise dimension to hold a frit for retaining
material above
the frit and maintain a consistent flow through the bored interior during a
flushing
procedure by only forming a pressure differential to expel material from the
vial,
wherein the precise dimension is consistent for each of the plurality of
vials; b. a
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top opening through which material is dispensed into the bored interior; c. a
bottom opening of a diameter to retain material within the bored interior when
no
pressure differential is applied and through which material is flushed during
the
flushing procedure; d. an exterior dimension to fit directly within a
receiving hole of
a cartridge to form a pressure-tight seal directly between the vial and the
cartridge
when the vial is inserted into a receiving hole of the cartridge, wherein the
exterior
dimension is consistent for each of the plurality of vials such that any of
the vials
will consistently fit within the receiving hole of the cartridge; and e. a
solid support
retained within the vial above the frit after the flushing procedure.
In another aspect, a multi-well rotary synthesizer includes a
controller, a plurality of precision fit vials circularly arranged in multiple
banks on a
cartridge, a drain corresponding to each bank of vials, a chamber bowl, a
plurality
of valves for delivering reagents to selective vials, and a waste tube system
for
purging material from the vials. The banks of vials can be selectively purged,
allowing the banks of vials to be used to synthesize different polymer chains.
Further, the multiple banks of valves provide an additional number of reagent
choices while operating in a serial mode and faster reagent distribution while
operating in a parallel mode.
The plurality of vials are held within the cartridge and are divided
among individual banks. Preferably, each individual bank of vials has a
corresponding drain. There is at least one waste tube system for expelling the
reagent solution from vials within a particular bank of vials when the waste
tube
system is coupled to the corresponding drain. The cartridge holding the
plurality
of vials rotates relative to the stationary banks of valves and the waste tube
system. The controller controls a motor to rotate the cartridge. The
controller also
operates the banks of valves and the waste tube system in response to the
required sequence of dispensing various reagent solutions and flushing
appropriate vials in order to create the desired polymer chain.
A frit is inserted into each vial and serves as a filter and to hold the
CPG within the vial. The interior of each vial is precision bored to ensure a
tight
consistent seal with the corresponding frit. This consistent seal with the
frit for
every vial also results in a consistent reagent solution flow through every
vial. The
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exterior of each vial also has a precise dimension to consistently fit within
the
cartridge and provide a pressure tight seal around each vial within the
cartridge.
BRIEF DESCRIPTION OF THE DRAWINGS:
Figure 1 illustrates a perspective view of the synthesizer of the
present invention.
Figure 2 illustrates the preferred cartridge of the present invention.
Figure 3 illustrates a perspective view of an alternate cartridge.
Figure 4 illustrates a cross-sectional view of the synthesizer of the
present invention.
Figure 5 illustrates a top view of the drain plate.
Figure 6 illustrates a cross-sectional view of the vial.
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Figure 7 illustrates a cross-sectional view of the
waste tube system.
Figure 8 illustrates the controlling computer coupled
to the synthesizer of the preferred embodiment of the present
invention.
Figure 9 illustrates a cross-sectional view of an
alternate waste tube system.
DETAILED DESCRIPTION OF THE PRESENT INVENTION
While the present invention will be described with
reference to several specific embodiments, the description is
illustrative of the present invention and is not to be
construed as limiting the invention. For the sake of clarity
and a better understanding of the present invention, common
components share common reference numerals throughout various
figures.
Figure 1 illustrates a synthesizer 100. The
synthesizer 100 is designed for building a polymer chain by
sequentially adding polymer units to a solid support in a
reagent solution. The solid support generally resides within a
vial and various reagent solutions are sequentially added to
the vial. Before an additional reagent solution is added to
the vial, the previous reagent solution is preferably purged
from the vial. Although, the synthesizer 100 is particularly
suited for building sequence defined oligonucleotides, the
synthesizer 100 is also configured to build any other desired
polymer chain or organic compound. The term "polymer chain" is
defined as a unit that is bound to other units of the same or
different kind to form a polymer chain, such as
oligonucleotides and peptide chains. It is important to note
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4a
that although the present invention is described in context of
specific applications, the present invention should not be
limited to these specific examples disclosed herein.
