U.S. patent application number 14/261263 was filed with the patent office on 2014-08-21 for method of making a formulation for deactivating nucleic acids.
This patent application is currently assigned to GEN-PROBE INCORPORATED. The applicant listed for this patent is Gen-Probe Incorporated. Invention is credited to Kenneth A. BROWNE, Lizhong DAI, Mark E. FILIPOWSKY, Daniel L. KACIAN, Margarita B. KAMINSKY, Norman C. NELSON, James RUSSELL.
Application Number | 20140231710 14/261263 |
Document ID | / |
Family ID | 34961462 |
Filed Date | 2014-08-21 |
United States Patent
Application |
20140231710 |
Kind Code |
A1 |
NELSON; Norman C. ; et
al. |
August 21, 2014 |
METHOD OF MAKING A FORMULATION FOR DEACTIVATING NUCLEIC ACIDS
Abstract
The disclosure relates to formulations for use in deactivating
nucleic acids and methods of making and using the same.
Inventors: |
NELSON; Norman C.; (San
Diego, CA) ; BROWNE; Kenneth A.; (Poway, CA) ;
DAI; Lizhong; (San Diego, CA) ; RUSSELL; James;
(Vista, CA) ; FILIPOWSKY; Mark E.; (San Marcos,
CA) ; KAMINSKY; Margarita B.; (San Diego, CA)
; KACIAN; Daniel L.; (San Diego, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Gen-Probe Incorporated |
San Diego |
CA |
US |
|
|
Assignee: |
GEN-PROBE INCORPORATED
San Diego
CA
|
Family ID: |
34961462 |
Appl. No.: |
14/261263 |
Filed: |
April 24, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13531924 |
Jun 25, 2012 |
8765652 |
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14261263 |
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11073085 |
Mar 4, 2005 |
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13531924 |
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60550749 |
Mar 5, 2004 |
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Current U.S.
Class: |
252/186.1 |
Current CPC
Class: |
A61L 2/186 20130101;
C12Q 1/6848 20130101; C12Q 1/68 20130101; C11D 3/3956 20130101 |
Class at
Publication: |
252/186.1 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A method of making a formulation for deactivating nucleic acids,
the method comprising the steps of: (a) separately dissolving solid
forms of a corrosion-inhibiting agent and a wetting agent, the
corrosion-inhibiting agent being phosphate, borate or sodium
bicarbonate, and the wetting agent being a surfactant or detergent;
(b) combining together the dissolved forms of the
corrosion-inhibiting agent and the wetting agent to form a first
mixture; (c) combining together the first mixture with a
solubilizing agent to form a second mixture, the solubilizing agent
being an organic solvent or an emulsifying agent; and (d)
instructing a user to combine the second mixture with a
deactivating agent to form the formulation, the deactivating agent
being sodium hypochlorite or dichloroisocyanurate, whereby the
concentration of the corrosion-inhibiting agent in the formulation
is from about 10 mM to about 750 mM; whereby the concentration of
the wetting agent in the formulation is from about 0.005% to about
1% (w/v); whereby the concentration of the solubilizing agent in
the formulation is from about 0.001% to about 20% (v/v); whereby
the concentration of the deactivating agent in the formulation is
from about 0.06% to about 3% (w/v) if the deactivating agent is
sodium hypochlorite; whereby the concentration of the deactivating
agent in the formulation is from about 5 mM to about 400 mM if the
deactivating agent is dichloroisocyanurate; and whereby each agent
of the formulation will remain substantially in solution at
22.degree. C.
2. The method of claim 1, wherein the deactivating agent is sodium
hypochlorite.
3. The method of claim 2, wherein the sodium hypochlorite is to be
present in the formulation at a concentration of from about 0.18%
to about 1.8% (w/v).
4. The method of claim 2, wherein the sodium hypochlorite is to be
present in the formulation at a concentration of from about 0.6% to
about 1.5% (w/v).
5. The method of claim 2, wherein the sodium hypochlorite is to be
present in the formulation at a concentration of from about 0.6% to
about 1.2% (w/v).
6. The method of claim 1, wherein the deactivating agent is
dichloroisocyanurate.
7. The method of claim 6, wherein the dichloroisocyanurate is
present in the formulation at a concentration of from about 10 mM
to about 200 mM.
8. The method of claim 6, wherein the dichloroisocyanurate is
present in the formulation at a concentration of from about 20 mM
to about 100 mM.
9. The method of claim 6, wherein the dichloroisocyanurate is
present in the formulation at a concentration of from about 40 mM
to about 80 mM.
10. The method of claim 1, wherein the corrosion-inhibiting agent
is sodium bicarbonate.
11. The method of claim 1, wherein the wetting agent is SDS or
LLS.
12. The method of claim 1, wherein the solubilizing agent is an
organic solvent.
13. The method of claim 12, wherein the organic solvent is benzyl
acetate, polysorbate 20 (PS20), or isopropanol.
14. The method of claim 1, wherein the solubilizing agent is an
emulsifying agent.
15. The method of claim 14, wherein the emulsifying agent is
polyoxyethylene sortitan mono-palmitate, lecithin, or ethylene
glycol distearate.
16. The method of claim 1, wherein the solubilizing agent is a
fragrance.
17. The method of claim 1, further comprising dissolving a solid
form of the solubilizing agent prior to step (c).
18. The method of claim 1, wherein the second mixture is 600 mM
sodium bicarbonate, pH 9.3, 0.1% SDS, and 0.05% fragrance.
19. The method of claim 1, wherein the formulation is 0.6% sodium
hypochlorite, 90 mM sodium bicarbonate, pH 9.3, 0.015 SDS, and
0.0075% fragrance.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 13/531,924, filed on Jun. 25, 2012, now
pending, which is a divisional of U.S. patent application Ser. No.
11/073,085, now pending, filed on Mar. 4, 2005, which claims the
benefit of U.S. Provisional Application No. 60/550,749, filed on
Mar. 5, 2004, the contents of each of which applications are hereby
incorporated herein by reference in their entirety.
FIELD
[0002] The present disclosure relates to formulations, methods and
kits containing or employing an agent for use in deactivating
nucleic acids present on a surface or in a solution.
BACKGROUND
[0003] Procedures for qualitatively or quantitatively determining
the presence of particular organisms or viruses in a test sample
routinely rely upon nucleic acid-based probe testing. To increase
the sensitivity of these procedures, an amplification step is often
included to increase the copy number of potential nucleic acid
target sequences present in the test sample. During amplification,
polynucleotide chains containing the target sequence and/or its
complement are synthesized in a template-dependent manner from
ribonucleoside or deoxynucleoside triphosphates using
nucleotidyltransferases known as polymerases. There are many
amplification procedures in general use today, including the
polymerase chain reaction (PCR), Q-beta replicase, self-sustained
sequence replication (3SR), transcription-mediated amplification
(TMA), nucleic acid sequence-based amplification (NASBA), ligase
chain reaction (LCR), strand displacement amplification (SDA) and
loop-mediated isothermal amplification (LAMP), each of which is
well known in the art. See, e.g., Mullis, "Process for Amplifying
Nucleic Acid Sequences," U.S. Pat. No. 4,683,202; Erlich et al.,
"Kits for Amplifying and Detecting Nucleic Acid Sequences," U.S.
Pat. No. 6,197,563; Walker et al., Nucleic Acids Res., 20:1691-1696
(1992); Fahy et al., "Self-sustained Sequence Replication (3SR): An
Isothermal Transcription-Based Amplification System Alternative to
PCR," PCR Methods and Applications, 1:25-33 (1991); Kacian et al.,
"Nucleic Acid Sequence Amplification Methods," U.S. Pat. No.
5,399,491; Davey et al., "Nucleic Acid Amplification Process," U.S.
Pat. No. 5,554,517; Birkenmeyer et al., "Amplification of Target
Nucleic Acids Using Gap Filling Ligase Chain Reaction," U.S. Pat.
No. 5,427,930; Marshall et al., "Amplification of RNA Sequences
Using the Ligase Chain Reaction," U.S. Pat. No. 5,686,272; Walker,
"Strand Displacement Amplification," U.S. Pat. No. 5,712,124;
Notomi et al., "Process for Synthesizing Nucleic Acid," U.S. Pat.
No. 6,410,278; Dattagupta et al., "Isothermal Strand Displacement
Amplification," U.S. Pat. No. 6,214,587; and Lee et al., Nucleic
Acid Amplification Technologies: Application To Disease Diagnosis
(1997).
[0004] Nucleic acid products formed during an amplification
procedure (i.e., amplicon) can be analyzed either during the course
of the amplification reaction (real-time) or once the amplification
reaction has been generally completed (end-point) using detectable
probes. While the probes are designed to screen for
target-containing amplicon, other products may be produced during
an amplification procedure (e.g., primer-dimers formed in a typical
PCR reaction) that have the potential to interfere with the desired
amplification reaction. Following completion of the amplification
procedure and exposure to detectable probes, the resulting reaction
mixture is discarded.
[0005] During the steps of an assay or synthesis procedure which
includes an amplification procedure, it is possible to contaminate
work surfaces or laboratory equipment with nucleic acids used or
formed in the assay through spills, mishandling, aerosol formation,
etc. This nucleic acid can then carry-over and contaminate future
amplification and other nucleic acid assay procedures performed
using the same laboratory equipment and/or on the same work
surfaces. The presence of carryover products can result in the
unwanted consumption of amplification reagents or, in the case of
target-containing amplicon from a previous amplification procedure,
it can lead to an erroneous result, as amplification procedures are
capable of detecting the presence of even minute amounts of target
nucleic acid. In the case of a synthetic amplification reaction,
the desired nucleic acid product may become contaminated by
carry-over products and/or synthesis yields may be reduced.
[0006] Various methods have been devised to limit carryover
contamination. A PCR amplification product, for example, can be
deactivated from further amplification by irradiation with UV
light. See Ou et al., BioTechniques, 10:442-446 (1991); and Cimino
et al., Nucleic Acids Res., 19:99-107 (1991). Such irradiation in
the absence or presence of a DNA binding photoactivatable ligand
(e.g., isopsoralen) makes the product DNA nonamplifiable but
retains the specific hybridization property. In addition, use of a
3'-ribose primer in a PCR reaction produces nucleic acid that can
be readily destroyed by an alkali (e.g., NaOH). See Walder et al.,
Nucleic Acids Res., 21:4339-4343 (1993). Similarly, other
procedures are used to produce specific modified nucleic acids that
can be selectively destroyed by treatment with a specific enzyme.
Such modified nucleic acids have been produced by amplification in
the presence of dUTP as a substrate in a PCR reaction. Deoxy
U-containing product DNA can be deactivated by a U-specific enzyme
making the DNA nonamplifiable. See Integrated DNA Technologies
Technical Bulletin, Triple C primers (1992); and Longo et al.,
Gene, 93:125-128 (1990). Many of these methods function well with
DNA but require expensive reagents and affect the course of the
amplification procedure (e.g., requiring longer times and specific
reagents).
[0007] In a preferred method, work surfaces and laboratory
equipment exposed to nucleic acid products are treated with a 50%
bleach solution (i.e., a bleach solution containing about 2.5% to
about 3.25% (w/v) sodium hypochlorite) to deactivate nucleic acids.
See GEN-PROBE.RTM. Aptima Combo 2.RTM. Assay Package Insert, IN0037
Rev. A/2003-08. While this bleach solution is effective at
deactivating nucleic acids present on treated surfaces, it tends to
create noxious fumes in poorly ventilated areas and corrodes
laboratory equipment over time. Therefore, it is an object of the
present disclosure to provide a formulation containing a nucleic
acid deactivating agent that is stable in solution, has a tolerable
odor, and which is non-corrosive or is substantially less corrosive
than a standard 50% bleach solution.
SUMMARY
[0008] The present disclosure satisfies this objective by providing
a formulation that contains or can be combined with a nucleic acid
deactivating agent ("deactivating agent") in an amount sufficient
to deactivate nucleic acids contacted with the formulation in
solution or on a solid surface. By "deactivate" is meant that the
nucleic acid is altered such that it can no longer function as it
did prior to deactivation. For example, the nucleic acid may no
longer be capable of acting as a template in, or otherwise
interfering with (e.g., through the formation of primer-dimers), an
amplification reaction, binding to another nucleic acid or protein,
or serving as a substrate for an enzyme. The term "deactivate" does
not imply any particular mechanism by which the deactivating agent
of the formulation alters nucleic acids. The components of the
formulation include a corrosion-inhibiting agent, a wetting agent,
a solubilizing agent and, optionally, a deactivating agent. When
the formulation is comprised of all four components, the
corrosion-inhibiting agent is present in an amount sufficient to
reduce the corrosiveness of the deactivating agent, the wetting
agent is present in an amount sufficient to improve the dispersion
properties of the deactivating agent and/or to increase the
solubility of the deactivating agent and/or other material present
on a solid surface or in a solution, the solubilizing agent is
present in an amount sufficient to increase the solubility of the
deactivating agent, or the corrosion inhibiting agent, or the
wetting agent, or various combinations thereof, and the
deactivating agent is present in an amount sufficient to
substantially deactivate nucleic acids contacted with the
formulation. If the formulation does not include the deactivating
agent, then the amounts of the corrosion-inhibiting agent, the
wetting agent and the solubilizing agent are concentrated to
account for their decreased concentrations when combined with the
deactivating agent and any diluents (e.g., water) which may be used
to form a final working solution capable of deactivating nucleic
acids.
[0009] Deactivating agents of the present disclosure are selected
for their ability to substantially deactivate nucleic acids present
on a surface or in a solution, thereby preventing the nucleic acids
from acting as unintended templates in an amplification reaction or
otherwise contaminating a workspace, laboratory equipment or
materials, or working solutions. For certain applications, the
deactivating agents of the present disclosure may be used without
the corrosion-inhibiting agent, the wetting agent and/or the
solubilizing agent referred to above. Preferred deactivating agents
include bleach, sodium hypochlorite (NaOCl) (or hypochlorous acid
(HOCl), which results when chlorine ions are combined with water),
sodium hypochlorite and sodium bromide (NaBr), dichloroisocyanurate
(DCC), hydrogen peroxide (H.sub.2O.sub.2) and metal ions,
preferably copper ions (Cu.sup.++) (e.g., cupric sulfate
(CuSO.sub.4) or cupric acetate (Cu(CH.sub.3COO).sub.2.H.sub.2O)),
hydrogen peroxide in combination with metal ions and piperazine or
piperazine-containing formulations, acetate or ascorbate,
percarbonate (2Na.sub.2CO.sub.3.3H.sub.2O.sub.2), peroxymonosulfate
(KHSO.sub.5), peroxymonosulfate and potassium bromide (KBr),
hypobromite ions (OBr--) (e.g., hypobromous acid (HOBr)) and
halohydantoins (e.g., 1,3-dihalo-5,5-dimethylhydantoins).
Hypochlorite and hypobromite ions may be delivered to a solution
using a salt, such as sodium. Particularly preferred are
deactivating agents containing chloronium ions (Cl.sup.+), such as
sodium hypochlorite, a component of household bleach, or DCC. The
DCC may be substantially pure or it may be part of a DCC-containing
solution, such as ACT 340 PLUS 2000.RTM. disinfectant, containing
sodium dichloroisocyanurate dihydrate at 40% p/p. An advantage of
DCC is that it is less corrosive and, in some cases, more resistant
to inactivation by contaminating organic material than
hypochlorite.
