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Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan 106
A protocol based on aminated diamond nanocrystals has detection limit as well as to increase mass measurement
been developed to isolate, concentrate, purify, and digest accuracy,9-15 both of which are of importance in analyzing complex
DNA oligonucleotides in one microcentrifuge tube for or low-concentration samples, or both. The biotin-streptavidin
matrix-assisted laser desorption/ionization (MALDI) time- system is one of the technologies developed to selectively extract
of-flight (TOF) mass spectrometry. It is shown that use of and preconcentrate DNA prior to MS analysis.16,17 In this method,
diamond nanocrystals as a solid-phase extraction support DNA molecules or fragments are biotinylated and then captured
not only permits concentration of oligonucleotides in by streptavidin-coated magnetic microbeads, while nonbiotinylated
highly diluted solutions but also facilitates separation of components are removed by washing. Although the method has
oligonucleotides from proteins in heavily contaminated become a routine protocol in nucleic acids research, it is
solutions. Enzymatic digestions can be conducted on inapplicable to analysis of nonbiotinylated DNA, unknown DNA,
particle, and additionally, the digests can be easily recov- or DNA fragments that are difficult to be amplified by polymerase
ered from the solution for base sequencing. In this chain reactions.
method, the aminated diamond nanocrystals (∼100 nm Poly(L-lysine) (PL) is a polyelectrolyte frequently used as a
in diameter) were prepared by noncovalent coating of DNA delivery tool.18,19 The compound forms stable complexes with
carboxylated/oxidized diamonds with poly(L-lysines) (PL), oligonucleotides, enhancing their cellular uptake via nonspecific
which form stable complexes with DNA oligonucleotides. endocytosis. While PL has attracted much interest used as a gene
While the complexes are sufficiently stable to sustain carrier, its application to facilitate MALDI-TOF MS of DNA is little
repeated washing with deionized water, the DNA mol- explored, except for proteins.20 In a previous work,21 we found
ecules can be readily eluted after incubation of the that carboxylated/oxidized diamond nanocrystals are remarkably
diamond adducts in aqueous ammonium hydroxide at good adsorbents for proteins and polypeptides in highly diluted
elevated temperatures. No preseparation of PL or dia- solution because of their high affinity for amino acids with basic
mond nanocrystals is required for subsequent MALDI- side-chain groups. In particular for PL, the adsorption is so strong
TOF mass analysis. that a PL coating can endure repeated washing with deionized
(7) Gut, I. G.; Jeffery, W. A.; Pappin, D. J. C.; Beck, S. Rapid Commun. Mass
Matrix-assisted laser desorption/ionization (MALDI) time-of- Spectrom. 1997, 11, 43-50.
flight (TOF) mass spectrometry (MS)1 is an effective diagnostic (8) Tang, W.; Zhu, L.; Smith, L. M. Anal. Chem. 1997, 69, 302-312.
(9) Berlin, K.; Gut, I. G. Rapid Commun. Mass Spectrom. 1999, 13, 1739-
tool for mass analysis of biopolymers including proteins and
1743.
nucleic acids.2 However, due to low ionization efficiency and facile (10) Langley, G. J.; Herniman, J. M.; Davies, N. L.; Brown, T. Rapid Commun.
fragmentation of oligonucleotides, the overall performance of the Mass Spectrom. 1999, 13, 1717-1723.
(11) Koomen, J. M.; Russell, W. K.; Hettick, J. M.; Russell. D. H. Anal. Chem.
technique is less satisfactory for nucleic acids than for proteins.2
2000, 72, 3860-3866.
Earlier reports on DNA MALDI-TOF MS mainly focused on the (12) Smirnov, I. P.; Hall, L. R.; Ross, P. L.; Haff, L. A. Rapid Commun. Mass
selection of matrixes and improvement of sample deposition Spectrom. 2001, 15, 1427-1432.