The synthesizer 100 preferably comprises at least a
bank of valves and at least one bank of vials. Within each
bank of vials, there is at least one vial for holding the solid
support and for containing a reagent solution such that a
polymer chain can be synthesized. Within the bank of valves,
there are preferably a plurality of valves configured for
selectively dispensing a reagent solution into one of the
vials. The synthesizer 100 is preferably configured to allow
each bank of vials to be selectively purged of the presently
held reagent solution. Additional banks of valves provide the
synthesizer 100 with greater flexibility. For example, each
bank of valves can be configured to distribute reagent
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solutions to a particular bank of vials in a parallel fashion to minimize the
processing time.
Alternatively, multiple banks of valves can be configured to distribute
reagent solutions to
a particular bank of vials in series thus allowing the synthesizer 100 to hold
a larger
number of different reagent solutions. thus being able to create complex
polymer chains.
5 Figure 1 illustrates an exterior perspective view of a rotary synthesizer
100. As
illustrated in Figure 1. the synthesizer 100 includes a base 105, a cartridge
170, a first bank
of vials 115, a second bank of vials 125, a plurality of dispense lines 140, a
plurality of
fittings 150, a first bank of valves 110 and a second bank of valves 120.
Within each of
the banks of valves 110 and 120, there is preferably at least one valve.
Within each of the
banks of vials 115 and 125, there is preferably at least one vial. Each of the
valves is
capable of selectively dispensing a reagent solution into one of the vials. As
stated before.
each of the vials is preferably configured for retaining a solid support such
as CPG and
holding a reagent solution. Further, as each reagent solution is sequentially
deposited
within the vial and sequentially purged therefrom, a polymer chain is
generated.
Preferably, there is a plurality of reservoirs (not shown) each containing a
specific
reagent solution to be dispensed to one of the plurality of valves 130. Each
of the valves
within the first bank and second bank of valves 110 and 120, is coupled to a
corresponding
reservoir. Each of the plurality of reservoirs is pressurized. As a result, as
each valve is
opened, a particular reagent solution from the corresponding reservoir is
dispensed to a
corresponding vial.
Each of the plurality of dispense lines 140 is coupled to a corresponding one
of the
valves within the first and second banks of valves 110 and 120. Each of the
plurality of
dispense lines 140 provides a conduit for transferring a reagent solution from
the valve to a
corresponding vial. Each one of the plurality of dispense lines 140 is
preferably configured
to be flexible and semi-resilient in nature. Preferably, the plurality of
dispense lines 140
are each coated with Teflon which is more resistant to deterioration upon
contact with
reagent solutions and provides an adequate seal between the plurality of
valves 130 and the
plurality of fittings 150. Further, each of the plurality of fittings 150 is
preferably coupled
to one of the plurality of dispense lines 140. The plurality of fittings 150
are preferably
configured to prevent the reagent solution from splashing outside the vial as
the reagent
solution is dispensed from a cap to a particular vial positioned below the
cap.
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As shown in Figure 1. the first and second banks of valves 110 and 120 each
have
thirteen valves. In Figure 1, the number of valves in each bank is merely for
exemplary
purposes. It is preferable to have fifteen valves for each bank even though -
the illustrated
cartridge 170 only has twelve vials per bank. The present invention provides
greater
flexibility in creating complex polymer chains by including a greater number
of valves than
vials per bank. It should be apparent to those skilled in the art that any
appropriate
number of valves can be included within each bank of valves.
Each of the vials within the first bank of vials 115 and the second bank of
vials 11'5
is presently shown resting in one of a plurality of receiving holes 185 within
the cartridge
170. Preferably, each of the vials within the corresponding plurality of
receiving holes 185
is positioned in a substantially vertical orientation. Each of the vials is
configured to retain
a. solid support such as CPG and hold a reagent solution. Preferably CPG is
utilized as this
solid support. Alternatively, any other appropriate solid support can be used
to support the
polymer chain being synthesized.
