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On-chip Isotachophoresis for Separation of Ions and Purification of Nucleic Acids

互联网2013-11-13

1385

实验材料

Name	Company	Catalog Number	Comments
Distilled water	GIBCO	10977	RNase/DNase free
Clorox Ultra	Clorox	02489CT
sodium hydroxide (NaOH)	Mallinckrodt	7708
hydrochloric acid (HCl)	EMD Chemicals	HX0603-4
Trizma base (tris)	Sigma-Aldrich	T6066
polyvinylpyrrolidone (PVP)	Polysciences Inc.	06067	MW 1,000,000
HEPES	Sigma-Aldrich	H-4034
Alexa Fluor 488 carboxylic acid	Invitrogen	A20000
tricine	Sigma-Aldrich	T-9784
bis-tris	Sigma-Aldrich	B4429
EDTA	GIBCO	AM9260G
Triton-X 100	Sigma-Aldrich	X100
lysozyme	Sigma-Aldrich	L6876
SYBR Green II	Invitrogen	S7564
ethanolamine	Sigma-Aldrich	411000
Rhodamine 6G	Acros Organics (Geel, Belgium)	CAS 989-38-8
L-Amino Acids	Sigma-Aldrich	LAA21
Power SYBR Green RNA-to-C_T 1-Step Kit	Applied Biosystems	4389986
PCR primers	Integrated DNA Technologies
Borosilicate microfluidic chip	Caliper Life Sciences Inc.	NS12A	Supplied with or without plastic caddy
Vacuum pump	Gast	DOA-P104-AA
Sourcemeter	Keithley	2410	Constant current and constant voltage operation modes
Inverted epifluorescent microscope	Olympus	IX70	Use mercury lamp (Olympus) or LED (Thorlabs) for illumination
Filter cube	Omega	XF115-2	Excitation/emission: blue/green
Safe-lock microcentrifuge tubes	Eppendorf	022363204	1.5mL capacity
Centrifuge	Eppendorf	5417C

实验步骤

1. Physics of ITP

ITP forms a sharp moving boundary between ions of like charge. The technique can be performed with anionic or cationic samples, but we tailor this introduction to anionic ITP and note the same principles apply to cationic ITP. We choose LE and TE buffers such that LE ions have higher magnitude effective electrophoretic mobility. The effective electrophoretic mobility, μ = U/E , is the proportionality constant between applied electric field, E , and ion drift velocity, U .¹³ We establish a diffuse interface between the LE and TE and apply an electric field directed from the high-conductivity LE zone to the low-conductivity TE zone. The system quickly establishes a strong gradient in electric field at the ITP interface, due to the non-uniform conductivity profile. As per its name (from Greek, "isos" means "equal", "takhos" means "speed"), TE and LE ions travel at the same, uniform velocity, as a result of the non-uniform electric field and conservation of current (this is the so-called "ITP condition", see Figure 1).

The ITP interface is self-sharpening: LE ions that diffuse into the TE zone experience a strong restoring flux and return to the leading zone (and vice versa for TE ions in the LE zone). Sample ions focus at this interface if their effective mobility in the TE zone is greater than those of the TE co-ions, and if their effective mobility in the LE zone is less than that of the LE co-ions (see Figure 1). The self-sharpening and focusing properties of ITP contribute to the robustness of this technique and make ITP relatively insensitive to disturbances of the interface (e.g. due to pressure-driven flow or changes in geometry, such as contractions, expansions, and turns).

In peak mode ITP (see Figure 2a and Videos 1-2), sample ion concentrations are at all times significantly lower than LE and TE ion concentrations and therefore contribute negligibly to local conductivity. The distribution of sample ions is determined by the self-sharpening interface between neighboring zones (here the TE and LE) and the value of the sample effective mobility relative to these zones.¹⁴ Multiple sample ions focus within the same narrow ITP interface region as largely overlapping peaks. The interface and peak widths, as well as the associated preconcentration factor, scale inversely with the applied current (see experiments in Figure 2b).¹⁴

For sufficiently high initial sample concentrations and sufficient accumulation time, sample ions reach a threshold concentration value. For fully-ionized species, this value is determined by the Kohlrausch regulating function (KRF).¹⁵ For weak electrolytes, it is determined by the Alberty and Jovin functions.^16,17 In plateau mode, as depicted in Figure 3 and Video 3, sample ions separate and purify into zones of locally uniform and constant concentration in an order determined by their effective mobility. Very dilute ions may still focus in peak mode between plateau zones. In ITP, sample ions can be introduced in a finite injection between the TE and LE (see Figure 3) or alternately mixed together with the TE and/or LE (see Figure 2). We refer to mixing in the TE zone as "semi-infinite" injection, which can be used to accumulate analyte ions continuously. Continuous sample accumulation increases sensitivity in both peak and plateau mode assays. However, finite injections are more common in plateau mode. This is likely because high initial analyte concentrations in semi-infinite injection can substantially increase TE conductivity and lower focusing rates. Also, full purification is not possible in semi-infinite injection (since there remains a finite concentration in TE).