(13) Distler, A. M.; Allison, J. Anal. Chem. 2001, 73, 5000-5003.
methods.3-8 Recently, increasingly more efforts are made to lower
(14) Kjellstrom, S.; Jensen, O. N. Anal. Chem. 2004, 76, 5109-5117.
(15) Weng, M. F.; Chen, Y. C. Rapid Commun. Mass Spectrom. 2004, 18, 1421-
* To whom correspondence should be addressed. E-mail: hcchang@ 1428.
po.iams.sinica.edu.tw. (16) Jurinke, C.; van den Boom, D.; Collazo, V.; Luchow, A.; Jacob, A.; Koster,
(1) Karas, M.; Hillenkamp, F. Anal. Chem. 1988, 60, 2299-2301. H. Anal. Chem. 1997, 69, 904-910.
(2) Dass, C. Principles and Practices of Biological Mass Spectrometry; Wiley: (17) Kim, S.; Ruparel, H. D.; Gilliam, T. C.; Ju, J. Nat. Rev. Gen. 2003, 4, 1001-
New York, 2001. 1008.
(3) Wu, K. J.; Shaler, T. A.; Becker, C. H. Anal. Chem. 1994, 66, 1637-1645. (18) Molas, M.; Bartrons, R.; Perales, J. C. Biochim. Biophys. Acta 2002, 1572,
(4) Wang, B. H.; Biemann, K. Anal. Chem. 1994, 66, 1918-1924. 37-44.
(5) Kirpekar, F.; Nordhoff, E.; Kristiansen, K.; Roepstorff, P.; Hahner, S.; (19) Parker, A. L.; Oupicky, D.; Dash, P. R.; Seymour, L. W. Anal. Biochem.
Hillenkamp, F. Rapid Commun. Mass Spectrom. 1995, 9, 525-531. 2002, 302, 75-80.
(6) Liu, Y. H.; Bai, J.; Liang, X.; Lubman, D. M.; Venta, P. J. Anal. Chem. 1995, (20) Zhang, L.; Orlando, R. Anal. Chem. 1999, 71, 4753-4757.
67, 3482-3490. (21) Huang, L. C. L.; Chang, H.-C. Langmuir 2004, 20, 5879-5884.
10.1021/ac050213c CCC: $30.25 © 2005 American Chemical Society Analytical Chemistry, Vol. 77, No. 13, July 1, 2005 4273
Published on Web 05/20/2005
water and is stable in aqueous solution over several months. This
unique feature endows PL-coated diamond nanocrystals with the
potential to be used as solid-phase extraction (SPE) supports for
DNA oligonucleotides.
In adsorption of oligomeric DNA molecules, polystyrene
particles are often used as the affinity substrate. Detailed studies
of the adsorption have been made for single-stranded DNA
fragments on amino polystyrene nanospheres.22 It is found that
high-affinity capture of DNA occurs at neutral pH, and the amount
of the DNA fragments captured decreases smoothly with solution
pH, evidence that the adsorption is dominated by electrostatic
forces. The maximal amount of DNA adsorbed at pH 5 is 0.8 mg/
m2, independent of the chain length of the oligonucleotides Figure 1. Comparison between the maximal amounts of d(ATCG-
investigated, suggesting that the molecules are attached to the GCTAATCGGCTA) adsorbed to 100-nm PL-coated diamonds (O) and
surface in a flat configuration.22 carboxylated/oxidized diamonds (9) as a function of solution pH. The
PL-coated diamond crystallites of an average size of 100 nm typical error involved in these measurements is (3 mg/g as indicated
are chosen as the DNA SPE supports in this work. The particles at pH 7.
are crystalline, easy to purify, and therefore, undesirable ion
entrapment during synthesis of nanoparticles (such as porous in dilute NaOH and HCl solutions, the particles were thoroughly
silica nanoparticles23) does no occur. Previous infrared spectro- washed with deionized water and collected by centrifugation. Such
scopic measurements21 indicated that PL is adsorbed to the surface oxidative acid-treated powders were then mixed with PL in boric
of carboxylated/oxidized diamonds with multiple adsorption sites acid buffers, forming noncovalently coated diamond nanocrystals.