In use, each of the valves selectively dispenses a reagent solution through
one of the
plurality of dispense lines 140 and fittings 150. The first and second banks
of valves 110
and 120 are preferably coupled to the base 105 of the synthesizer 100. Each of
the first
and second bank of valves 110 and 120 have a corresponding fitting 150 within
a first
bank of fittings 102 and a second bank of fittings 104, respectively. The
cartridge 170
which contains the plurality of vials 181 rotates relative to the synthesizer
100 and relative
to the first and second banks of valves 110 and 120. By rotating the cartridge
170. a
particular vial 181 can be positioned under a specific valve such that the
corresponding
reagent solution from this specific valve is dispensed into this vial.
Further, the first and
second banks of valves 110 and 120 are capable of simultaneously and
independently
dispensing reagent solutions into corresponding vials.
Figure 2 illustrates a detailed view of the cartridge 170. Preferably, the
cartridge
170 is circular in shape such that the cartridge 170 is capable of rotating in
a circular path
relative to the base 105 and the first and second banks of valves 110 and 120.
The
cartridge 170 has a plurality of receiving holes 185 on its upper surface
around the
peripheral edge of the cartridge 170. Each of the plurality of receiving holes
185 is
configured to hold one of the vials 181 within the first bank of vials 115 and
the second
bank of vials 125. The plurality of receiving holes 185 as shown on the
cartridge 170 are
divided up among four banks. A bank 180 illustrates one of the four banks on
the
cartridge 170 and contains twelve receiving holes wherein each receiving hole
is configured
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to hold a vial. An exemplary vial 181 is shown being inserted into one of the
plurality of
receiving holes 185. The total number of receiving holes shown on the
cartridge 170
includes forty-eight (48) receiving holes divided into four banks of twelve
receiving holes
each. The number of receiving holes and the configuration of the banks of
receiving holes
is shown on the cartridge 170 for exemplary purposes only. It should be
apparent to those
skilled in the art that any appropriate number of receiving holes and banks of
receiving
holes can be included in the cartridge 170. Preferably, the receiving holes
185 within the
cartridge each have a precise diameter for accepting the vials 181. which also
each have a
corresponding precise exterior dimension to provide a pressure-tight seal when
the vials
181 are inserted into the receiving holes 185.
Figure 3 illustrates an alternative cartridge 300. The cartridge 300 is
similar to the
cartridge 170 shown in Figures 1 and 2. Each of the receiving holes 320 is
configured to
hold a vial 181. A plurality of receiving holes are grouped together to form a
bank of
receiving holes 310. The cartridge 300 contains a total of ninety-six (96)
receiving holes
grouped into twelve banks, each bank including eight receiving holes. The
number of
receiving holes and the configuration of the banks of receiving holes included
on the
cartridge 300 is exemplary only.
Figure 4 illustrates a cross sectional view of the synthesizer 100. As
illustrated in
Figure 4, the synthesizer 100 includes the base 105, a set of valves 470, a
motor 445, a
gear box 440, a chamber bowl 400, a drain plate 410, a drain 740, the
cartridge 170, a
chamber seal 450, a motor connector 465, a waste tube system 430. a controller
480, and a
clear window 460. The valves 470 are coupled to the base 105 of the
synthesizer 100 and
are preferably positioned above the cartridge 170 around the outside edge of
the base 105.
This set of valves 470 preferably contains fifteen individual valves which
each deliver a
corresponding reagent solution in a specified quantity to a vial held in the
cartridge 170
positioned below the valve. Each of the valves may dispense the same or
different reagent
solutions depending on the user-selected configuration. When more than one
valve
dispenses the same reagent solution, the set of valves 470 is capable of
simultaneously
dispensing a reagent solution to multiple vials within the cartridge 170. When
the valves
470 each contain different reagent solutions, each one of the valves 470 is
capable of
dispensing a corresponding reagent solution to any one of the vials within the
cartridge
170.