[0010] While the deactivating agents of the present disclosure may
be provided, alone or as part of a formulation, in any amount
sufficient to deactivate nucleic acids, preferred concentration
ranges of above-described deactivating agents are as follows: (i)
from about 0.06% to about 3% (w/v), about 0.18% to about 1.8%
(w/v), about 0.6% to about 1.5% (w/v), or about 0.6% to about 1.2%
(w/v) sodium hypochlorite, or sodium hypochlorite and sodium
bromide, where the sodium hypochlorite:sodium bromide ratio is
about 5:1 to about 1:5, about 2:1 to about 1:2, or about 1:1; (ii)
from about 5 mM to about 400 mM, about 10 mM to about 200 mM, about
20 mM to about 100 mM, or about 40 mM to about 80 mM DCC; (iii)
from about 100 mM to about 880 mM, about 200 mM to about 880 mM, or
about 250 mM to about 800 mM percarbonate; (iv) from about 50 mM to
about 300 mM or about 100 mM to about 200 mM peroxymonosulfate or
peroxymonosulfate and potassium bromide, where the
peroxymonosulfate:potassium bromide ratio is about 2:1 to about 1:2
or about 1:1. These ranges reflect concentrations in final working
solutions to be used directly on a surface or in a solution and may
be adjusted where the formulation is a concentrate. The preferred
concentration ranges of hydrogen peroxide containing formulations
are described below.
[0011] When chlorine is a component of the deactivating agent
(e.g., sodium hypochlorite or DCC), the potential organic load on a
surface or in a solution that will be exposed to the deactivating
agent is a factor in determining the concentration of the
chlorine-containing component. This is because organic materials,
especially compounds containing primary amine and sulfhydryl
groups, react with chloronium ions and effectively scavenge them
from solution. Therefore, when selecting the concentration of the
chlorine containing component to use in the formulation for
deactivating nucleic acids, consideration must be given not only to
the expected amount of nucleic acid on the surface or in the
solution to be treated, but also to the expected organic load, as
well as sources of interfering substances of a non-organic origin.
Interfering substances may also affect non-chlorine based
deactivating agents and, for this reason, their influence on a
deactivating agent should be evaluated when determining the
concentration of the deactivating agent needed to deactivate
nucleic acids on a surface or in a solution.
[0012] The corrosion-inhibiting agents of the formulation are
selected to counter the corrosive effects of the deactivating
agent. As an example, bleach is a highly corrosive material that
can damage laboratory equipment and fixtures over time, requiring
early replacement. We unexpectedly discovered that the
corrosion-inhibiting agents do not interfere with the activity of
the deactivating agents. Corrosion-inhibiting agents of the present
disclosure include phosphate, borate, sodium bicarbonate,
detergents and other corrosion-inhibiting agents known in the art.
Particularly preferred is sodium bicarbonate. The concentration of
the corrosion-inhibiting agent present in the formulation, when
combined with the deactivating agent in a final working solution
for direct use on a surface or in a solution, is preferably in the
range of from about 10 mM to about 750 mM. The pH of the
corrosion-inhibiting agent should be selected to limit any loss in
the activity of the deactivating agent over time, yet still be
effective in reducing the corrosiveness of the deactivating agent.
By way of example, sodium salts of phosphate were found to
destabilize sodium hypochlorite at pH 6.4 and 7.5 but not at pH 9.1
and 9.5. Conversely, sodium salts of phosphate were found to
destabilize DCC at pH 9.1 and 9.5 but not at pH 6.4 and 7.5.
[0013] The wetting agent is included in the formulation to ensure
that the deactivating agent makes sufficient contact with the
surface being treated and/or to improve the solubility of the
deactivating agent and/or other material that may be present on a
surface or in a solution to be decontaminated (e.g., nucleic acids,
organic substances, oils or films, etc.). Detergents and
surfactants are preferred wetting agents because they reduce
surface tension and allow for more complete wetting of surfaces
with the deactivating agent. Additionally, detergents and
surfactants help to solubilize materials to be removed from
surfaces or deactivated in a solution. But because detergents and
surfactants tend to foam, detergent and surfactant types and
concentrations should be selected to limit foaming while providing
good wetting and solubilization qualities in the final working
solution. Preferred detergents and surfactants include sodium
dodecyl sulfate (SDS), lithium lauryl sulfate (LLS), Photo-Flo.RTM.
200 Solution (Eastman Kodak Company, Rochester, N.Y.; Cat. No.
146-4502), saponin, cetyl trimethylammonium bromide (CTAB),
Alconox.RTM. detergent containing 10-30% (w/w) sodium
dodecylbenzenesulfonate, 7-13% (w/w) sodium carbonate, 10-30% (w/w)
tetrasodium pyrophosphate and 10-13% (w/w) sodium phosphate
(Alconox, Inc., White Plains, N.Y.; Cat. No. 1104-1), MICRO-90.RTM.
cleaning solution containing less than 20% (w/w) glycine,
N,N'-1,2-ethanediylbis-(N-(carboxymethyl)-,tetra-sodium salt, less
than 20% (w/w) benzenesulfonic acid, dimethyl-, ammonium salt, less
than 20% (w/w) benzenesulfonic acid, dodecyl-, cpd. with
2,2',2''-nitrilotris (ethanol), and less than 20% (w/w)
poly(oxy-1,2-ethanediyl),alpha-(undecyl)-omega-hydroxy
(International Products Corporation, Burlington, N.J.), and
polyoxyethylene detergents (e.g., Triton.RTM. X-100). Most
preferred are SDS and LLS at a concentration range preferably of
from about 0.005% to about 1% (w/v), about 0.005% to about 0.1%
(w/v), or about 0.005% to about 0.02% (w/v) in the final working
solution.
[0014] The formulation further includes the solubilizing agent for
helping to maintain the components of the formulation in solution.
The solubilizing agent may contain, for example, an organic solvent
or an emulsifying agent, such as that found in Fragrance No.
2141-BG, a citrus fragrance available from International Flavors
and Fragrances (IFF) of Hazlet, N.J. Fragrances may have the
additional advantage of masking the odor of the deactivating agent
(e.g., sodium hypochlorite). Organic solvents that may be included
in the formulation include benzyl acetate, PS20 and isopropanol.
Emulsifying agents that may be included in the formulation include
polyoxyethylene sorbitan mono-palmitate (Tween.RTM. 40), lecithin
and ethylene glycol distearate. In some cases, the inventors
discovered that the wetting agent was necessary to maintain the
solubilizing agent in solution when combined with the
corrosion-inhibiting agent and that the solubilizing agent was
necessary to maintain the detergent in solution when combined with
the corrosion-inhibiting agent. And, when the formulation also
include the deactivating agent, all four components remained in
solution. When the solubilizing agent is a fragrance, such as IFF
Fragrance No. 2415-BG or 2141-BG, the preferred concentration of
the solubilizing agent in a final working solution which contains
the deactivating agent is in a range from about 0.001% to about 20%
(v/v), about 0.001% to about 2% (v/v), or about 0.002% to about
0.2% (v/v). The concentration of the solubilizing agent selected
should be such that it has no substantial impact on the activity
and stability of the deactivating agent and the
corrosion-inhibiting agent.
[0015] In a particularly preferred formulation of the present
disclosure, a 6.7.times. concentrate is prepared having the
following formulation: 600 mM sodium bicarbonate, pH 9.3+0.1% SDS
(w/v)+0.05% (v/v) IFF Fragrance No. 2145-BG. When the formulation
further includes a deactivating agent, a particularly preferred
formulation is as follows: 0.6% (w/v) sodium hypochlorite+90 mM
sodium bicarbonate, pH 9.3+0.015% (w/v) SDS+0.0075% (v/v) IFF
Fragrance No. 2145-BG. Of course, the components and concentrations
of these preferred formulations can be modified in the manner
described herein, without the exercise of undue experimentation, to
arrive at alternative formulations that are stable and capable of
deactivating nucleic acids on a surface or in a solution while
minimizing the potential corrosive effect of the deactivating agent
selected.
[0016] Based on our discovery that the order in which the agents
are combined can be important to preventing the formation of
precipitates or an otherwise non-homogenous formulation, a further
embodiment of the present disclosure is directed to a method of
making the above-described formulations. This method includes the
following ordered steps: (i) separately dissolving solid forms of a
corrosion-inhibiting agent and a wetting agent; (ii) combining
together the dissolved forms of the corrosion-inhibiting agent and
the wetting agent to form a mixture; and (iii) combining together a
solubilizing agent and the mixture to form a formulation comprising
the corrosion-inhibiting agent, the wetting agent and the
solubilizing agent, where the agents of this formulation remain
substantially in solution at 22.degree. C. (approximately room
temperature). If the solubilizing agent is provided in a solid
form, it too may be dissolved prior to combining the solubilizing
agent with the mixture. The deactivating agent can then be added to
the formulation, where the deactivating agent may be added directly
to the formulation or it may be dissolved prior to combining it
with the formulation. If water is used to dissolve any of the solid
forms of the agents, it is preferably distilled or deionized water.
For many of the formulations tested, it was discovered that
deviating from the above-ordered steps for combining the agents
resulted in the formation of non-homogenous solutions (e.g., the
solubilizing agent was first combined with either the
corrosion-inhibiting agent or the wetting agent).
[0017] For those applications that do not require a wetting agent,
we discovered that the deactivating agent and the
corrosion-inhibiting agent may be combined without substantially
affecting the ability of the deactivating agent to deactivate
nucleic acids. Therefore, formulations of the present disclosure
containing corrosive deactivating agents are not required to
include a wetting agent and a solubilizing agent.
[0018] Another preferred deactivating agent of the present
disclosure comprises hydrogen peroxide and metal ions, such as, for
example, copper, cobalt, iron or manganese ions (e.g., cupric
sulfate or cupric acetate). For solution-based applications in
particular, we found that the metal ions (e.g., copper ions) can be
stabilized in a chemical configuration that is active with hydrogen
peroxide at deactivating nucleic acids when the deactivating agent
further includes piperazine or reagents that contain the piperazine
group, such as the buffer HEPES
(N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid)), acetate,
and like compounds and reagents. Surprisingly, we further
discovered that piperazine can stimulate the deactivation of
nucleic acids in the presence of hydrogen peroxide and copper ions.
The hydrogen peroxide of this deactivating agent is preferably
present at a concentration range of from about 0.5% to about 30%
(w/v), about 1% to about 15% (w/v), or about 1% to about 6% (w/v).
Where, for example, copper sulfate is the source of the metal ions,
the preferred concentration range of copper sulfate is from about
0.1 mM to about 5 mM, about 0.5 mM to about 2.5 mM, or about 1 mM
to about 2.5 mM. And if piperazine is used to stimulate the
deactivation of nucleic acids, the preferred concentration range of
piperazine is from about 0.5 mM to about 250 mM, about 1 mM to
about 200 mM, or about 10 mM to about 100 mM. A preferred
formulation of this embodiment comprises 3% (w/v) hydrogen
peroxide+2 mM CuSO.sub.4+50 mM piperazine, pH 5.5. This
deactivating agent has the advantage of being non-corrosive and
odorless.
[0019] In a further embodiment, the present disclosure relates to a
method for deactivating nucleic acids suspected of being present on
a surface. In this method, a first amount of a first reagent
comprising a deactivating agent is applied to the surface. Where
warranted by the expected presence of interfering substances (e.g.,
organic load and/or oily films or residue on the surface), and to
ensure adequate deactivation of nucleic acids present on the
surface, a second amount of a second reagent comprising a
deactivating agent can be applied to the surface. The first and
second reagents of this method may be the same or different and one
or both of the reagents may comprise one of the formulations
described above. In a preferred embodiment, the reagents are
removed from the surface, such as by wiping with an absorbent
material (e.g., a paper towel or cotton gauze), before the reagents
have had an opportunity to completely evaporate. By wiping before
the reagents have completely evaporated, nucleic acids that may not
have been chemically deactivated by the reagents can be
mechanically removed by the absorbent material. Additionally, by
wiping with an absorbent material after the first application,
other materials solubilized by the first reagent that might consume
all or part of the deactivating agent in the second application can
be removed. Therefore, in a particularly preferred mode, there is
no substantial "soak time" between the applying and removing steps
of the preferred embodiment. This means that the delay between
application of a reagent to the surface and its removal therefrom
is no more than a few minutes, preferably no more than one minute,
and, more preferably, the removal of the reagent from the surface
immediately follows its application thereto. Also, to avoid all
possible sources of contamination, it is recommended that the
reagents for deactivating nucleic acids be applied with one gloved
hand and that removal of the reagents be performed with another
gloved hand.
[0020] To reduce the organic load on a surface prior to application
of the first reagent, the surface may be pre-treated with an
application of a detergent. Additionally, for surface applications,
it is recommended that the surface not be cleaned with water
following removal of the first or second reagents from the surface,
as the water may contain amplifiable nucleic acids or nucleic acids
or other chemicals that could interfere with an amplification
reaction.
[0021] In still another embodiment, the present disclosure relates
to a method for deactivating nucleic acids suspected of being
present in one or more conduits using a formulation described
above. The conduits may be present, for example, in one or more
pipettes or an aspirator manifold. In this method, the formulation
containing the deactivating agent is drawn into the one or more
conduits, such as by suctioning. The formulation is then dispensed
from the one or more conduits. After dispensing the formulation,
the one or more conduits may be exposed to a wash solution by
drawing the wash solution into the one or more conduits and then
dispensing the wash solution from the conduits. The wash solution
may be, for example, purified water or a reagent solution and is
used to rinse residual amounts of the formulation from the
conduits.
[0022] In yet another embodiment, the present disclosure relates to
a kit comprising, in one or more receptacles, a formulation as
described above for use in deactivating nucleic acids. In one
embodiment, if the kit includes a deactivating agent, the
deactivating agent is preferably contained in a receptacle separate
from one or more receptacles containing the corrosion-inhibiting
agent, the wetting agent and/or the solubilizing agent. One or more
of the components of the formulation may be provided in a
pre-measured amount suitable for making a specific volume of final
solution or as a bulk powder. If pre-measured, powder forms of the
component or components may be provided in packets or capsules or
as tablets to be dissolved in water before being combined with the
other components of the formulation. The kit may further include
instructions recorded in tangible form (e.g., paper, diskette,
CD-ROM, DVD or video cassette) for combining the deactivating agent
and the other components of the formulation. The kit may also
include one or more reagents for performing a nucleic acid
amplification reaction. Such reagents may include one or more
enzyme reagents (e.g., an RNA or a DNA polymerase) for use in
amplifying a nucleic acid sequence of interest. Enzyme reagents for
use in performing a transcription-based amplification, for example,
include a reverse transcriptase and an RNA polymerase (e.g., T7 RNA
polymerase). Other amplification reagents may also be included,
such as, for example, amplification oligonucleotides (e.g.,
primers, promoter-primers and/or splice templates), nucleotide
triphosphates, metal ions and co-factors necessary for enzymatic
activity.