2. Device cleaning and preparation

For the assays presented in this protocol we use isotropically wet-etched (roughly D-shaped cross section) glass microfluidic chips with a cross-channel design (see Figure 1). The following cleaning and preparation protocol is optimized for borosilicate and fused silica channels, but can also be used with glass/PDMS chips. Perform this cleaning procedure prior to experiments to ensure run-to-run repeatability and successful application of dynamic coatings needed to suppress electroosmotic flow (EOF). Omission of this protocol may result in strong dispersion of the ITP interface.¹⁴

1) To decontaminate the channel, fill the North, East, and South reservoirs with 10-20 μL of 10% bleach and apply vacuum at the West reservoir for 2 min. If using a standard Caliper chip caddy, vacuum can be effectively applied by simply attaching the wide end of a 200 μL (unfiltered) pipette tip to the chip reservoir and connecting the vacuum line to a 2 mm inner diameter tube.

2) Empty the reservoirs and rinse the channel (as in step 1) with 1 M sodium hydroxide for 2 min. This gently etches the channel walls, yielding a clean borosilicate surface to help establish uniform surface properties.

3) Empty the reservoirs and clean with de-ionized water (DI), then rinse the channel with LE for ~2 min. During this period surface properties and dynamic coatings equilibrate within the channel.

3. Fluorophore focusing in peak mode ITP

1) Prepare 1 mL LE consisting of 100 mM HCl, 200 mM tris, and 1% PVP.

2) Prepare 1 mL TE consisting of 100 mM HEPES and 200 mM tris. Combine 90 μl of TE with 10 μl of 1 μM Alexa Fluor 488 (AF488).

3) After rinsing with LE as described in Part 2, empty the West reservoir and clean a few times with DI in order to dilute any LE remaining in the reservoir. Fill this reservoir with 20 μL TE containing AF488.

4) Place the positive electrode in the East reservoir and the ground (negative) electrode in the West reservoir and apply 2 μA (constant current). The sample peak will migrate at a constant velocity from the West reservoir to the East reservoir (see Figure 1) and the voltage between these reservoirs will increase as the lower conductivity TE fills the channel.

4. Extraction and purification of nucleic acids from cultured E. coli

The ability to selectively focus ionic species makes ITP an ideal technique for biological sample preparation. We purify nucleic acids from untreated cell lysate by selecting a trailing anion with an effective mobility magnitude lower than the target nucleic acid but higher than co-ionic PCR inhibitors (e.g. anionic detergents, proteins, and organic solvents, even if present in high concentration). Cationic PCR inhibitors (e.g. alkali metals and cationic proteins and detergents) migrate in the opposite direction and so are also left behind. ITP extracts and focuses target nucleic acids from the sample reservoir, while leaving slower PCR-inhibiting species behind (see Figure 4).

1) Obtain a sample of or culture E. coli cells to a density greater than 10⁸ CFU/mL.

2) Transfer 1 mL cell culture into a safe-lock microcentrifuge tube and pellet by centrifugation at 4000g for 6 min.

3) Re-suspend the pellet in 80 μL RNase-free water and add 10 μL of lysing agent consisting of 10 mM tricine, 10 mM bis-tris, 2 mM EDTA, 0.1 % Triton-X, and 5 mg/mL lysozyme. Mix gently and incubate for 5 mins. at room temperature (lysing protocol adapted from Bercovici et al. ¹¹ ).

4) Add 10 μL of 1 M sodium hydroxide to raise the lysate pH to ~12.5. Gently actuate the pipette up and down until the solution becomes clear, at which point lysing is complete.

5) Combine 10 μL of lysate with 90 μL of 50 mM tricine and 100 mM bis-tris. This solution can now be used as the TE.

6) Prepare 1 mL of LE consisting of 500 mM bis-tris, 250 mM HCl, 1% PVP, and 1X SYBR Green II. Fill the microfluidic chip with LE as described in Part 3.

7) In order to extract the purified nucleic acid for off-chip analysis following ITP, replace the contents of the East reservoir with a PCR-compatible LE containing 50mM bis-tris, 25 mM HCl, and 0.1% PVP. Apply 1000 V between the East and West wells to begin the experiment. The current between these reservoirs will decrease.

8) At the end of the experiment the sample elutes into the LE reservoir. Coincident with this elution, the current versus time for this system typically reaches a plateau value (since resistance is now dominated by TE ions uniformly distributed within channel). Gently mix the reservoir contents by repeated pipetting and extract a 5 μL volume for analysis by quantitative RT-PCR.

5. Separation of amino acids with cationic plateau mode ITP and non-focusing tracer (NFT) for visualization

ITP can be used to separate and focus small ions into adjoining and detectable plateaus between the TE and LE. This allows detection and identification based on physicochemical properties, such as local conductivity, UV absorbance, temperature sensing, or index of refraction. Here we demonstrate a non-focusing tracer (NFT) assay where a fluorescent, co-ionic species is added to the LE. This fluorescent species does not focus, but its concentration adapts to a local electric field and thereby enables visualization of purified plateau zones (see Figure 5).