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Although not specifically shown in Figure 4. the synthesizer 100 may have
multiple
sets of valves. The plurality of valves within the multiple sets of valves may
he configured
in a variety of ways to dispense the reagent solutions to a select one or more
of the vials.
For example, in one configuration, where each set of valves is identically
configured. the
synthesizer 100 is capable of simultaneously dispensing the same reagent
solution in
parallel from multiple sets of valves to corresponding banks of vials. In this
configuration.
the multiple banks of vials may be processed in parallel. In the alternative.
each individual
valve within multiple sets of valves may contain entirely different reagent
solutions such
that there is no duplication of reagent solutions among any individual valves
in the multiple
sets of valves. This configuration allows the synthesizer 100 to build polymer
chains
requiring a large variety of reagent solutions without changing the reagent
solutions
associated with each valve.
The motor 445 is preferably mounted to the base 105 through the gear box 440
and
the motor connector 465. The chamber bowl 400 preferably surrounds the motor
connector
465 and remains stationary relative to the base 105. The chamber bowl 400 is
designed to
hold any reagent solution spilled from the plurality of vials during the
purging process.
Further, the chamber bowl 400 is configured with a tall shoulder to insure
that spills are
contained within the bowl 400. The chamber lip seal 450 preferably provides a
seal
around the motor connector 465 in order to prevent the contents of the chamber
bowl 400
from flowing into the gear box 440. The chamber seal 450 is preferably
composed of a
flexible and resilient material such as Teflon or elastomer which conforms to
any
irregularities of the motor connector 465. Alternatively, the chamber seal can
be composed
of any other appropriate material. Additionally, the chamber seal 450 has
frictionless
properties which allow the motor connector 465 to rotate freely within the
seal. For
example, coating this flexible material with Teflon helps to achieve a low
coefficient of
friction.
The drain plate 410 is coupled to the motor connector 465. The cartridge 170
is
coupled to the drain plate 410. More specifically, the drain plate 410 is
attached to the
motor connector 465 which rotates the drain plate 410 while the motor 445 is
operating
and the gear box 440 is turning. The cartridge 170 and the drain plate 410 are
preferably
configured to rotate as a single unit. The drain plate 410 is configured to
catch and direct
the reagent solutions as the reagent solutions are expelled from the plurality
of vials.
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While operating, the motor 445 is configured to rotate both the cartridge 170
and the drain
plate 410 through the gear box 440 and the motor connector 465. The chamber
seal 450
allows the motor connector 465 to rotate the cartridge 170 and the drain plate
410 through
a portion of the chamber bowl 400 while still containing any reagent solutions
in the
chamber bowl 400.
The controller 480 is coupled to the motor 445 to activate and deactivate the
motor
445 in order to rotate the cartridge 170 and the drain plate 410. The
controller 480
provides embedded control to the synthesizer and controls not only the
operation of the
motor 445, but also the operation of the valves 470 and the waste tube system
430.
Figure 5 illustrates a detailed top view of the drain plate 410. The drain
plate 410
has a plurality of securing holes 780 for attaching to the motor connector
465. The drain
plate 410 also has a top surface 715 which attaches to the underside of the
cartridge 170.
As stated previously. the cartridge 170 holds the plurality of vials grouped
into the plurality
of banks.
The drain plate 410 preferably has four collection areas 705. 710. 720 and
730, to
correspond to the four banks within the cartridge 170. Each of these four
collection areas
705, 710, 720 and 730 forms a recessed area below the top surface 715 and is
designed to
contain and direct material flushed from the vials within the bank above the
collection area.
Each of the four collection areas 705, 710, 720 and 730 is positioned below a
corresponding one of the banks of vials on the cartridge 170. The drain plate
410 is
rotated with the cartridge 170 to keep the corresponding collection area below
the
corresponding bank.
There are four drains 740, 750, 760 and 770, each of which is located within
one of
the four collection areas 705, 710, 720 and 730, respectively. In use. the
collection areas
705, 710, 720 and 730 are configured to contain material flushed from
corresponding vials
and pass that material through the drains 740. 750, 760 and 770, respectively.