BRIEF DESCRIPTION OF THE DRAWINGS
[0023] FIG. 1 is an electrophoretogram showing the results of a
fixed amount of a 71-mer, single-stranded DNA oligonucleotide
reacted with varying concentrations of bleach following
polyacrylamide gel electrophoresis (PAGE).
[0024] FIG. 2 is an electrophoretogram showing the results of a
fixed amount of a 60-mer, single-stranded DNA/RNA chimera
oligonucleotide reacted with varying concentrations of bleach
following PAGE. The RNA consisted of 2'-O-methyl
ribonucleotides.
[0025] FIG. 3 is comprised of two electrophoretograms showing the
results of a fixed amount of a 71-mer, single-stranded DNA
oligonucleotide reacted with varying concentrations of
dichloroisocyanurate or bleach, respectively, following PAGE.
[0026] FIG. 4 is an electrophoretogram showing the results of a
fixed amount of a 71-mer, DNA oligonucleotide reacted with varying
concentrations of hydrogen peroxide alone or in combination with a
fixed concentration cupric sulfate following PAGE.
[0027] FIG. 5 is an electrophoretogram showing the results of a
fixed amount of a 71-mer, DNA oligonucleotide reacted with varying
concentrations of hydrogen peroxide and a fixed amount of cupric
sulfate following PAGE.
[0028] FIG. 6 is comprised of two electrophoretograms showing the
results of a fixed amount of a 71-mer, single-stranded DNA
oligonucleotide reacted with varying concentrations of bleach in
the presence or absence of NALC following PAGE.
[0029] FIG. 7 is an electrophoretogram showing the results of a
fixed amount of a 71-mer, single-stranded DNA oligonucleotide
reacted with varying concentrations of hydrogen peroxide and a
fixed amount of cupric sulfate in the presence or absence of a
fixed amount of NALC or human serum following PAGE.
[0030] FIG. 8 is a graph showing the results of a real-time
amplification after reacting a target nucleic acid with varying
concentrations of bleach in a pure system.
[0031] FIGS. 9A-9H show assay results for nucleic acid deactivation
by bleach.
[0032] FIGS. 10A-10F show real-time transcription-mediated
amplification (TMA) results for nucleic acid deactivation by bleach
in the presence of organic load.
[0033] FIGS. 11A-11D show PAGE results for nucleic acid
deactivation by bleach in the presence of organic load.
[0034] FIG. 12 shows PAGE results illustrating scavenging effects
of Enzyme Dilution Buffer on DCC and bleach.
DETAILED DESCRIPTION
[0035] The present disclosure is directed in part to formulations,
methods and kits which are useful for deactivating nucleic acids.
These formulations, methods and kits are described above and in the
examples and claims which follow. In addition, the examples
describe screening methods for selecting formulations of the
present disclosure which are useful for deactivating nucleic acids
on work surfaces, laboratory equipment and/or in solution, or which
could be used as, for example, disinfectants. Such formulations may
also be useful for deactivating biological molecules, like proteins
and lipids. The examples further consider the effect of a number of
exemplary formulations in both pre- and post-amplification
applications.
EXAMPLES
[0036] The examples set forth below illustrate but do not limit the
disclosure.
Example 1
Effect of Various Concentrations of Bleach on Visualization of DNA
by Gel Electrophoresis
[0037] An experiment was conducted in which a 71-mer DNA
oligonucleotide was reacted with various concentrations of Ultra
Clorox.RTM. Bleach (The Clorox Company, Oakland, Calif.) at a
concentration of 6.15% (w/v) sodium hypochlorite, and the reaction
products were analyzed using polyacrylamide gel electrophoresis
(PAGE). Ten samples were prepared by mixing 2 .mu.L of the DNA
oligonucleotide, at a concentration of 173 .mu.g/mL, with distilled
water in sample vials before adding varying concentrations of
bleach to bring the total volume of each sample to 20 .mu.L. The
samples were mixed by vortexing for about 10 seconds and then
provided with 20 .mu.L of a 2.times.TBE-Urea sample buffer
containing 180 mM Tris base, 180 mM boric acid, 4 mM
ethylenediaminetetraacetic acid (EDTA), pH 8.0 (Invitrogen
Corporation, Carlsbad, Calif.; Cat. No. LC 6876), bringing the
total volume of each sample to 40 .mu.L. The samples were again
mixed by vortexing for about 10 seconds. Final bleach
concentrations in the samples ranged from 0 to 50% bleach, as set
forth in Table 1 below. A 10 .mu.L aliquot of each sample was
loaded into one of the 10 lanes of a 10% polyacrylamide TBE-Urea
gel, and the gel was run for 40 minutes at 180 V. When the run was
completed, the gel was removed from its cast, contacted with 100 mL
of a SYBR.RTM. Green I nucleic acid gel stain (Molecular Probes,
Eugene Oreg.; Cat. No. 57563) diluted 1/10,000 with distilled
water, and mixed at 10 rpm for 30 minutes. After staining, the gel
was photographed using a ChemiImager.TM. System 4400 (Alpha
Innotech Corporation, San Leandro, Calif.). The separated products
stained on a gel are commonly referred to as bands. A copy of the
resulting electrophoretogram is presented in FIG. 1.
TABLE-US-00001 TABLE 1 Bleach Concentrations Lane % Bleach 1 0 2
0.01 3 0.03 4 0.1 5 0.3 6 1 7 3 8 10 9 20 10 50
[0038] From the results illustrated in the electrophoretogram of
FIG. 1, it can be seen that the last visible band appears in lane
3. These results suggest that between 0.03% (0.25 mM) and 0.1%
(0.82 mM) sodium hypochlorite was needed to substantially alter the
DNA present in the samples. From the DNA oligonucleotide
concentration indicated above, it was determined that the
nucleotide concentration in the samples was 0.52 mM. Thus, the
sodium hypochlorite to nucleotide molar ratio was approximately
1:1, suggesting that about one mole sodium hypochlorite reacted
with about one mole nucleotide. Another similar experiment
comparing incubation times of 0 to 20 minutes showed no changes in
the appearance of oligonucleotide bands over the time course of
hypochlorite incubation, suggesting the reaction rate is rapid.
Example 2
Effect of Various Concentrations of Bleach on Visualization of a
DNA/RNA Chimera by Gel Electrophoresis
[0039] The experiment of Example 1 was repeated, substituting a
60-mer DNA/RNA chimeric oligonucleotide at a concentration of 200
ng/mL for the DNA oligonucleotide of that experiment. The RNA of
the chimera consisted of 2'-O-methyl ribonucleotides. A copy of the
resulting electrophoretogram appears in FIG. 2 and shows that most
of the oligonucleotide band disappeared at 0.1% bleach, again about
a 1:1 molar ratio of sodium hypochlorite to nucleoside. The
concentrations of bleach used in the various lanes of the gel of
this experiment are the same as those described in the experiment
of Example 1.
Example 3
Effect of Various Concentrations of Bleach on Visualization of DNA
by Gel Electrophoresis
[0040] Dichloroisocyanuric acid, sodium salt (DCC) (Sigma-Aldrich,
Milwaukee, Wis.; Prod. No. 21, 892-8) and Ultra Clorox.RTM. Bleach
(6.15% (w/v) sodium hypochlorite) were examined at varying
available chlorine concentrations in this experiment for their
comparative abilities to react with nucleic acid. The chlorine
concentrations tested are set forth in Table 2 below. In all other
aspects, including the use of the 71-mer DNA oligonucleotide, this
experiment was identical to the experiment detailed in Example
1.
TABLE-US-00002 TABLE 2 Chlorine Concentrations Lane Chlorine (mM) 1
0 2 0.8 3 0.24 4 0.8 5 2.4 6 8 7 24 8 80 9 160 10 400
[0041] The results of this experiment are illustrated in FIG. 3 and
indicate that pure DCC causes the disappearance of the DNA band at
lower concentrations than the bleach solution at the same chlorine
concentration.
Example 4
Effect of Various Concentrations of Hydrogen Peroxide and Hydrogen
Peroxide plus Cupric Sulfate on Visualization of DNA by Gel
Electrophoresis
[0042] In this experiment, a 71-mer DNA oligonucleotide present at
a concentration of 53 ng/mL was reacted with various concentrations
of 30% (w/v) hydrogen peroxide (Fisher Scientific, Tustin, Calif.;
Cat. No. BP2633-500) and 30% (w/v) hydrogen peroxide plus cupric
sulfate (Sigma-Aldrich, Milwaukee, Wis.; Prod. No. 45, 165-7), and
the reaction products were analyzed using polyacrylamide gel
electrophoresis (PAGE). Ten samples were prepared in the manner
indicated in Table 3 below, with the DNA and water being combined
prior to adding 30% (w/v) hydrogen peroxide (8.8 M) and/or 1 mM
cupric sulfate. The remaining procedural details of this experiment
are the same as those set forth in Example 1. The concentration of
peroxide in each lane is set forth in Table 4 below.
TABLE-US-00003 TABLE 3 Sample Mixtures Components (.mu.L) DNA
CuSO.sub.4 H.sub.2O.sub.2 H.sub.2O Sample 1 2 0 0 18 Number 2 2 2 0
16 3 2 0 16 2 4 2 2 0.33 15.7 5 2 2 1 15 6 2 2 2 14 7 2 2 4 12 8 2
2 8 8 9 2 2 12 4 10 2 2 16 0
TABLE-US-00004 TABLE 4 Hydrogen Peroxide Concentrations Lane %
H.sub.2O.sub.2 (w/v) 1 0 2 0 3 24 4 0.5 5 1.5 6 3 7 6 8 12 9 18 10
24
[0043] The resulting electrophoretogram appears in FIG. 4 and
indicates that the peroxide and the cupric sulfate do not
independently cause the disappearance of the DNA oligonucleotide
bands at the indicated concentrations. However, the
electrophoretogram does appear to demonstrate that mixtures of
peroxide and cupric sulfate are effective at causing the
disappearance of the DNA oligonucleotide bands at all
concentrations tested. This suggests that the cupric sulfate may
function as a catalyst for the peroxide in the degradation of
nucleic acids.
Example 5
Effect of Various Concentrations of Hydrogen Peroxide in the
Presence of Cupric Sulfate on Visualization of DNA by Gel
Electrophoresis
[0044] The experiment of Example 4 was repeated using lower
concentrations of the hydrogen peroxide component and 100 .mu.M
cupric sulfate in all lanes of the gel. The final concentration of
peroxide in each lane of the gel is set forth in Table 5 below.
TABLE-US-00005 TABLE 5 Peroxide Concentrations Lane %
H.sub.2O.sub.2 (w/v) 1 0 2 0.0005 3 0.005 4 0.01 5 0.02 6 0.04 7
0.1 8 0.2 9 0.4 10 1
[0045] A copy of the resulting electrophoretogram appears in FIG. 5
and shows no band at 0.2% (w/v) hydrogen peroxide and only a faint
band at 0.1% (w/v) hydrogen peroxide.
Example 6
Effect of NALC Upon Reaction of Bleach with DNA
[0046] Bleach is known to react with a variety of organic
materials. These materials may thus interfere with the deactivation
of nucleic acids by reacting with and consuming the bleach. The
presence of these organic materials thus constitutes an "organic
load" that must be compensated for by the presence of sufficient
bleach to react with both the DNA and the organic materials. In
this experiment, the scavenging effect of N-acetyl-L-cysteine
(NALC), an organic load compound (i.e., a compound that may be
expected to consume bleach), was examined in the presence of
varying concentrations of Ultra Clorox.RTM. Bleach. NALC is a
reducing agent found in some enzyme reagents intended for use in
amplification reactions. Two sets of 10 samples were prepared in
this experiment, each sample containing 2 .mu.L of a 71-mer DNA
oligonucleotide at a concentration of 173 mg/mL. The first set of
samples contained no NALC, while each sample of the second set of
samples contained 16 .mu.L NALC at a concentration of 11.4 mg/mL.
The samples were prepared by first providing the DNA and NALC (if
any) to sample vials and mixing the samples containing NALC by
vortexing for about 10 seconds. The bleach was then added to both
sets of samples at varying concentrations, along with distilled
water, to bring the total volume of each sample to 20 .mu.L. The
samples were mixed by vortexing for about 10 seconds before adding
20 .mu.L of a 2.times.TBE-Urea sample buffer (Invitrogen
Corporation; Cat. No. LC 6876), bringing the total volume of each
sample to 40 .mu.L. The samples were again mixed by vortexing for
about 10 seconds. Final bleach concentrations in the samples ranged
from 0% to 50% bleach, as set forth in Table 6 below. A 10 .mu.L
aliquot of each sample was loaded into one of 10 lanes of a 10%
polyacrylamide TBE-Urea gel, a separate gel being provided for each
of the two sets of samples, and the gels were run for 40 minutes at
180V. When the runs were completed, the gels were removed from
their casts, contacted with 100 mL of a SYBR.RTM. Green I nucleic
acid gel stain (Molecular Probes; Cat. No. S7563) diluted 1/10,000
with distilled water, and mixed at 10 rpm for 30 minutes. After
staining, the gels were photographed using a ChemiImager.TM. System
4400, and a copy of the resulting electrophoretogram is presented
in FIG. 6.
TABLE-US-00006 TABLE 6 Bleach Concentrations Lane % Bleach 1 0 2
0.01 3 0.03 4 0.1 5 0.3 6 1 7 3 8 10 9 20 10 50
[0047] From the results illustrated in the electrophoretograms of
FIG. 6, it can be seen that the last clearly visible band appears
in lane 3 (0.03% (v/v) bleach) of the gel having samples containing
no NALC and in lane 8 (10% (v/v) bleach) of the gel having samples
containing NALC. These results indicate that the concentration of
bleach needed to cause the disappearance of the DNA bands is
affected by the presence of NALC, which likely competes with the
DNA for reaction with bleach.
Example 7
Effect of NALC and Human Serum Upon Reaction of Hydrogen Peroxide
and Cupric Sulfate Mixture with DNA
[0048] In this experiment, the effect of NALC and human serum upon
the reaction of various concentrations of hydrogen peroxide and
cupric sulfate with DNA was examined. A set of 11 samples was
prepared, each sample containing 2 .mu.L of a 71-mer DNA
oligonucleotide at a concentration of 53 .mu.g/mL. Other components
of the samples included 100 .mu.M cupric sulfate, 30% (w/v)
hydrogen peroxide, and NALC at a concentration of 11.4 mg/mL. The
amount of each component in the sample vials is set forth in Table
7 below. The samples were prepared by combining all sample
components, except the hydrogen peroxide, in sample vials and
mixing by vortexing for about 10 seconds. After mixing, the
hydrogen peroxide was added to the samples at varying
concentrations, bringing the total volume of sample 1 to 20 .mu.L
and samples 2-11 to 22 .mu.L and giving the final concentrations
indicated in Table 8 below. The samples were again mixed by
vortexing for about 10 seconds before adding 20 .mu.L of a
2.times.TBE-Urea sample buffer (Invitrogen Corporation; Cat. No. LC
6876), bringing the total volume of sample 1 to 40 .mu.L and
samples 2-11 to 42 .mu.L. The remainder of the procedure and
sources of the reagents were identical to that set forth in Example
6 above. A copy of the resulting electrophoretogram is presented in
FIG. 7.