1) Prepare 1 mL LE consisting of 100 mM ethanolamine, 200 mM tricine, and 1% PVP, and 100 μM of the cationic fluorophore Rhodamine 6G.

2) Prepare 1 mL TE consisting of 20 mM tris, 40 mM tricine. Prepare sample by mixing 90 μL of TE with 10 μL each of 50 mM arginine and 50 mM lysine.

3) Dispense 20 μL LE in the West and North reservoirs and sample in the East reservoir. Apply vacuum at South reservoir for 1 min.

4) Rinse the East well with DI and replace with TE (TE without sample).

5) Apply 500 V between the East and West reservoirs.

6. Representative Results

We show isotachopherograms of peak mode experiments in Figure 2b and nucleic acid extraction experiments in Figure 4. In peak mode experiments with a fluorescent reporter (e.g. AF488, SYBR Green II), the overall fluorescence intensity can be integrated and compared against a calibration curve to obtain quantitative concentration information.¹² Additionally, in nucleic acid extraction experiments, sample is allowed to elute into the LE reservoir and extracted with a pipette for analysis by quantitative RT-PCR.^10,12 We show plateau mode isotachopherograms for amino acid separation in Figure 5. Fluorescence intensity (relative to LE or TE zone intensity) can be used for zone identification, while zone widths enable quantitation.

1. Jung, B., Bharadwaj, R., & Santiago, J.G. On-chip millionfold sample stacking using transient isotachophoresis. Anal. Chem. 78 (7), 2319 (2006).

2. Jung, B., Zhu, Y., & Santiago, J.G. Detection of 100 am fluorophores using a high-sensitivity on-chip CE system and transient isotachophoresis. Anal. Chem. 79 (1), 345 (2007).

3. Everaerts, F.M., Beckers, J.L., & Verheggen, T.P.E.M. Isotachophoresis: Theory, instrumentation, and applications. Elsevier Science & Technology. , (1976).

4. Khurana, T.K. & Santiago, J.G. Preconcentration, separation, and indirect detection of nonfluorescent analytes using fluorescent mobility markers. Anal. Chem. 80 (1), 279 (2008).

5. Bercovici, M., Kaigala, G.V., Backhouse, C.J., & Santiago, J.G. Fluorescent carrier ampholytes assay for portable, label-free detection of chemical toxins in tap water. Anal. Chem. 82 (5), 1858 (2010).

6. Bercovici, M., Kaigala, G.V., & Santiago, J.G. Method for analyte identification using isotachophoresis and a fluorescent carrier ampholyte assay. Anal. Chem. 82 (5), 2134 (2010).

7. Kaigala, G.V., et al. Miniaturized system for isotachophoresis assays. Lab Chip. 10 (17), 2242 (2010).

8. Chambers, R.D. & Santiago, J.G. Imaging and quantification of isotachophoresis zones using nonfocusing fluorescent tracers. Anal. Chem. 81 (8), 3022 (2009).

9. Schoch, R.B., Ronaghi, M., & Santiago, J.G. Rapid and selective extraction, isolation, preconcentration, and quantitation of small RNAs from cell lysate using on-chip isotachophoresis. Lab Chip. 9 (15), 2145 (2009).

10. Persat, A., Marshall, L.A., & Santiago, J.G. Purification of nucleic acids from whole blood using isotachophoresis. Anal. Chem. 81 (22), 9507 (2009).

11. Bercovici, M., et al. Rapid detection of urinary tract infections using isotachophoresis and molecular beacons. Anal. Chem. 83 (11), 4110 (2011).

12. Marshall, L.A. & Santiago, J.G. Extraction of DNA from malaria-infected erythrocytes using isotachophoresis. Anal. Chem. 83 (24), 9715 (2011).

13. Persat, A., Chambers, R.D., & Santiago, J.G. Basic principles of electrolyte chemistry for microfluidic electrokinetics. Part I: Acid-base equilibria and pH buffers. Lab Chip. 9 (17), 2437 (2009).

14. Garcia-Schwarz, G., Bercovici, M., Marshall, L.A., & Santiago, J.G. Sample dispersion in isotachophoresis. J. Fluid Mech. 1 (1), 1 (2011).

15. Kohlrausch, F. Über concentrations-verschiebungen durch electrolyse im inneren von lösungen und lösungsgemischen. Ann. Phys. 298 (10), 209 (1897).

16. Alberty, R.A. Moving boundary systems formed by weak electrolytes. Theory of simple systems formed by weak acids and bases. J. Am. Chem. Soc. 72 (6), 2361 (1950).

17. Jovin, T.M. Multiphasic zone electrophoresis. I. Steady-state moving-boundary systems formed by different electrolyte combinations. Biochem. 12 (5), 871 (1973).

18. Persat, A. & Santiago, J.G. MicroRNA profiling by simultaneous selective isotachophoresis and hybridization with molecular beacons. Anal. Chem. (2011).

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