in an extended configuration, covering the particles with amino DNA Adsorption. An UV-visible spectrophotometer served
groups. Although the ionic interaction between protonated PL and to determine the amounts of DNA adsorbed to PL-coated
deprotonated DNA is strong, which can be a serious impediment diamonds in 20 mM phosphate buffers at pH 3-9. The specific
to MS analysis, we found that incubation of the complexes in pH as reported in Figure 1 was achieved by fine adjustment of
aqueous ammonium hydroxide at elevated temperatures ef- the pH value of the buffer with 1 N HCl and NaOH.28 The
fectively elutes the oligonucleotides (and/or the whole complexes) adsorbed quantities were determined from the changes in optical
from the aminated diamond surfaces. Direct analysis of the target density of dissolved oligonucleotides before and after addition of
molecules without preseparation of the particles is viable for the diamond nanocrystals to the solution. To ensure equilibration
MALDI-TOF MS. The method is general and applicable to of the adsorption, the oligonucleotide solution and the diamond
biotinylated DNA, nonbiotinylated DNA, and DNA fragments from suspension were thoroughly mixed by vortexing for 2 h, after
enzymatic digestion.24-26 which the mixture was centrifuged and the supernatant was
collected for optical absorption measurement at 260 nm.
EXPERIMENTAL SECTION MADLI-TOF MS. The matrix solution consisted of 3.3 mg of
Chemicals and Materials. Synthetic abrasive diamond pow-
THAP and 4 mg of ammonium citrate in 500 µL of 50% aqueous
ders with a nominal size of 100 nm were obtained from Kay
acetonitrile, optimized empirically for detection of DNA oligo-
Industrial Diamond.27 Biological samples including snake venom
nucleotides. The sample for MALDI-TOF MS was prepared by
phosphodiesterase (SVP), ubiquitin, d(ATCGGCTAATCGGCTA)
adding 1 µL of diamond suspension (typically 10 mg/mL) to 500
(mass 4881), poly(L-lysine) (mass ∼30 000), and chemicals includ-
µL of oligonucleotide solution (typically 50 nM) in a microcen-
ing urea, sodium dodecyl sulfate (SDS), 2,4,6-trihydroxyacetophe-
trifuge tube. After incubation for 2 min and removal of the
none (THAP), and ammonium citrate were all from Sigma and
supernatant from centrifugation, an aliquot (2 µL) of 28% am-
used without further purification. Components (Na2HPO4 and
monium hydroxide solution was added to rinse the inner wall of
NaH2PO4) for phosphate buffers were obtained from Acros
the tube and immerse the centrifuged diamonds. The resulting
Organics.
slurry was then mixed with 2 µL of matrix solution, from which
PL-Coated Diamond Nanocrystals. Poly(L-lysine)s were
1 µL of the mixture was sampled and deposited on the probe. In
noncovalently coated on carboxylated/oxidized diamonds, de-
the cases that DNA oligonucleotides cannot be effectively eluted
scribed in detail previously.21 Briefly, diamond powers were
from the PL-coated diamond nanocrystals, the slurry was heated
carboxylated and oxidized in concentrated H2SO4/HNO3 (9:1
in the original centrifuge tube to 90 °C for 2 min prior to MALDI
volume ratio) at room temperature. After subsequent treatments
analysis.
(22) Ganachaud, F.; Elaissari, A.; Pichot, C.; Laayoun, A.; Cros, P. Langmuir Mass spectra were acquired in the negative ion mode using a
1997, 13, 701-707. home-built delayed ion extraction linear time-of-flight mass
(23) Turney, K.; Drake, T. J.; Smith, J. E.; Tan, W.; Harrison, W. W. Rapid
Commun. Mass Spectrom. 2004, 18, 2367-2374.
spectrometer with a flight length of 2.2 m and at an acceleration
(24) Nordhoff, E.; Crammer, R.; Karas, M.; Hillenkamp, F.; Kirpekar, F.; voltage of -20 kV.29 A pulsed Nd:YAG laser operating at 355 nm
Kristiansen, K.; Roepstorff, P. Nucleic Acids Res. 1993, 21, 3347-3357.