TABLE-US-00007 TABLE 7 Sample Mixtures Components (.mu.L) Human DNA
CuSO.sub.4 H.sub.2O.sub.2 NALC Serum H.sub.2O Sample 1 2 0 0 0 0 18
Number 2 2 2 1 0 0 17 3 2 2 4 0 0 14 4 2 2 12 0 0 6 5 2 2 1 4 0 13
6 2 2 4 4 0 10 7 2 2 12 4 0 2 8 2 2 0 0 4 14 9 2 2 1 0 4 13 10 2 2
4 0 4 10 11 2 2 12 0 4 2
TABLE-US-00008 TABLE 8 Peroxide Concentrations Lane %
H.sub.2O.sub.2 (w/v) 1 0 2 1.36 3 5.45 4 16.36 5 1.36 6 5.45 7
16.36 8 0 9 1.36 10 5.45 11 16.36
[0049] The results illustrated in the electrophoretograms of FIG. 7
show that NALC and serum interfere with the reaction of the
hydrogen peroxide and cupric sulfate mixture with DNA. Thus, these
results demonstrate that the amount of hydrogen peroxide needed to
cause the disappearance of the DNA bands is affected by the
presence of NALC and human serum, which likely compete with the DNA
for reaction with bleach.
Example 8
Reaction of Nucleic Acids with Bleach in a Pure System
[0050] This experiment was conducted to evaluate the ability of
various bleach concentrations to deactivate purified ribosomal RNA
derived from Neisseria gonorrhoeae ("target") in a pure system.
Eight sample tubes were initially set up to contain 4 .mu.L of
target-containing water and 4 .mu.L of bleach in the concentrations
indicated in Table 9. For sample tubes 6 and 8, 4 .mu.L of water
was used in place of a bleach solution). The bleach used in this
experiment was Ultra Chlorox.RTM. Bleach (6.15% (w/v) sodium
hypochlorite). After set up, the contents of the sample tubes were
incubated for 5 minutes at room temperature.
TABLE-US-00009 TABLE 9 Bleach Concentrations Initial Target Initial
Bleach Final Bleach Sample Concentration Concentration
Concentrations Tube (copies/.mu.L) % (v/v) % (v/v) 1 10.sup.8 40 20
2 10 5 3 4 2 4 1 0.5 5 0.4 0.2 6 0 0 7 0 40 20 8 0 0
[0051] Following the room temperature incubation, 392 .mu.L of
water (chilled on ice) was added to each sample tube. The samples
then were analyzed by a real-time Transcription-Mediated
Amplification (TMA) assay. In the assay, amplification reaction
mixtures were prepared by combining a 4 .mu.L aliquot from each
sample tube with 300 .mu.L of an Amplification Reagent (44.1 mM
HEPES, 2.82% (w/v) trehalose, 33.0 mM KCl, 9.41 mM rATP, 1.76 rCTP,
11.76 rGTP, 1.76 mM UTP, 0.47 mM dATP, 0.47 mM dCTP, 0.47 mM dGTP,
0.47 mM dTTP, 30.6 mM MgCl.sub.2, 0.30% (v/v) ethanol, 0.1% (w/v)
methyl paraben, 0.02% (w/v) propyl paraben, and 0.003% (w/v) phenol
red) at pH 7.7 and spiked with 25.6 pmol of a T7 promoter-primer
and 20.0 pmol of a non-T7 primer for amplifying a region of the
target following a Transcription-Mediated Amplification (TMA)
procedure (see Kacian et al., U.S. Pat. No. 5,399,491) and 80 pmol
of a molecular beacon probe for detecting the resulting amplicon in
real-time (see Tyagi et al., "Detectably Labeled Dual Conformation
Oligonucleotide Probes, Assays and Kits," U.S. Pat. No. 5,925,517).
The probes and primers of this experiment were synthesized on an
Expedite.TM. 8909 Nucleic Acid Synthesizer (Applied Biosystems,
Foster City, Calif.) using standard phosphoramidite chemistry. See,
e.g., Caruthers et al., Methods in Enzymology, 154:287 (1987). The
molecular beacon probes were synthesized to include interacting
CyTM5 and BHQTM dyes using Cy5-CE phosphoramidite (Glen Research
Corporation, Sterling, Va.; Cat. No. 10-5915-90) and 3'-BHQ-2
Glycolate CPG (BioSearch Technologies, Inc., Novato, Calif.; Cat.
No. CG5-5042G-1).
[0052] Amplification reaction mixtures were then set up in a
96-well Microtiter.RTM. plate (Thermo Labsystems, Helsinki,
Finland; Cat. No. 9502887) in replicates of three, each well
containing 75 .mu.L of a light mineral oil and 75 .mu.L of the
amplification reaction mixture. The plates were covered with
ThermalSeal sealing film (Sigma-Aldrich Co., St. Louis, Mo.;
Product No. Z36, 967-5) and incubated in a Solo HT Microplate
Incubator (Thermo Electron Corporation; Milford, Mass.) for 15
minutes at 62.degree. C. to permit hybridization of the
promoter-primer to the target, followed by a second 15 minute
incubation in the Solo HT Microplate Incubator at 42.degree. C.
After incubating the contents of the plate, a multi-channel
pipettor was used to add 25 .mu.L of an Enzyme Reagent (50 mM
N-acetyl-L-cysteine (NALC), 58 mM HEPES, 3.03% (w/v) trehalose, 10%
Triton.RTM. X-100 detergent, 1.04 mM EDTA, 20% (v/v) glycerol, 120
mM KCl, 120 RTU/.mu.L Moloney murine leukemia virus ("MMLV")
reverse transcriptase, and 80 U/.mu.L T7 RNA polymerase, where one
"unit" of activity is defined as the synthesis and release of 5.75
fmol cDNA in 15 minutes at 37.degree. C. for MMLV reverse
transcriptase, and the production of 5.0 fmol RNA transcript in 20
minutes at 37.degree. C. for T7 RNA polymerase) at pH 7.0 to each
sample Immediately after each set of Enzyme Reagent additions, the
contents of the reaction wells were mixed by stirring with the
corresponding pipette tips held by the pipettor. To measure the
formation of amplicon in real-time, the plate was transferred to a
Fluoroskan Ascent microplate fluorometer (Thermo Electron
Corporation; Product No. 5210470) and incubated for 60 minutes at
42.degree. C. Fluorescence from the reaction wells was measured in
30 second increments using a 639 nm excitation filter and 671 nm
emission filter.
[0053] The results of this experiment are reported in the graph of
FIG. 8, which plots relative fluorescent units (RFU) on the y-axis
and time in minutes on the x-axis. The results show that even at
0.2% bleach, the lowest bleach concentration tested, the target
nucleic acid in this pure system was deactivated, such that it
could not be detectably amplified. Detectable amplification in this
experiment would have been RFU value more than two-fold the
background RFU value (sample tube 8) in a 60 minute amplification
period.
Example 9
Further Characterization of Nucleic Acid Deactivation in a Pure
Bleach System
[0054] Several formulations were tested for efficacy in
deactivating nucleic acids using multiple assays.
[0055] A. Real-time TMA Results
[0056] Neisseria gonorrhoaea (Ngo) ribosomal RNA (rRNA) was reacted
with 0-20% commercial bleach, where the lowest bleach concentration
was 0.2%, in a pure system and reaction products were analyzed by
real-time TMA assays (see Example 8). Even at the lowest bleach
concentration the rRNA was inactivated within the limits of
sensitivity of the real-time assay (FIG. 9A).
[0057] Chlamydia trachomatis (Ctr) rRNA also was reacted with 0-20%
bleach, where the lowest bleach concentration was 0.016%, in a pure
system and reaction products were analyzed by real-time TMA assays.
The lowest bleach concentration also inactivated the rRNA (FIG.
9B).
[0058] B. Capillary Electrophoresis Results
[0059] Ribosomal RNA was reacted with bleach in solution and
products were analyzed by capillary electrophoresis. An Agilent
2100 Bioanalyzer was utilized to characterize nucleic acids exposed
to deactivation solutions. In a 10 .mu.L total reaction, the
following were added (in order): (a) Milli-Q H.sub.2O or buffer,
(b) an indicated amount of reagent (e.g., --OCl from bleach or
H.sub.2O.sub.2), and (c) 0 nM (blank) or 150 nM (718 .mu.M=470
ng/.mu.L nt) Mycobacterium tuberculosis (Mtb) rRNA or 15 nM (71.8
.mu.M=47.0 ng/.mu.L nt) Mtb rRNA. The reactants were incubated for
10 min at room temperature (ca. 23.degree. C.), and 90 .mu.L 1 mM
sodium ascorbate (900 .mu.M final) then was added. As in the
LabChip.RTM. protocol (Agilent Technologies, Inc.; Palo Alto,
Calif.), the RNA ladder was denatured at 70.degree. C. for 2 min,
and then 1 .mu.L of each reaction was loaded into wells on RNA 6000
Nano LabChip.RTM. or Pico LabChip.RTM. (Agilent Technologies, Inc.;
Palo Alto, Calif.) containing 5 .mu.L sample buffer. The components
were mixed and the assay Prokaryote Total RNA was run in the Bio
Sizing program (Agilent Technologies, Inc.; Palo Alto, Calif.).
[0060] Results from the capillary electrophoresis analysis showed a
1:1 ratio of hypochlorite-to-rRNA nucleotide substantially
eliminated rRNA peaks (FIG. 9C to 9F). A time course of the
reaction between rRNA and bleach also was performed (FIGS. 9G and
9H). The reaction with both the 16S and 23S subunits is very fast,
essentially over within 1 min, with pseudo-first order rate
constants for the decay of rRNA approaching at least 0.02
s.sup.-1.
[0061] C. Conclusions
[0062] Reaction of bleach (hypochlorite) with nucleic acids in a
pure system was rapid and essentially complete at a 1:1 ratio of
hypochlorite to nucleoside. These data suggested that any observed
lack of decontamination of nucleic acids in the laboratory using
bleach was not due to an inherently slow reaction of hypochlorite
with the nucleic acids or the need for a high molar excess of
bleach over the nucleic acids.
Example 10
Further Characterization of Nucleic Acid Deactivation by Bleach in
the Presence of Organic Load
[0063] Effects of N-acetyl-L-cysteine (NALC), an organic load
material, on the reaction between bleach and oligonucleotides were
characterized by PAGE in Example 6. Presented hereafter is a
characterization of the effects of NALC and other organic load
materials on the reaction between oligonucleotides and bleach using
PAGE and other characterization methods.
[0064] A. Real-Time TMA Results
[0065] Ribosomal RNA was reacted with bleach in the presence of
different amounts of various organic load materials. The ability of
this RNA to be amplified was then tested using real-time TMA.
Organic load materials included Amplification, Hybridization,
Enzyme and Selection Reagents from the Aptima Combo 2.RTM. Assay
kit (Catalog No. 1032; Gen-Probe Incorporated; San Diego, Calif.),
and mixtures thereof, urine transport medium (UTM; Catalog No. 1040
Aptima Combo 2.RTM. Assay Urine Specimen Collection Kit for Male
and Female Urine Specimens; Gen-Probe), swab transport medium
(STM), KOVA-Trol.TM. (Hycor Biomedical Inc.; Garden Grove, Calif.),
bovine serum albumin (BSA), lithium lauryl sulfate (LLS) and human
plasma. Of these compounds, UTM and Enzyme Reagent were most
effective at interfering with reaction of the bleach with RNA. In
one experiment, 20% commercial bleach was required to overcome the
effects of UTM, which is in contrast to the very rapid and complete
reaction of rRNA with 0.016% bleach in the absence of organic load
materials (FIGS. 10A-10F).
[0066] B. PAGE Results
[0067] PAGE was performed using a procedure similar to that
disclosed in Example 1. Briefly, a known amount of a 71-mer
oligonucleotide was incubated with a formulation having a known
concentration of candidate reagent. A 1.times. volume of
2.times.TBE-urea loading buffer (180 mM Tris, 180 mM boric acid, 4
mM EDTA, pH 8.0) was added to the mixture solution and vortexed for
10 seconds. Ten microliters of sample was loaded in each lane of a
10% polyacrylamide TBE-Urea gel. The gel was run in 1.times.TBE
running buffer at 180 V for 35 to 40 minutes depending on the
length of oligonucleotide. The gel then was removed from the cast
and stained in 1/10,000 SYBr Green I dye solution for 20 minutes.
The stained gel was imaged using a ChemiImager.TM. 4400.
[0068] Oligonucleotides were reacted with bleach in the presence of
various concentrations of organic load compounds, and reaction
products were analyzed by PAGE. Serum, Amplification Reagent and
the NALC in Enzyme Dilution Buffer interfered with the reaction of
bleach with the oligonucleotide (FIGS. 11A-11D).
[0069] C. RP-HPLC Results
[0070] Reverse phase (RP) HPLC was utilized to characterize nucleic
acids exposed to deactivation solutions using standard procedures.
Specifications for the HPLC apparatus and methodology utilized were
as follows. A Zorbax.RTM. Eclipse XDB C-8 Reverse Phase Column
(Agilent Technologies, Inc.; Palo Alto, Calif.) having a 4.6 mm
internal diameter and a 15 cm length was utilized. Triethyl
ammonium acetate (TEAA)/acetonitrile was utilized as the mobile
phase, where Buffer A contained 0.1 M TEAA and Buffer B contained
100% acetonitrile. A gradient of 5%-100% Buffer B was utilized in a
time interval of 15 minutes at a flow rate of 0.5 mL/min. 50 .mu.L
oligonucleotide samples having an optical density of 2.0 OD
(oligonucleotide 26mer=10 .mu.M) were injected on the column and
column output was detected at a wavelength of 254 nm.
[0071] Reaction of bleach with a 26mer DNA oligomer in the presence
of NALC and subsequent chromatography using RP-HPLC revealed that
NALC interfered with the reaction of bleach with DNA. These results
confirmed PAGE findings in Example 6.
[0072] D. Conclusions
[0073] Materials that effectively interfered with the reaction of
bleach with nucleic acids were Urine Transport Medium (UTM) and the
NALC in Enzyme Dilution Buffer (EDB). Materials that moderately
interfered with the reaction of bleach with nucleic acids were Swab
Transport Medium (STM), Hybridization Reagent, Amplification
Reagent and human serum. Materials that weakly interfered with the
reaction of bleach with nucleic acids (or not at all) were
Selection Reagent, Aptima Combo 2.RTM. Assay Target Capture
Reagent, lithium lauryl sulfate and KOVA-Trol.TM.. From this
analysis, it was determined that organic load material, especially
materials containing primary amine and sulfhydryl groups, reacted
with bleach and consumed it so that it was not all available to
deactivate the nucleic acids. Loss of decontamination power of
bleach at lower concentrations was not due to slow reaction rates
or the need for excess hypochlorite over nucleotides, but rather
consumption of bleach by other compounds.
Example 11
Further Screens of Alternative Formulations and Conditions
[0074] Alternative formulations to bleach, such as solutions
containing dichloroisocyanuric acid (DCC) or hydrogen peroxide and
copper ions, were characterized in Examples 3 and 4 by PAGE. These
and additional alternative formulations were characterized by PAGE
and other assays as described hereafter.