Preferably.
there is a collection area and a drain corresponding to each bank of vials
within the
cartridge 170. Alternatively, any appropriate number of collection areas and
drains can be
included within a drain plate.
The clear window 460 (Figure 4) is attached to a top plate of the base 105 and
covers the area above the cartridge 170. The top plate of the base 105 opens
up allowing
an operator or maintenance person access to the interior of the synthesizer
100. The clear
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window 460 allows the operator to observe the synthesizer 100 in operation
while
providing a pressure sealed environment within the interior of the synthesizer
100. As
shown in Figure 4. there are a plurality of through holes 520 in the clear
window 460 to
allow the plurality of dispense lines 140 to extend through the clear plate
460 to dispense
5 material into the vials.
The clear window 460 also includes a gas fitting 530 attached therethrough.
The
gas fitting 530 is coupled to a gas line 540. The gas line 540 preferably
continuously
emits a stream of inert gas which flows into the synthesizer 100 through the
gas fitting 530
and flushes out traces of air and water from the plurality of vials 160 within
the synthesizer
10 100. Providing the inert gas flow through the gas fitting 530 into the
synthesizer 100
prevents the polymer chains being formed within the vials from being
contaminated
without requiring the plurality of vials 160 to be hermetically sealed and
isolated from the
outside environment.
The drain 740 is attached to the drain plate 410 and is positioned to
correspond
with a bank of vials held within the cartridge 170. The drain 740 corresponds
to a single
bank of vials and is primarily utilized for flushing material from this single
bank of vials.
As described above, preferably, each bank of vials has a corresponding drain.
The waste tube system 430 is preferably utilized to provide a pressurized
environment for flushing material including reagent solutions from the
plurality of vials
located within a corresponding bank of vials and expelling this material from
the
synthesizer 100. Alternatively, the waste_ tube system 430 can be used to
provide a vacuum
for drawing material from the plurality of vials located within a
corresponding bank of
vials.
An isolated cross-sectional view of the waste tube system 430 is illustrated
in
Figure 7. The waste tube system 430 comprises a stationary tube 490 and a
mobile waste
tube 500. The stationary tube 490 and the mobile waste tube 500 are slidably
coupled
together. The stationary tube 490 is attached to the chamber bowl 410 and does
not move
relative to the chamber bowl 400. In contrast, the mobile tube 500 is capable
of sliding
relative to the stationary tube 490 and the chamber bowl 400. When in an
inactive state.
the waste tube system 430 does not expel any reagent solutions. During the
inactive state.
both the stationary tube 490 and the mobile tube 500 are preferably mounted
flush with the
bottom portion of the chamber bowl 400.
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11
When in an active state, the waste tube system 430 purges the material from
the
corresponding bank of vials. During the active state. the mobile tube 500
rises above the
bottom portion of the chamber bowl 400 towards the drain plate 410. The drain
plate 410
is rotated over to position a drain corresponding to the bank to be flushed.
above the waste
tube system 430. The mobile tube 500 then couples to this drain and the
material is
flushed out of the corresponding bank of vials and into the drain plate 420.
The reagent
solution is purged from the corresponding bank of vials due to a sufficient
pressure
differential between a top opening 610 (Figure 6) and a bottom opening 640
(Figure 6) of
each vial. This sufficient pressure differential is preferably created by
coupling the mobile
waste tube 500 to the corresponding drain. Alternatively, the waste tube
system 430 may
also include a vacuum device 510 coupled to the stationary tube 490 wherein
the vacuum
device 510 is configured to provide this sufficient pressure differential to
expel material
from the corresponding bank of vials. When this sufficient pressure
differential is
generated, the excess material within the vials being flushed, then flows
through the
corresponding drain and is carried away via the waste tube system 430.
When engaging the corresponding drain to flush a bank of vials, preferably the
mobile tube 500 slides over the corresponding drain such that the mobile tube
500 and the
drain act as a single unit. Alternatively, as illustrated in Figure 9 the
waste tube system
530 includes a mobile tube 520 which engages the corresponding drain by
positioning itself
directly below the drain and then sealing against the drain without sliding
over the drain.