[0075] A. PAGE Results
[0076] A 71-mer oligonucleotide was reacted with various candidate
compounds and the products were analyzed using PAGE. Solutions
containing DCC or hydrogen peroxide with copper sulfate were
tested, among other formulations. As shown in Example 3, DCC, which
is less corrosive than bleach, was as effective as bleach for
deactivating the oligonucleotide, if not more so. The effects of
scavengers including Enzyme Dilution Buffer (EDB) and serum on DCC
were also tested and compared with their effects on bleach. Similar
effects were observed as shown in FIG. 12 (results are for EDB;
serum results not shown). As shown in Examples 4, and 7, a solution
containing hydrogen peroxide and copper sulfate, which was odorless
and non-corrosive, was reasonably effective at (1) changing
oligonucleotide migration or oligonucleotide band retention, and
(2) overcoming the effects of organic load.
[0077] Other candidate solutions were characterized by incubating
them with oligonucleotide and analyzing the resulting reaction
products by PAGE. The following reagents exhibited little or no
changes to nucleic acid migration or band intensity in this assay:
(1) peroxymonosulfate (KHSO.sub.5) with or without copper sulfate;
(2) perborate; (3) percarbonate; (4) hydrogen peroxide with KBr;
and (5) NucleoClean.TM. (Chemicon International, Inc.; Temecula,
Calif.).
[0078] B. RP-HPLC Results
[0079] The RP-HPLC retention shift assay (described previously) was
used to screen several bleach alternative candidates in the
presence or absence of organic load material (NALC). A summary is
provided in Table 10 below of the efficacy of the alternative
formulations tested as compared to 10% bleach, where "=" is roughly
equivalent, "<" is less effective and ">" is more
effective.
TABLE-US-00010 TABLE 10 Effectiveness of Bleach Alternative
Formulations Bleach Alternative Reagent Organic Load Effectiveness
NaBr/NaOCl 70 mM NALC > KBr/peroxomonosulfate 70 mM NALC <
ClO2 70 mM NALC < 10% bleach/peroxide 70 mM NALC = Citric Acid
None < citric acid/peroxide None < 10% bleach/citric acid/ 70
mM NALC = peroxide 10% bleach/peroxide/ 70 mM NALC = sodium
hydroxide phosphoric acid/peroxide None < peroxide/CuSO.sub.4
None =, > peroxide/CuSO.sub.4 70 mM NALC =, >
peroxide/CuSO4/phosphoric 70 mM NALC < acid 10% bleach/peroxide
70 mM NALC = Citric Acid None <
Formulations comprising (a) NaBr/NaOCl or (b) peroxide/CuSO.sub.4
were as effective or more effective for deactivating nucleic acids
as compared to bleach alone under the conditions of this
experiment.
[0080] C. Capillary Electrophoresis Results
[0081] Ribosomal RNA was reacted with various candidate
formulations in solution and the products were analyzed using a
capillary electrophoresis assay. In the assay, 1 mM
dichloroisocyanurate (DCC) and 17.5 mM peroxymonosulfate
(Virkon.RTM. S; DuPont Animal Health Solutions, United Kingdom),
tested separately, substantially eliminated peaks corresponding to
0.72 mM rRNA oligonucleotide. In situ-generated Cl.sub.2 (10 mM
peroxymonosulfate+20 mM KCl) partially eliminated 72 .mu.M rRNA
oligonucleotide. Tested separately, (a) in situ-generated Br.sub.2
(10 mM peroxymonosulfate+20 mM KBr), (b) between 10 and 100 .mu.M
dichloro-hydantoin or dibromo-hydantoin, (c) between 10 and 100
.mu.M hypobromite, and (d) 10 mM peroxymonosulfate+metal ions (1 mM
Cu.sup.2+, 1 or 10 mM Fe.sup.2+) substantially eliminated 72 .mu.M
rRNA oligonucleotide.
[0082] D. Real-Time TMA Results
[0083] Ribosomal RNA was reacted with various compounds in
solution, and the ability of the RNA to be amplified was then
tested using the real-time TMA assay described in Example 8. The
efficacies of certain formulations are described hereafter.
[0084] Virkon.RTM. S (Peroxymonosulfate).
[0085] The nucleic acid was reacted with a 2.5% Virkon.RTM. S
solution (about 8.7 mM peroxymonosulfate), which was a
substantially lower concentration than the organic load included in
the reaction (Enzyme Dilution Buffer (EDB) or Urine Transport
Medium (UTM) here). Thus, 2.5% Virkon.RTM. S solution did not
substantially inactivate the nucleic acid target in the presence of
5 .mu.L EDB or UTM.
[0086] DCC.
[0087] An 83 mM DCC solution, which was determined as approximately
equivalent to 10% bleach, inactivated target in the presence of
EDB.
[0088] Peroxymonosulfate/KBr.
[0089] Target rRNA in the presence of UTM was inactivated with 0.25
M peroxymonosulfate/0.25 M KBr. Other ratios tested were not as
effective, and an optimum ratio is determined by varying the ratio
in additional runs of the assay. At 0.25 M of each component,
intensive coloration and odor were observed (due to the Br.sub.2),
and after addition to UTM/Target mix, a residue formed. The residue
dissolved upon a 50.times. dilution in water. The stability of this
formulation may be characterized further by varying reaction
conditions in additional runs of the assay. If formulations
including these components are found to have limited stability,
they can be provided in dry powder formulations and the solutions
can be prepared shortly before use.
[0090] Perborate and Percarbonate.
[0091] Perborate was not sufficiently soluble at concentrations
useful in solution. Percarbonate was soluble to 880 mM (roughly the
equivalent of 3% peroxide). When combined with copper(II),
percarbonate at this concentration reacted with nucleic acid
essentially with the efficacy of 3% hydrogen peroxide. Percarbonate
evolved oxygen quite readily when mixed with copper(II), however,
indicating the stability of the active reagents would require
additional testing by the assay. Also, when percarbonate was
combined with copper(II)/piperazine, a yellow residue formed.
Enhanced activity was observed in solution (as with hydrogen
peroxide/copper(II)/piperazine), but the solution characteristics
were not ideal (lower solubility, foamy). Accordingly, while the
percarbonate solutions were effective nucleic acid deactivators,
the solution properties were less favorable than hydrogen peroxide
formulations. Provision of the components in dry form to prepare
solutions just prior to use would overcome some of these
disadvantages.
[0092] From these results, the compounds that were especially
effective (at appropriate concentrations) included bleach+peroxide,
KHSO.sub.5+KBr, DCC and peroxide+UTM. Compounds that were not as
effective under the particular conditions of the experiments
include 15% peroxide alone; peroxide+potassium, sodium or iron
ions; 5 mM bromo- or chloro-hydantoin and KMnO.sub.4. The
effectiveness of peroxide+copper was not determined at the time of
these studies since the corresponding control failed (i.e., the
reaction mix itself inhibited TMA). It also was determined 1 mM
CuSO.sub.4/3% H.sub.2O.sub.2 inactivated rRNA oligonucleotide to a
greater degree than 1 mM CuBr.sub.2/3% H.sub.2O.sub.2,
CuCl.sub.2/3% H.sub.2O.sub.2, or Cu(NO.sub.3).sub.2/3%
H.sub.2O.sub.2. Additionally, 1 mM Cu(OAc).sub.2/3% H.sub.2O.sub.2
inactivated rRNA to a greater degree than 1 mM CuSO.sub.4/3%
H.sub.2O.sub.2.
[0093] Results from the analytical methods described herein are
summarized in the following Table 11 below. In the Table, "+"
indicates the compound was deactivating; "-" indicates the compound
was not substantially deactivating under the conditions and by the
methods used; "*" indicates equivocal results were obtained and
further results can be obtained by repeating the assay at the
conditions shown; no notation indicates the conditions were not
examined by the indicated assay.
TABLE-US-00011 TABLE 11 Effectiveness of Deactivating Reagents
HPLC, Compound Bioanalyzer TMA MS PAGE HOCl + + + + HOBr + Cl.sub.2
(from - peroxymonosulfate + KCl) Br.sub.2 (from + + -
peroxymonosulfate + KBr) I.sub.2 (from peroxymonosulfate + - KI)
DCC (ACT 340 PLUS + + + 2000 .RTM. disinfectant) DCC + +
halo-hydantoins + + HOCl + tertiary amines - NaBr + NaOCl +
ClO.sub.2 - H.sub.2O.sub.2 - - - H.sub.2O.sub.2 + metal ions + +
H.sub.2O.sub.2 + metal ions + + ascorbate H.sub.2O.sub.2 + HOCl - -
H.sub.2O.sub.2, acidic - H.sub.2O.sub.2, acidic + metal ions +
H.sub.2O.sub.2, acidic + HOCl (two - step addition) H.sub.2O.sub.2,
basic + HOCl (two - step addition) H.sub.2O.sub.2 + KBr or NaCl - -
Chloramine-T - peracetic acid (Peroxill - 2000) perborate - -
percarbonate * - Virkon .RTM. S solution +/- - (peroxymonosulfate)
peroxymonosulfate + + peroxymonosulfate + - Cu(II) DNA AWAY .TM.
solution - DNA-OFF .TM. cleansing - solution DNAZAP .TM. +
decontamination solution NucleoClean .TM. - - decontamination
solution Citric acid -
In this Table, DNA AWAY.TM. is an alkali hydroxide solution
(Molecular BioProducts, Inc., San Diego, Calif.; Cat. No. 7010),
DNAZap.TM. is a pair of PCR DNA degradation solutions (Ambion,
Inc., Austin, Tex.; Cat. No. 9890), DNA-OFF.TM. is a non-alkaline
cleaning solution (Q-biogene, Inc., Irvine, Calif.; Cat. No.
QD0500), and NucleoClean.TM. is a PCR decontamination solution
(Chemicon International, Temecula, Calif.; Cat. No. 3097S). These
results showed bleach (at reduced levels), dichloroisocyanurate
(DCC), H.sub.2O.sub.2/Cu(II), peroxymonosulfate,
peroxymonosulfate/KBr (generates Br.sub.2) and hypobromite
displayed especially potent nucleic acid deactivation activity in
solution.
Example 12
Further Characterization of Nucleic Acid Deactivation Formulations
and Methods in a Nucleic Acid Amplification Procedure
[0094] Multiple formulations and various methods of applying them
were characterized for nucleic acid deactivation efficacy in an
Aptima Combo 2.RTM. Assay (described hereafter) and associated
components. Following is a list of materials utilized for the assay
and characterization process:
[0095] Amplification Reagent
[0096] Amplification Reconstitution Solution
[0097] Target Capture Reagent
[0098] Target Capture Reagent B
[0099] CT Positive Control
[0100] GC Positive Control
[0101] Oil Reagent
[0102] Wash Buffer
[0103] Urine Transport Media (UTM)
[0104] Swab Transport Media (STM)
[0105] Enzyme Reagent
[0106] Enzyme Reconstitution Solution
[0107] CT rRNA
[0108] GC rRNA
[0109] KOVA-Trol.TM. (Normal)
[0110] Probe Reagent
[0111] Probe Reconstitution Solution
[0112] Selection Reagent
[0113] Detection Reagent I
[0114] Detection Reagent II
[0115] Endocervical swabs
[0116] Household liquid bleach (Chlorox.RTM.)
[0117] Dichloroisocyanurate (DCC)
[0118] Household hydrogen peroxide, 3% U.S.P. (H.sub.2O.sub.2)
[0119] Cupric sulfate (Cu(II))
[0120] Peroxymonosulfate (KHSO.sub.5)
Following is a description of several analytical processes employed
for the characterization procedures.
[0121] A. Preparation of Positive and Negative Amplification
Reactions
[0122] Oil reagent (200 microliters) was added to 80 reaction tubes
(12.times.75 mm) 4.2.times.10.sup.10 copies of Chlamydia
trachomatis (CT) and Neisseria gonorrhoeae (GC) rRNA were spiked
into 3.15 mL of reconstituted Amplification Reagent. Seventy-five
microliters (1.times.10.sup.9 copies (.about.2.5 ng)) of this
spiked Amplification Reagent was added to 40 of the reaction tubes
(positive samples). Seventy-five microliters of Amplification
Reagent without target (negative samples) was added to the other 40
tubes. All 80 samples were incubated for 10 min at 62.degree. C.,
then 5 min at 42.degree. C. Twenty-five microliters of
reconstituted Enzyme Reagent was added to each tube, the rack was
removed from the water bath, the rack was shaken to mix tube
contents, and the rack then was quickly returned to the water bath.
Reaction tube contents were incubated 60 min at 42.degree. C.
(amplification), then for 10 min at 80.degree. C. (inactivation of
enzymes). Thirty-eight of the positive samples and 38 of the
negative samples were pooled and oil was removed from each pool.
The two remaining positive and negative samples were assayed
according to the standard Aptima Combo 2.RTM. manual assay protocol
(described above).
[0123] B. Preparation of CT+GC rRNA Samples
[0124] 5.times.10.sup.8 copies of CT and GC rRNA prepared by
standard procedures were added to 100 microliters of
UTM:KOVA-Trol.TM. in a 1:1 ratio (in some cases (indicated in the
table below), samples were added to 100 microliters of STM). The
desired number of replicates of this mixture can be prepared as a
pool before spotting on the surface.
[0125] C. Deacontamination Assay Protocol
[0126] Surface.
[0127] Decontamination assays were performed on 2.times.4 ft
sections of ChemSurf laboratory bench ("surface"). Before, between
and after the various experiments, the surface was cleaned with a
50% bleach solution (household liquid bleach (e.g., Ultra
Clorox.RTM. Bleach) diluted 1:1 with water) followed by a water
rinse. Wiping was accomplished with paper towels or large
Kimwipes.
[0128] Sample Application.
[0129] One-hundred microliters of each selected sample (see below)
was applied to the surface in a circular spot of about 1.5 inches
in diameter. Approximately eight samples were applied, evenly
spaced, on the surface. Samples were allowed to dry for
approximately 15-30 min.
[0130] Sample Collection.
[0131] A Gen-Probe endocervical swab was placed in 3 mL of Swab
Transport Medium (STM) in a transport tube labeled with the name of
the sample to be collected. The swab was removed from the transport
tube and, using a circular motion, each spot was swabbed where the
sample was applied. Each swab was returned to its transport tube,
the end of the swab was carefully snapped-off at the scoreline, and
the tube was closed using its penetrable cap, and then
vortexed.
[0132] Deactivation Formulations Tested.
[0133] Among the formulations tested were:
TABLE-US-00012 a) 10% bleach one application b) 10% bleach two
applications c) 40 mM DCC one application d) 40 mM DCC two
applications e) 3% H.sub.2O.sub.2, 1 mM Cu(II) one application f)
3% H.sub.2O.sub.2, 1 mM Cu(II) two applications g) 1%
H.sub.2O.sub.2, 1 mM Cu(II) one application h) 1% H.sub.2O.sub.2, 1
mM Cu(II) two applications i) 200 mM KHSO.sub.5 one application j)
200 mM KHSO.sub.5 two applications
[0134] Decontamination Protocol.
[0135] The decontamination protocol utilized included the following
steps:
[0136] 1. The surface was cleaned (see above).
[0137] 2. For negative controls a sample was collected from a
circular area of .about.1.5 inch in diameter, selected randomly on
the surface, before any positive samples were applied to the
surface.
[0138] 3. Approximately eight replicate CT & GC rRNA in
UTM:KOVA-Trol.TM. (1:1) (or S.TM.) samples (100 microliters each)
were spotted and evenly spaced on the surface.
[0139] 4. Spot 1 was treated with decontamination condition "a"
above (10% bleach, one application) as follows: the area containing
the sample (about 7.times.7 inch square with sample in the center)
was wetted with approximately 2 mL of reagent (in some cases
(indicated in table below) approximately 3 mL was used) and then
immediately wiped with a paper towel or large Kimwipe until it was
dry (the towel sometimes was flipped over during the process if
necessary to complete the drying). The towel and the glove that was
on the hand that performed the wiping were carefully discarded (the
other glove was discarded if there was a possibility it became
contaminated). A sample from the original spot of application was
collected using an endocervical swab as described above.
[0140] 5. Spot 2 was treated with condition "b" using the same
general method described in "4" above, but also with a second
application of the decontamination reagent.
[0141] 6. The sample spots then were treated with the
decontamination conditions listed above until all samples on the
surface were treated.
[0142] 7. The surface was cleaned as described above, and a
sufficient number of sample replicates were applied to complete
testing of the decontamination conditions plus one additional spot
(to be used as a positive control).
[0143] 8. Testing of decontamination conditions then was
completed.
[0144] 9. For last remaining sample spot (positive control), the
spot was swabbed directly without any application of
decontamination reagent.
[0145] 10. Steps 1-9 were completed for the negative amplification
and the positive amplification samples.
[0146] Assay Protocol.
[0147] Replicates (2.times.400 .mu.L) of each of the samples
collected in the decontamination studies described above were
assayed using an Aptima Combo 2.RTM. Assay, described below. The
assay amplified Chlamydia trachomatis (referred to herein as "CT"
or "Ctr") and Neisseria gonorrhoeae (referred to herein as "GC" or
"Ngo") template rRNA prepared by standard methodology ("positive
Amp") and also was run without template rRNA ("negative Amp"). The
assay was performed using the following general protocol: [0148] 1.
Reconstitute reagents using the docking collars. Reconstitute
Amplification Reagent with Amplification Reconstitution Solution,
Enzyme Reagent with Enzyme Reconstitution Solution, and Probe
Reagent with Probe Reconstitution Solution. [0149] 2. Dilute Target
Capture Reagent (TCR) Component B into Target Capture Reagent at a
1:100 dilution and mix well by hand. [0150] 3. Dispense 100 .mu.L
of the TCR:Component B mix into each reaction tube of a Ten-Tube
Unit (TTU, Catalog No. TU002; Gen-Probe). [0151] 4. Pierce the cap
and pipette 400 .mu.L of the controls into the appropriate tube in
the following order: Tube 1 (CT Positive Control) then Tube 2 (GC
Positive Control). [0152] 5. Transfer 400 .mu.L of each sample into
the appropriate tube of the TTU. [0153] 6. When all samples are
loaded in an appropriate rack (Catalog No. 4579; Gen-Probe), place
a sealing card on the TTU, and mix the samples by gently shaking by
hand. Do not vortex the rack. [0154] 7. Incubate at 62.degree. C.
in a water bath for 30 minutes. [0155] 8. Place the rack on the
bench and incubate for 30 minutes. [0156] 9. Load a Target Capture
System (TCS, Catalog No. 5210, Gen-Probe) with Ten-Tip cassettes
(Catalog No. 4578; Gen-Probe). Ensure that the wash bottle is
connected to the pump. [0157] 10. Prime the pump lines with two
flushes of Wash Reagent. [0158] 11. Place the rack on the TCS
magnetic base, remove sealing cards and cover with new cards (do
not stick down). Incubate for 5 minutes. [0159] 12. Turn on the
vacuum for the aspirator. The vacuum gauge must read between 9 and
11 in. Hg with the system correctly set up. Aspirate all liquid by
lowering the aspiration manifold slowly into the bottom of the
tubes. Tap the bottom of the tubes with the tips briefly. Avoid
holding the tips at the bottom of the tube. Aspirate until the all
foam is removed from the tube. [0160] 13. Add 1.0 mL of Wash
Reagent into each tube, by pumping the wash bottle once. [0161] 14.
Cover tubes with a sealing card and vortex on the multi-vortexer.
[0162] 15. Place rack on the TCS magnetic base for 5 minutes.
[0163] 16. Aspirate all liquid. [0164] 17. Add 75 .mu.L of the
reconstituted Amplification Reagent. [0165] 18. Add 200 .mu.L of
Oil Reagent. [0166] 19. Cover tubes with a sealing card and vortex
on the multi-vortexer. [0167] 20. Incubate the rack in a 62.degree.
C. water bath for 10 minutes. [0168] 21. Transfer the rack to a
circulating water bath at 42.degree. C. and incubate for 5 minutes.
[0169] 22. With the rack in the water bath, remove the sealing
card, and add 25 nL of the Enzyme Reagent to all of the reactions.
[0170] 23. Immediately cover with a sealing card, briefly remove
from the waterbath, and mix the reactions, gently shaking by hand.
[0171] 24. Incubate the rack at 42.degree. C. for 60 minutes.
[0172] 25. Remove the rack from the water bath and transfer to the
HPA area. Add 100 .mu.L of the reconstituted Probe Reagent. [0173]
26. Vortex on the multi-vortexer. [0174] 27. Incubate the rack in a
circulating water bath at 62.degree. C. for 20 minutes. [0175] 28.
Remove the rack from the water bath and incubate on the bench-top,
at room temperature, for 5 minutes. [0176] 29. Add 250 .mu.L of
Selection Reagent. [0177] 30. Cover tubes with a sealing card and
vortex on the multi-vortexer. [0178] 31. Incubate the rack at
62.degree. C. in a circulating water bath for 10 minutes. [0179]
32. Incubate the rack on the bench-top, at room temperature, for 15
minutes. [0180] 33. Light-off the reactions in a LEADER.RTM. HC+
Luminometer (Catalog No. 4747; Gen-Probe) Combo software.
[0181] Before assay, Ngo/Ctr rRNA samples were prepared by spiking
amplification-negative samples with 0.5 fg of CT rRNA (about
2.times.10.sup.2 copies) and 50 fg of GC rRNA (about
2.times.10.sup.4 copies). In addition, 5-10 negative assay controls
(STM only) were performed. Acceptance criteria were as follows:
TABLE-US-00013 Specifications Controls Amplification Positive
Control, CT CT Positive, GC Negative Amplification Positive
Control, GC CT Negative, GC Positive Samples Negative control CT
Negative, GC Negative (swipes from clean, control area) Positive
control CT Positive, GC Positive (swipes from sample spot w/ no
cleaning) rRNA and positive amplicon swipes CT Negative, GC
Negative (cleaned areas) Negative amplicon (cleaned areas) CT
Positive, GC Positive
[0182] Follow-Up Testing.
[0183] Any samples not meeting the above specifications were stored
at room temperature and re-tested the following day. The acceptance
criteria for the follow-up testing are the same as the acceptance
criteria for the initial testing (see above).
[0184] D. Characterization Results of Nucleic Acid Deactivation
Using Various Formulations and Application Methods
[0185] Table 12 below depicts results collected using the protocols
described above. "NA Source" is the nucleic acid source, "# App" is
the number of reagent applications, "kRLU" is relative light units
times a factor of 1000, and "pip" is piperazine. Expected Ctr and
Ngo results are negative (Neg) for Ngo/Ctr rRNA, Neg for Pos
Amplification and positive (Pos) for Neg Amp. The majority of Ctr
and Ngo results from the tests were valid, and invalid results are
not included in the table.
TABLE-US-00014 TABLE 12 Effectiveness of Reagents Used for Surface
Decontamination Ctr Ngo Reagent NA Source # App. kRLU Result Result
10% Bleach Ngo/Ctr rRNA 1 10 Neg Neg 1 6 2 5 1 3 1 3 1 3 2 2 2 2
Positive 1 3 Amplification 1 3 (100 .mu.L) 2 3 2 3 1 2 1 2 2 3 2 2
Negative 1 828 Pos Pos Amplification 1 859 (100 .mu.L) 2 825 2 870
1 1004 1 1020 2 996 2 1008 10% Bleach, Ngo/Ctr rRNA 1 9 Neg Neg
0.1M Bicarb, 1 9 Neg Neg 0.025% LLS 2 10 Neg Neg 2 10 Neg Neg 1 10
Neg Neg 1 10 Neg Neg 1 12 Neg Neg 1 11 Neg Neg 2 10 Neg Neg 2 11
Neg Neg Positive 1 10 Neg Neg Amplification 1 11 Neg Neg (100
.mu.L) 2 11 Neg Neg 2 11 Neg Neg 1 8 Neg Neg 1 8 Neg Neg 2 10 Neg
Neg 2 12 Neg Neg 1 9 Neg Neg 1 7 Neg Neg 2 11 Neg Neg 2 11 Neg Neg
Negative 1 2243 Pos Pos Amplification 1 2269 Pos Pos (100 .mu.L) 2
2240 Pos Pos 2 2259 Pos Pos 1 2213 Pos Pos 1 2348 Pos Pos 2 2353
Pos Pos 2 2277 Pos Pos 10% Bleach, Ngo/Ctr rRNA 1 10 Neg Neg 0.1M
PB, 1 11 Neg Neg 0.05% SDS 2 10 Neg Neg 2 11 Neg Neg 1 8 Neg Neg 1
8 Neg Neg 1 11 Neg Neg 1 10 Neg Neg 2 9 Neg Neg 2 8 Neg Neg
Positive 1 11 Neg Neg Amplification 1 13 Neg Neg (100 .mu.L) 2 7
Neg Neg 2 8 Neg Neg 1 12 Neg Neg 1 11 Neg Neg 1 11 Neg Neg 1 11 Neg
Neg Negative 1 2192 Pos Pos Amplification 1 2285 Pos Pos (100
.mu.L) 2 2240 Pos Pos 2 2212 Pos Pos 1 806 Neg Pos 1 899 Pos Pos 2
2218 Pos Pos 2 2193 Pos Pos 40 mM DCC Ngo/Ctr rRNA 1 3 Neg Neg 1 3
Neg Neg 2 3 Neg Neg 2 3 Neg Neg 1 3 Neg Neg 1 2 Neg Neg 2 3 Neg Neg
2 3 Neg Neg 1 12 Neg Neg Positive 1 3 Neg Neg Amplification 1 3 Neg
Neg (100 .mu.L) 2 3 Neg Neg 2 3 Neg Neg 1 15 Neg Neg 2 2 Neg Neg 2
2 Neg Neg 1 7 Neg Neg 1 8 Neg Neg Negative 1 812 Pos Pos
Amplification 1 795 Pos Pos (100 .mu.L) 2 726 Pos Pos 2 668 Pos Pos
1 886 Pos Pos 1 919 Pos Pos 2 937 Pos Pos 2 919 Pos Pos Ngo/Ctr
rRNA 1 6 Neg Neg 1 3 Neg Neg 2 3 Neg Neg 2 3 Neg Neg 1 3 Neg Neg 1
3 Neg Neg 2 8 Neg Neg 2 3 Neg Neg 3% peroxide, Positive 2 11 Neg
Neg 1 mM Amplification CuSO.sub.4 (10 .mu.L) Negative 2 870 Pos Pos
Amplification 2 865 Pos Pos (100 .mu.L) Negative 2 781 Pos Pos
Amplification 2 784 Pos Pos (100 .mu.L) 3 mL 3% Positive 2 7 Neg
Neg peroxide, 1 mM Amplification 2 6 Neg Neg CuSO.sub.4 (10 .mu.L)
3% peroxide, Ngo/Ctr rRNA 2 8 Neg Neg 1 mM CuSO.sub.4, 1 21 Neg Neg
25 mM pip 1 8 Neg Neg 2 8 Neg Neg 2 9 Neg Neg 3% peroxide, Ngo/Ctr
rRNA 2 8 Neg Neg 1 mM CuSO.sub.4, 2 22 Neg Neg 50 mM pip 1 158 Neg
Neg 2 10 Neg Neg 2 12 Neg Neg 2 10 Neg Neg 2 3 Neg Neg Ngo/Ctr rRNA
2 10 Neg Neg in STM 2 11 Neg Neg 3% peroxide, Ngo/Ctr rRNA 2 7 Neg
Neg 2 mM CuSO.sub.4, Ngo/Ctr rRNA 2 11 Neg Neg 50 mM HEPES in STM 2
10 Neg Neg 3% peroxide, Ngo/Ctr rRNA 1 9 Neg Neg 2 mM CuSO.sub.4, 2
10 Neg Neg 50 mM pip 2 9 Neg Neg (10 day Cu/pip) 1 7 Neg Neg 2 8
Neg Neg 2 8 Neg Neg 3% peroxide, Ngo/Ctr rRNA 2 11 Neg Neg 2 mM
cupric 2 12 Neg Neg acetate 2 9 Neg Neg 2 9 Neg Neg 2 10 Neg Neg 2
10 Neg Neg Ngo/Ctr rRNA 2 11 Neg Neg in STM 2 10 Neg Neg 3%
peroxide, Ngo/Ctr rRNA 2 9 Neg Neg 2 mM CuSO.sub.4 2 9 Neg Neg 2 10
Neg Neg 2 9 Neg Neg Ngo/Ctr rRNA 2 10 Neg Neg in STM 2 9 Neg Neg 1%
peroxide, Ngo/Ctr rRNA 1 3 Neg Neg 1 mM CuSO.sub.4 1 3 Neg Neg 2 3
Neg Neg 2 3 Neg Neg 2 3 Neg Neg 2 2 Neg Neg 1 7 Neg Neg Positive 2
7 Neg Neg Amplification 2 7 Neg Neg (100 .mu.L) 200 mM KHSO.sub.5
Ngo/Ctr rRNA 1 3 Neg Neg 1 3 Neg Neg 2 3 Neg Neg 2 3 Neg Neg
The results in the table show bleach-containing reagents--including
those that also contain a corrosion inhibitor and a
surfactant--effectively deactivated rRNA and positive and negative
TMA reactions on surfaces. The same was true for solutions
containing 40 mM DCC. Solutions containing peroxide and copper
effectively deactivated rRNA on surfaces, and were not as
efficacious as bleach for consistently decontaminating surfaces of
positive or negative TMA reactions under the conditions tested.
Adding piperazine or HEPES to the peroxide/copper solutions did not
significantly alter deactivation performance on surfaces under the
conditions tested. Peroxymonosulfate deactivated rRNA on surfaces,
but not positive and negative TMA reactions under the conditions
tested.
Example 13
Characterization of Nucleic Acid Deactivation Formulations
[0186] Effects of including corrosion inhibitors, surfactants and
fragrances in nucleic acid deactivation formulations were assessed.