The mobile tube 520 includes a drain seal 540 positioned on top of the mobile
tube 520.
In this embodiment, during a flushing operation, the mobile tube 520 is not
locked to the
corresponding drain. In the event that this drain is accidentally rotated
while the mobile
waste tube 520 is engaged with the drain, the drain and mobile tube 500 of the
synthesizer
100 will simply disengage and will not be damaged. If this occurs while
material is being
flushed from a bank of vials, any spillage from the drain is contained within
the chamber
bowl 400.
Configuring the waste tube system 430 to expel the reagent solution while the
mobile waste tube 500 is coupled to the drain allows the present invention to
selectively
purge individual banks of vials. Instead of simultaneously purging all the
vials within the
synthesizer 100, the present invention selectively purges individual banks of
vials such that
only the vials within a selected bank or banks are purged.
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12
Preferably. the synthesizer 100 includes two waste tube systems 430 for
flushing
two banks of vials simultaneously. Alternatively, any appropriate number of
waste tube
systems can be included within the synthesizer 100 for selectively flushing
banks of vials.
Figure 6 illustrates a cross sectional view of a vial 181. The vial 181 is an
integral
portion of the synthesizer 100. Generally, the polymer chain is formed within
the vial 181.
More specifically, the vial 181 holds a CPG 650 on which the polymer chain is
grown. As
stated previously, to create the polymer chain, the CPG 650 is sequentially
submerged in
various reagent solutions for a predetermined amount of time. With each
deposit of a
reagent solution. an additional unit is added to the resulting polymer chain.
Preferably, the
CPG 650 is held within the vial 181 by a frit 620. The vial 181 includes a top
opening
610 and a bottom opening 640. During the dispensing process, the vial 181 is
filled with a
reagent solution through the top opening 610. Then. during the purging
process. the vial
181 is drained of the reagent solution through the bottom opening 640. The
frit 620
prevents the CPG 650 or other support from being flushed away during the
purging
process. A precision bored interior 630 holds the frit 620 in place and
provides a
consistent compression and seal with the fit 620. As a result of the precision
bored
interior 630, there is a consistent flow of the reagent solution through each
vial during both
the dispensing and purging processes.
The exterior of each vial 181 also has a precise dimension around the support
660.
This support 660 fits within the receiving hole 185 within the cartridge 170
and provides a
pressure tight seal around each vial within the cartridge 170. Preferably,
each vial 181 is
formed of polyethylene by a molded process. Alternatively, the vials 181 can
be formed
using any appropriate process and any appropriate material.
In use, the controller 480 which is coupled to the motor 445. the valves 470,
and
the waste tube system 430 coordinates the operation of the synthesizer 100.
The controller
480 controls the motor 445 such that the cartridge is rotated to align the
correct vials with
the dispense lines 140 corresponding to the appropriate valves 470 during
dispensing
operations and that the correct one of the drains 740. 750. 760 and 770. are
aligned with an
appropriate waste tube system 430 during a flushing operation.
Figure 8 illustrates a computer system 800 coupled to the synthesizer 100. The
computer system 800 preferably provides the synthesizer 100 and specifically
the controller
480 with operating instructions. These operating instructions include rotating
the cartridge
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13
170 to a predetermined position. dispensing one of a plurality of reagent
solutions into
selected vials through the valves 470 and dispense lines 140. flushing the
first bank of vials
115 and/or the second bank of vials 125. and coordinating a timing sequence of
these
synthesizer functions. Preferably, the computer system 800 allows the user to
input data
representing reagent solution sequences to form a polymer chain.
oligonucleotides. and
other organic compounds via a graphical user interface. After the user inputs
this data. the
computer system 800 instructs the synthesizer 100 to perform appropriate
functions without
any further input from the user. The computer system 800 preferably includes a
processor
810. an input device 820 and a display 830. The computer 800 can be configured
as a
laptop or a desktop.