Bleach, and to a lesser but still significant extent DCC, cause
corrosion of metals and other materials. Nucleic acid deactivation
activity of various candidate anti-corrosion compounds, including
the sodium salts of phosphate (PB), borate, bicarbonate and dodecyl
sulfate (SDS), were tested in solution prior to analysis using
real-time TMA and PAGE (e.g., Example 8 and Example 1). Studies
were performed to test the activity of bleach and DCC when mixed
together with the candidate corrosion inhibitors. Phosphate at pH
6.4 and 7.5 destabilized bleach (loss of activity increased with
time) whereas phosphate at pH 9.1 or 9.5 did not. The converse was
true for DCC, where the higher pH phosphate's (9.1 and 9.5) were
destabilizing whereas the lower pH phosphate's (6.4 and 7.5) were
not. Bleach was stable in borate at pH 7.6 or 9.1 and bicarbonate
at pH 9.3. SDS did not have any apparent effect on the activity of
bleach.
[0187] Anti-corrosion formulations with bleach were also tested
with the surface decontamination protocol described in Example 12.
All formulations tested were determined to be effective, thus
demonstrating the anti-corrosion agents have no apparent negative
effect on bleach activity. One application ("1 app") is one
application of the reagent and two applications ("2 app") is two
applications of the reagent. Results from the analysis are
presented in Table 13 below.
TABLE-US-00015 TABLE 13 Anti-Corrosion Formulations Reagent
Contamination Source Result 10% Bleach, 100 mM Bicarb., 0.025% LLS,
1 App. rRNA (Ctr/Ngo) Validated 10% Bleach, 100 mM Bicarb., 0.025%
LLS, 2 App. rRNA (Ctr/Ngo) Validated 10% Bleach, 100 mM Bicarb.,
0.025% LLS, 1 App. Pos. Amplicon (100 .mu.L) Validated 10% Bleach,
100 mM Bicarb., 0.025% LLS, 2 App. Pos. Amplicon (100 .mu.L)
Validated 10% Bleach, 100 mM Bicarb., 0.025% LLS, 1 App. Neg.
Amplicon (100 .mu.L) Validated 10% Bleach, 100 mM Bicarb., 0.025%
LLS, 2 App. Neg. Amplicon (100 .mu.L) Validated 10% Bleach, 100 mM
PB, 0.05% SDS, 1 App. rRNA (Ctr/Ngo) Validated 10% Bleach, 100 mM
PB, 0.05% SDS, 2 App. rRNA (Ctr/Ngo) Validated 10% Bleach, 100 mM
PB, 0.05% SDS, 1 App. Pos. Amplicon (100 .mu.L) Validated 10%
Bleach, 100 mM PB, 0.05% SDS, 2 App. Pos. Amplicon (100 .mu.L)
Validated 10% Bleach, 100 mM PB, 0.05% SDS, 1 App. Neg. Amplicon
(100 .mu.L) Validated 10% Bleach, 100 mM PB, 0.05% SDS, 2 App. Neg.
Amplicon (100 .mu.L) Validated
[0188] An assay for assessing corrosion was devised. The assay
comprised soaking stainless steel bolts (1'' long, 1/8'' diameter,
standard thread, hex-head stainless steel bolts) in candidate
solutions and visually scoring corrosion over time. Results from
the corrosion inhibition studies are summarized in Table 14
below.
TABLE-US-00016 TABLE 14 Corrosion Inhibition Result Agent Corrosion
Inhibition Phosphate, pH 9.1 High Phosphate, pH 9.5 High Borate, pH
7.6 Moderate Borate, pH 8.5 Moderate Bicarbonate, pH 9.3 High SDS*
Low to moderate SDS + other corrosion inhibitors SDS enhanced
activity of corrosion inhibitor *Other detergents/surfactants
(including lithium lauryl sulfate, Photo-Flo .RTM., saponin, Triton
.RTM. X-100 and General Use Hybridization Reagent (Gen-Probe)) were
tested, with similar results as for SDS.
[0189] Detergents and surfactants also were tested for effects on
the physical properties of bleach solutions on surfaces. These
agents decreased surface tension and allowed for more complete
wetting of the surface with the bleach solution (typically 0.6%
hypochlorite). To decrease foaming of the solution when applied to
the surface, detergent concentration was lowered to a level that
minimized foaming but retained effective surfactant qualities. SDS
and LLS levels of approximately 0.005% to 0.02% (w/v) minimized
foaming in this particular application.
[0190] Effects of fragrances on activity and stability of bleach
and DCC also were tested. Among the fragrances tested were 2141-BG,
2145-BG, and two other custom fragrances from International Flavors
and Fragrance. The fragrances exhibited no detectable effect on
activity and stability of 10% bleach and DCC according to PAGE
analysis. Also, the fragrances exhibited no detectable effect on
corrosion inhibition of various compounds tested (e.g., phosphate
and bicarbonate).
[0191] As a culmination of results for corrosion inhibitors,
detergent/surfactants and fragrances, formulations of these
reagents with bleach were developed. Unexpectedly, the balance
between components was critical for maintaining physical stability
of the solution. There were various combinations of these
components that were successful in this regard. One formulation was
as follows:
[0192] corrosion inhibitor/detergent/fragrance (6.7.times.
concentrate): 600 mM bicarbonate (pH 9.3), 0.1% SDS, 0.05%
2141-BG
[0193] finished decontamination reagent: 0.6% hypochlorite, 90 mM
bicarbonate (pH 9.3), 0.015% SDS, 0.0075% 2141-BG.
[0194] Solutions comprising peroxide and copper were further
characterized. It was discovered that UTM stimulated inactivation
of rRNA in solutions containing peroxide and Cu(II). The effects of
the individual components of the UTM formulation (150 mM HEPES, pH
7.6, 300 mM LLS, 10 mM (NH.sub.4).sub.2SO.sub.4) were examined, and
it was discovered that the HEPES was responsible for the
stimulation. Effects of pH and concentration on the observed
inactivation of rRNA then was examined. The activity of different
chemical components of HEPES (ethanol, ethanesulfonic acid and
piperazine) and PIPES, a buffer similar to HEPES, also were
examined. It was discovered piperazine was essentially as active as
HEPES, and piperazine at a pH of 5.5 was utilized for further
characterization. It also was discovered that piperazine stabilized
Cu(II) in solution in a chemical configuration that maintains
activity with peroxide for inactivating nucleic acids.
Example 14
Stability of Nucleic Acid Deactivation Formulations
[0195] Selected reagents were stored under a variety of conditions.
At selected time points, the formulations were assayed for the
ability to deactivate target nucleic acid using a solution assay,
in which rRNA was incubated with reagents in solution, diluted, and
an aliquot was assayed using real-time TMA (Example 8). Incubation
conditions were at room temperature with no protection from light.
Results are provided hereafter.
I. 40 mM CuSO.sub.4/1 M piperazine (Acetate), pH 5.5
TABLE-US-00017 Incubation Solution Stability Time (Days)
Characteristics (% Day 0) 0 Clear, royal blue 100 1 100 7 100 13
100 41 100 63 96 70 94 139 94 185 Getting lighter 85
II. 80 mM CuSO.sub.4/1 M Piperazine (Acetate), pH 5.5
TABLE-US-00018 [0196] Incubation Solution Stability Time (days)
Characteristics (% Day 0) 0 Clear, royal blue 100 83 100 129
100
III. 200 mM CuSO.sub.4 (in Water)
[0197] A. Stored at Room Temperature, No Protection from Light
TABLE-US-00019 Incubation Solution Stability Time (Days)
Characteristics (% Day 0) 0 Clear, pale blue 100 4 97 50 50
IV. 10% Bleach/Sodium Bicarbonate/SDS/IFF
[0198] A. 10% Bleach/0.2 M Sodium Bicarbonate (pH 9.3)/0.05%
SDS
TABLE-US-00020 Incubation Solution Stability Time (days)
Characteristics (% Day 0) 0 Clear 100 1 100 4 100 34 100 57 100 72
100
[0199] B. 10% Bleach/0.08M Sodium Bicarbonate (pH 9.3)/0.020%
SDS/0.025%2141-BG
TABLE-US-00021 Incubation Solution Stability time (Days)
Characteristics (% Day 0) 0 Clear, pale 100 15 yellow 100 20 100 26
100
[0200] C. 10% Bleach/0.09M Sodium Bicarbonate (pH 9.3)/0.015%
SDS/0.0075% 2141-BG
TABLE-US-00022 Incubation Solution Stability Time (days)
Characteristics (% Day 0) 0 Clear 100 7 100 28 100 58 96 103 100
148 100 214 40 242 35
V. Sodium Bicarbonate/SDS/2141-BG (Then Added to "Fresh"
Bleach)
[0201] A. 600 mM Sodium Bicarbonate (pH 9.3)/0.1% SDS/0.05% 2141-BG
(6.7.times. Solution)
TABLE-US-00023 Incubation Stability Time (days) Solution
Characteristics (% Day 0) 0 Clear, pale yellow; fine 100 2 white
particulate on 100 bottom of tube 31 Increased particulates 100 58
Same as day 31 100 103 100 148 100 214 100 242 100 276 100 330
100
[0202] B. 600 mM Sodium Bicarbonate (pH 9.3)/0.1% SDS/0.05% 2145-BG
(6.7.times. Solution)
TABLE-US-00024 Incubation Solution Stability Time (days)
Characteristics (% Day 0) 0 Clear 100 24 100 69 100 126 100 154 100
188 100 242 100
Example 15
Deactivation of Nucleic Acid on Laboratory Equipment
[0203] Formulations and procedures for deactivating nucleic acid on
several pieces of laboratory equipment, including a vacuum trap
system, an aspiration manifold, a rack and a deck, were assessed
for efficacy.
[0204] A. Vacuum Trap System
[0205] A vacuum system comprising an aspiration manifold, two
traps, an inline filter, and a vacuum pump connected in series by
tubing was utilized for conducting an amplification assay after
multiple target capture runs (both Ctr and Ngo rRNA). Contamination
was assessed without adding bleach to the first trap. After the
runs, swab samples were taken from various locations in the vacuum
system and assayed for presence of Ctr and Ngo rRNA using the
real-time TMA assay presented in Example 8. No detectable
contamination with Ngo rRNA was identified outside of the first
trap. Contamination with Ctr rRNA was identified in the tubing
between the first and second traps, in the second trap and in the
tubing between the second trap and the inline filter, and no
contamination was detected after the inline filter. These results
demonstrated that no detectable Ngo or Ctr rRNA escaped into the
environment, and it is therefore feasible to not to include bleach
in the first trap during usage.
[0206] B. Aspiration Manifold
[0207] One protocol for decontaminating a target capture aspiration
manifold utilized for a TMA assay (Aptima Combo 2.RTM. Assay)
included the step of soaking the manifold in 50% bleach for 10
minutes followed by thorough rinsing with water. This procedure
resulted in corrosion of the manifold and the relatively frequent
need to replace it.
[0208] To test other decontamination protocols and agents, the
manifold was intentionally contaminated, decontamination was
attempted, then contamination levels measured. Each of target
negative samples (10 replicates) remained negative using the
contaminated manifold, demonstrating that the target capture system
prevented contamination from entering new samples. In one
decontamination protocol, it was discovered that leaving the
manifold attached to the system and aspirating nucleic acid
deactivation formulations through it successfully decontaminated
the manifold. In such a procedure, it was determined 0.6%
hypochlorite (10% bleach) or 40 mM DCC (followed by a water rinse)
successfully decontaminated the manifold. A hydrogen
peroxide/copper solution also successfully decontaminated the
manifold, but this reagent was not as suitable for routine use as
it could vigorously evolve oxygen when under reduced pressure in
the vacuum system. It was determined that aspirating approximately
50 mL (about 5 mL per nozzle) of a 0.6% hypochlorite solution (with
corrosion inhibitor, detergent and fragrance) followed by
approximately 50 mL (about 5 mL per nozzle) of water, and then
leaving the vacuum pump on for at least 1 minute sufficiently
decontaminated the aspiration manifold.
[0209] C. Tecan Deck Decontamination
[0210] Leading bleach alternative candidates were tested for
decontamination of the deck of the DTS.RTM. Tecan Genesis System
(Catalog No. 5216 or 5203; Gen-Probe). The results in Table 15
below were observed.
Table 15
Deck Decontamination
TABLE-US-00025 [0211] Degree of Reagent Effectiveness 10% bleach
100% 40 mM DCC 100% 3% peroxide, 1 mM Cupric Sulfate 100%
Thus, multiple formulations and procedures effectively deactivated
nucleic acids that contaminated various laboratory equipment.
Example 16
Efficacy of Nucleic Acid Deactivation Formulation and Methods at
Two Laboratory Sites
[0212] Efficacy of two decontamination reagents and methods in a
clinical laboratory setting were characterized at two sites.
Reagent 1 (3% H.sub.2O.sub.2 (w/v), 2 mM cupric sulfate) and
Reagent 2 (0.6% hypochlorite (w/v), 90 mM bicarbonate, 0.015% SDS
(w/v), 0.0075% (v/v) 2141-BG), used according to the prescribed
protocol provided to each site (see below), were equivalent to the
protocol using 50% bleach described in the package insert for the
Aptima Combo 2.RTM. Assay kit (Catalog No. 1032) and at http
address www.gen-probe.com/pdfs/pi/IN0037-04RevA.pdf, and yielded
effective nucleic acid deactivation and decontamination control for
nucleic acid assay procedures in a clinical laboratory setting.
[0213] A. Materials
[0214] Following is a list of materials utilized at each site:
[0215] Reagent 1A (3% H.sub.2O.sub.2 USP grade) [0216] Reagent 1B
(copper sulfate, dry powder) [0217] Reagent 2A (600 mM sodium
bicarbonate, 0.1% (w/v) sodium dodecylsulfate, 0.05% 2415-BG
fragrance) [0218] Household bleach (.about.6% hypochlorite) [0219]
De-ionized (or higher quality) water [0220] Milli-Q (or equivalent
quality) water [0221] Aptima Combo 2.RTM. Test Kit [0222] Dual
Positive Control (CT and GC rRNA) [0223] Negative Control [0224]
Squirt bottle with a vented top (for Reagent 1)
[0225] B. Procedures
[0226] The following procedures were utilized at each site. For
each rack of samples (up to 10 Ten-Tube Units (TTUs; Catalog No.
TU0022; Gen-Probe) run in the Aptima Combo 2.RTM. Assay, included
were the usual two-run controls (Positive Control, CT and Positive
Control, GC), two Dual Positive Controls (see Materials), 16
Negative Controls (see Materials) and up to 80 patient specimens.
The assay was performed according to the standard protocol (package
insert).
[0227] If the two-run controls met run control criteria, the run
was valid (PASS). If one or both of the run controls did not meet
run control criteria, the run was invalid (FAIL) and all results in
the same run were invalid and were not reported. The run was then
repeated. Also, as usual for patient samples, initial equivocal or
invalid results were repeated.
[0228] Described below are the three phases of the research study.
Each stage was run between 2 and 4 weeks as less than 2 weeks might
not allow adequate evaluation of the decontamination protocol.
Three weeks was determined as being ideal, and the maximum duration
was four weeks. The entire study was expected to be completed in 9
weeks, with a maximum duration of 12 weeks. For each phase of the
study, 15 racks of samples were assayed, with all containing the
appropriate controls as described above.