The present invention forms custom defined sequences such as oligonucleotides.
polymers and other organic compounds. The present invention has a plurality of
vials
divided among a plurality of banks wherein a custom sequence can be
synthesized within
each vial. The present invention forms these custom sequences without constant
supervision by the user.
Each bank of vials has a drain and can be selectively purged. To perform a
purging
operation, the drain of the corresponding bank of vials is coupled to a mobile
waste tube.
After coupling the drain to the mobile waste tube, a pressure differential is
formed and the
material within each of the vials within the corresponding bank of vials is
expelled.
The present invention preferably utilizes a plurality of valves divided into a
plurality of banks of valves to perform a filling operation to dispense
reagent solutions to
various vials during the filling operation. Each of the plurality of valves
can be configured
to dispense different reagent solutions to form complex custom sequences. In a
parallel
configuration, the plurality of valves can be configured to dispense the same
reagent
solution simultaneously to more than one vial.
The present invention allows the user to enter the custom sequence into a
computer
system. This computer system controls the fill operation and the purge
operation such that
appropriate vials are filled with the correct reagent solutions and the
appropriate banks of
vials are purged at the appropriate times within the sequence. Further. the
computer
system ensures that the correct quantity of reagent solution is deposited and
that the reagent
solution remains in the appropriate vial for the correct amount of time.
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Each vial of the present invention has a precision bored interior that is
configured to
produce a consistent seal with a frit. By having the consistent seal with the
frit. the
reagent solutions flow evenly and predictably through each vial of the present
invention.
Each vial also includes a precise exterior dimension to consistently fit
within the cartridge
and provide a pressure tight seal around the vial within the cartridge.
In operation, when building sequence defined oligonucleotides, polymer chains
or
other organic compounds, the synthesizer 100 rotates the appropriate vials
under the
dispense tubes corresponding to the appropriate valves 470 at the appropriate
times to build
the desired sequence or compound. The synthesizer also rotates the banks of
vials over a
corresponding waste tube system 430 in order to flush material from the vials,
as
appropriate. As discussed above, the banks of vials held within a cartridge
can be
selectively purged to allow a user to potentially build different sequences or
compounds
within each vial. In this manner, one bank of vials can be purged. while
another bank of
vials is in a wait period. While purging one bank of vials, a dispense
operation could also
be performed on vials other than the bank or banks of vials being purged, if
the position of
the vials corresponds to the appropriate valves. However, during a purging
operation, the
cartridge 170 cannot be rotated or the drain 740 will disengage from the
mobile waste tube
500.
To perform a dispense operation for a selected vial, the motor 445 rotates the
cartridge 170 in response to the computer system 800 such that the vial 181 is
positioned
below the appropriate dispense line 140 corresponding to the valve 470. Once
the vial 181
is properly positioned below this dispense line 140, the valve is opened by
the controller
480 and the solution controlled by the valve 470 flows through the dispense
tube 140 into
the vial 181. The valve 470 is then closed after a predetermined period of
time
corresponding to the precise amount of solution to be dispensed into the vial
181.
To purge material from a bank of vials, the motor 445 rotates the cartridge
170 in
response to the computer system 800 such that the drain corresponding to the
bank of vials
to be purged is positioned above the waste tube system 430. The mobile waste
tube 500 is
then raised to engage the drain and the material within the bank of vials is
expelled from
the vials through the waste tube system 430.
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The present invention has been described in terms of specific embodiments
incorporating details to facilitate the understanding of the principles of
construction and
operation of the invention. Such reference herein to specific embodiments and
details
thereof is not intended to limit the scope of the claims appended hereto.
It will be apparent to those skilled in the art that modifications may be made
in the
embodiment chosen for illustration without departing from the spirit and scope
of the
invention. Specifically, it will be apparent to one of ordinary skill in the
art that the device
of the present invention could be implemented in several different ways and
the
embodiments disclosed above are only exemplary of the preferred embodiment and
the
10 alternate embodiments of the invention and is in no way a limitation.