[0229] Phase 1:
[0230] The standard Aptima Combo 2.RTM. protocol utilizing 50%
bleach was used for decontamination as described in the package
insert (http address www.gen-probe.com/pdfs/pi/IN0037-04RevA.pdf).
This approach was utilized to establish a baseline of results for
comparison with results obtained when the test decontamination
protocol was used.
[0231] Phase 2:
[0232] The test decontamination protocol was utilized (see
below).
[0233] Phase 3:
[0234] The test decontamination protocol (see below) was utilized,
except Reagent 2 was used when the protocol called for use of
Reagent 1. Reagent 2 still was utilized when the protocol called
for use of Reagent 2.
[0235] 1. Rack Set-Up
[0236] Each laboratory was instructed to utilize the following
procedure for setting-up racks of samples:
[0237] 1. Begin rack set-up in the standard fashion as described in
the package insert.
[0238] 2. Add 400 .mu.L of the Positive Control, CT, to reaction
tube 1.
[0239] 3. Add 400 .mu.L of the Positive Control, GC, to reaction
tube 2.
[0240] 4. Add 400 .mu.L of the Dual Positive Control to reaction
tubes 3-4.
[0241] 5. Add 400 .mu.L of the Negative Control to reaction tubes
5-20.
[0242] 6. Add 400 .mu.L of patient specimens into reaction tubes 21
up to 100.
[0243] 2. General Decontamination Protocol
[0244] Each laboratory was instructed to apply good physical
containment techniques in order to guard against spread of
contamination in the lab while decontaminating each workspace. Each
laboratory was cautioned that the glove on the hand used for
cleaning would become contaminated and that touching clean objects
with this hand should be avoided. It was recommended that one hand
should be reserved for cleaning only and the other hand (clean) for
application of reagent only. It also was recommended that used
towels and gloves should be discarded in a receptacle in which they
would be well-contained, making sure that no dripping occurred
between the area undergoing decontamination and the receptacle.
[0245] 3. Reagent Preparation
[0246] Each laboratory was instructed to prepare the following
reagents using the procedures outlined below:
[0247] a. Prepare Reagent 1B (every 2 weeks) [0248] i. Add 30 mL of
Milli-Q (or equivalent quality) water to 1 vial of Reagent 1B (dry
reagent). [0249] ii. Tightly cap and invert 30 times. Let stand for
1 minute. Invert 30 more times. Make sure all of the dry reagent is
dissolved. [0250] iii. Between uses (see section 2b below), store
Reagent 1B (liquid) at 2-8.degree. C. in the dark (the dry reagent
can be stored at room temperature). [0251] iv. After 2 weeks of
storage, discard Reagent 1B (liquid) and prepare a fresh
solution.
[0252] b. Prepare Reagent 1 (daily) [0253] i. Add 150 mL of Reagent
1A to a squirt bottle with a vented top (provided). [0254] ii. Add
1.5 mL of Reagent 1B to the squirt bottle. [0255] iii. Replace top
and thoroughly mix by swirling contents for 10-15 seconds [0256]
iv. Use contents as described below. If there is any escape of
Reagent 1 from the squirt bottle between uses, loosen the top and
then retighten immediately before resuming use. [0257] v. After the
last use of the day or 12 hours, whichever comes first, dispose of
any remaining Reagent 1 in the squirt bottle. Prepare fresh reagent
as described above when needed.
[0258] c) Prepare Reagent 2 (every 2 weeks)
[0259] The recipe provided below is for the preparation of 1 liter
of Reagent 2. The actual amount made is to be determined based on
the anticipated reagent usage in a given laboratory. The
preparation of Reagent 2 to be used for cleaning racks and other
equipment and may be performed in the vessel used for soaking.
[0260] i. Add 750 mL of de-ionized (or higher quality) water to an
appropriate vessel. Add 150 mL of Reagent 2A to the vessel,
followed by 100 mL of household bleach (this step can be performed
in a fume hood if so desired to avoid contact with bleach fumes).
[0261] ii. Close container and thoroughly mix by swirling contents
for 15-20 seconds. [0262] iii. Use contents as needed. [0263] iv.
At the end of 2 weeks, discard any unused Reagent 2 and prepare a
fresh solution as described above.
[0264] 4. Pre-Assay Procedures
[0265] Each laboratory was instructed to perform the following
pre-assay procedures. [0266] a. Turn on the water baths in the
pre-amp area, but not the post-amp area (if the water baths are
routinely left on 24 hours a day, this practice can be continued;
however, the person running the Aptima Combo 2.RTM. Assay in a
given day should not enter the post-amp area until the assay is
ready to proceed in that area (see below)). [0267] b. Clean all
surfaces in the pre-amp area as follows (in the order listed):
[0268] Tecan. Using a squirt bottle, wet a paper towel with Reagent
1 until the towel is saturated but not dripping. Thoroughly wet and
clean the Tecan deck with the wet towel (do not include a 1 minute
incubation time as in the current standard protocol) and continue
wiping until all the surfaces are dry. This may require additional
wetted towels as well as dry towels. Once the surface has been
cleaned and dried, repeat this procedure with a second application
of Reagent 1. Do not rinse with water. [0269] TCS Unit. Using a
squirt bottle, wet a paper towel with Reagent 1 until the towel is
saturated but not dripping. Thoroughly wet and clean surfaces of
the TCS (Catalog No. 5202; Gen-Probe) with the wet towel (do not
include a 1 minute incubation time as in the current standard
protocol) and continue wiping until all the surfaces are dry. This
may require additional wetted towels as well as dry towels. Once
the surface has been cleaned and dried, repeat this procedure with
a second application of Reagent 1. Do not rinse with water. [0270]
Bench surfaces. Liberally apply Reagent 1 to the bench surface
using a squirt bottle. Immediately clean the surface using a paper
towel, making certain that the entire surface has been thoroughly
wetted with the decontamination reagent yet taking care to not
splash the reagent onto the floor, into surrounding areas, etc. Do
not include a 1 minute incubation time as in the current standard
protocol. Continue wiping until the entire surface is dry. This may
require more than one paper towel. Repeat this procedure with a
second application of Reagent 1. Do not rinse with water. [0271]
Pipettors. Using a squirt bottle, wet a paper towel with Reagent 1
until the towel is saturated but not dripping. Thoroughly clean the
surfaces of the pipet with the wet towel (do not include a 1 minute
incubation time as in the current standard protocol) and continue
wiping until the pipet is dry. Repeat this procedure with a second
application of Reagent 1. Do not rinse with water. [0272] c. When
finished cleaning the pre-amp area, carefully discard both gloves.
Change gloves sooner if there is any suspicion of possible cross
contamination.
[0273] 5. Post-Specimen Preparation Procedures
[0274] Each laboratory was instructed to perform the following
post-specimen preparation procedures: [0275] a. Carefully discard
gloves used during specimen preparation and replace with clean
gloves. [0276] b. Clean the Tecan, items to be soaked (see below),
bench surfaces used in specimen processing area and any pipettors
used as follows: [0277] i. Tecan. Clean with Reagent 1 as described
above and carefully discard both gloves. [0278] ii. Items to be
soaked. After use, completely submerge racks, reagent reservoirs,
deck plates, disposable tip racks and waste chute (and any other
items that you currently soak) in Reagent 2 and allow to soak for
30-60 minutes. Rinse thoroughly with running water (do not soak in
a bath of rinse water) and then dry completely with paper towels
(air drying is acceptable). Carefully discard both gloves. [0279]
iii. Bench surfaces. Clean with Reagent 1 as described above.
Carefully discard both gloves [0280] iv. Pipettors. Clean with
Reagent 1 as described above. Carefully discard both gloves
[0281] 6. Post-Target Capture Procedures
[0282] Each laboratory was instructed to employ the following
post-target capture procedures: [0283] a. Aspiration manifold.
Place a new Ten-Tip Cassette (TTC; Catalog No. 4578; Gen-Probe)
into the TCS. Turn on the vacuum pump. Carefully attach the
manifold to the tips in the TTC. Carefully aspirate all Wash
Solution remaining from the Aptima Combo 2.RTM. Assay run from the
priming trough of the Wash Solution dispense station (the Wash
Solution dispense manifold will have to first be moved out of the
way). Add 100 mL of Reagent 2 to the trough, then carefully
aspirate it through the aspiration manifold. Add 100 mL of
de-ionized water to the trough, then carefully aspirate it through
the aspiration manifold. Eject the tips into their original TTC.
Leave the vacuum pump on for at least 1 minute after the last
aspiration. [0284] b. TCS, bench surfaces and pipettors. Clean with
Reagent 1 as described above. Carefully discard both gloves [0285]
c. Vacuum trap waste liquid. When required (see below),
decontaminate the liquid in the Waste Bottle. Attach the Waste
Bottle to the TCS unit empty (i.e., do not add bleach). Use the
Waste Bottle until it is 25% full (i.e., available capacity not to
exceed 25%) or for 1 week (whichever is first). Remove the Waste
Bottle from the system and carefully add 400 mL of undiluted bleach
(if desired, this procedure can be performed in a fume hood in
order to avoid release of fumes into the laboratory). Cap the Waste
Bottle and gently swirl the contents until fully mixed. Incubate 5
minutes, then pour the waste into a sink. Reconnect the empty Waste
Bottle to the TCS unit. Use universal precautions when handling and
disposing of liquid and solid waste. Dispose of liquid and solid
waste according to local, state, and federal regulations. The
contents of the Waste Bottle should be treated as a potential
source of assay contamination. Take precautions to avoid
contaminating the work surfaces. Carefully discard both gloves.
[0286] 7. Amplification Reaction b Procedures
[0287] Each laboratory was instructed to perform the following
procedures after each amplification reaction was started, which is
the last step performed in the pre-amp area. After starting the
reaction, each laboratory was instructed to clean the bench tops
surrounding the water baths, the handles to the lids of the water
baths and the pipettors using Reagent 1 according to the procedures
described above. Each laboratory was instructed to carefully
discard both gloves after performing these procedures.
[0288] 8. Post-Amp Area Procedures
[0289] Each laboratory was provided with the following instructions
concerning post-amplification area procedures. After the last
cleaning in the pre-amp area was completed and new gloves were
adorned, each laboratory was instructed to immediately turn on the
62.degree. C. water bath after entering the pre-amp area.
Instructions also were to pre-clean all surfaces in the post-amp
area (lab benches, pipettors, handles, and others) using Reagent 2
according to the specific procedures described above, and then to
carefully discard both gloves.
[0290] 9. Post Amplification Procedures
[0291] Each laboratory was provided with the following instructions
concerning post-amplification procedures. After adorning a clean
set of gloves, instructions were provided to carefully remove the
rack(s) from the 42.degree. C. water bath, and to avoid
contaminating the lid of the water bath.
[0292] 10. Post Detection Procedures
[0293] Each laboratory was provided with the following instructions
concerning post-detection procedures. Instructions were to (a)
remove TTU's from the luminometer and deactivate reactions using
the current procedure in the product insert; (b) clean all surfaces
(bench surfaces, pipettors, handle on water bath lid, exterior of
the LEADER.RTM. HC+ Luminometer, and others) using Reagent 2
according to the specific procedures described above, (c) every two
weeks, or as needed, clean the interior of the HC+ with DI water as
currently described in the operator's manual and soak the HC+
cassettes in Reagent 2 for 30-60 minutes, and (d) carefully discard
both gloves.
[0294] 11. Acceptance Criteria
[0295] Each laboratory was instructed to use the following
acceptance criteria.
TABLE-US-00026 Controls Specifications Amplification Positive
Control, CT CT Positive, GC Negative Amplification Positive
Control, GC CT Negative, GC Positive Negative Controls CT Negative,
GC Negative Dual Positive Controls CT Positive, GC Positive
[0296] C. Results
[0297] Reagents 1 and 2 used according to the prescribed protocol
were equivalent to the protocol using 50% bleach provided with the
Aptima Combo 2.RTM. Assay kit, and yielded effective
decontamination control for the Aptima Combo 2.RTM. Assay in a
clinical setting (see Table 16 below).
TABLE-US-00027 TABLE 16 Analysis of Negative and Positive Control
Data Fisher's Lab- Phase Exact P oratory Sample Result I II III
Total Value Lab- Negative Equivocal 1 0 2 3 0.625 oratory I Control
Low 1 0 2 3 Positive Negative 238 240 252 730 Total 240 240 256 736
Positive High 30 30 32 92 Control Positive Negative 0 0 0 0 Total
30 30 32 92 Lab- Negative Equivocal 1 0 0 1 0.110 oratory II
Control High 1 0 0 1 Positive Low 1 0 0 1 Positive Negative 237 240
240 717 Total 240 240 240 720 Positive High 30 30 30 90 Control
Positive Negative 0 0 0 0 Total 30 30 30 90
When the new decontamination reagents and protocol were used, 540
of 540 (100%) control samples for Phase II and 554 of 558 (99.3%)
control samples for Phase III yielded the expected results. When
50% bleach with the standard protocol was used (Phase I), 535 of
540 (99.1%) control samples yielded the expected results. A
Fisher's exact test (a statistical hypothesis test method to
demonstrate statistical differences between multiple groups with
qualitative outcomes; Categorical Data Analysis by Alan Agresti
(1990), pages 59-67, 68, 70, 78, 488, John Wiley & Sons, New
York, N.Y.) was performed on the data using SAS Version 8.2
software. It is widely accepted that P<0.05 suggests a
significant difference between groups while P>0.05 is indicative
of no statistical difference. The Fisher's exact test yielded a p
value of 0.625 for assays run at Laboratory 1 and 0.110 for assays
run at Laboratory II. These results indicate statistical
equivalence between the conditions of all three phases.
[0298] The entirety of each patent, patent application, publication
and document referenced herein hereby is incorporated by reference.
Citation of the above patents, patent applications, publications
and documents is not an admission that any of the foregoing is
pertinent prior art, nor does it constitute any admission as to the
contents or date of these publications or documents. Incorporation
by reference of these documents, standing alone, should not be
construed as an assertion or admission that any portion of the
contents of any document is considered to be essential material for
satisfying any national or regional statutory disclosure
requirement for patent applications. Notwithstanding, the right is
reserved for relying upon any of such documents, where appropriate,
for providing material deemed essential to the claimed subject
matter by an examining authority or court.
[0299] Modifications may be made to the foregoing without departing
from the basic aspects of the disclosure. Although the disclosure
has been described in substantial detail with reference to one or
more specific embodiments, those of ordinary skill in the art will
recognize that changes may be made to the embodiments specifically
disclosed in this application, and yet these modifications and
improvements are within the scope and spirit of the disclosure. The
disclosure illustratively described herein suitably may be
practiced in the absence of any element(s) not specifically
disclosed herein. Thus, for example, in each instance herein any of
the terms "comprising", "consisting essentially of", and
"consisting of" may be replaced with either of the other two terms.
Thus, the terms and expressions which have been employed are used
as terms of description and not of limitation, equivalents of the
features shown and described, or portions thereof, are not
excluded, and it is recognized that various modifications are
possible within the scope of the disclosure. Embodiments of the
disclosure are set forth in the following claims.
* * * * *
References