(25) Smirnov, I. P.; Roskey, M. T.; Juhasz, P.; Takach, E. J.; Martin, S. A.; Haff, (28) Concentrations of the buffers were maintained in the range of 2 × 10-2 M.
L. A. Anal. Biochem. 1996, 238, 19-25. In this range, the ionic strength plays an insignificant role in the DNA
(26) Zhang, L. K.; Rempel, D.; Gross, M. L. Anal. Chem. 2001, 73, 3263-3273. adsorption process (ref 22).
(27) Abrasive diamond nanocrystals are relatively inexpensive with a cost of (29) Lynn, E. C.; Chung, M. C.; Tsai, W. C.; Han, C.-C. Rapid Commun. Mass
∼1 US dollar per carat. Spectrom. 1999, 13, 2022-2027.
evaporated and ionized the molecules under vacuum for detection adsorption of proteins on carboxylated/oxidized diamonds, to
with a z-stacked triple microchannel plate. All mass spectra were which the amounts of the proteins attached increase with solution
acquired by signal averaging of 30 laser shots. pH and reach their maximums at the respective isoelectric points.30
Concentration and Extraction. Sample solutions were diluted Since PL is protonated up to pH 10.5 and DNA oligonucleotides
serially with deionized water. The diluted solutions were mixed are polyelectrolytes containing only negatively charged (phos-
with the diamond suspensions and analyzed directly with MALDI- phate) groups, such a monotonic decrease is a reflection that
TOF MS following the procedures described above. The same electrostatic forces dominate the adsorption process.
procedures applied to analysis of DNA extracted from highly The maximal amount of the DNA oligonucleotide adsorbed to
contaminated solutions containing 2 M urea, 0.1% SDS, or ubiquitin the PL-coated diamond surface at neutral pH is ∼22 mg/g (Figure
at a 500-fold higher concentration. In these experiments, to 1). Given a specific surface area of ∼40 m2/g (determined by BET
facilitate elimination of undesired molecules or ions, the oligo- isotherms31) for the diamond powders, an adsorbate density of
nucleotide-bound diamond nanocrystals were additionally rinsed ∼0.6 mg/m2 is revealed at saturation. With reference to the area
with deionized water twice (500 µL in each rinse) prior to addition of 20 Å × 3.4 Å occupied by each nucleotide pair for a double-
of ammonium hydroxide and matrix solutions. stranded DNA helix,32 this measured density suggests that nearly
Enzymatic Digestion. DNA oligonucleotides were digested half of the diamond surface is covered with the single-stranded
in solution by mixing 1 µL of SVP (0.01 munit/µL in pH 8.8 DNA oligonucleotides. The full coverage can be reached only at
ammonium citrate solution) with 100 µL of 200 nM DNA solution. pH e3.
The mixture was incubated at 40 °C for 3 min. A 1-µL aliquot was In Figure 1, we also include the adsorption of DNA to
removed for direct MALDI-TOF mass analysis, while the remain- carboxylated/oxidized diamonds for comparison. No adsorption
ing was mixed with 4 µL of the PL-coated diamond suspension of the oligonucleotides is detected within the experimental
for 2 min and then analyzed by MALDI. uncertainty of our measurements in the pH range 7-9. Significant
On-particle enzymatic digestion was conducted by adding 40 adsorption occurs only at pH e5 when the repulsion between the
µg of PL-coated diamonds to 100 µL of 200 nM DNA solution. negatively charged surface groups and DNA oligonucleotides
The DNA adducts, after one wash with deionized water, were diminishes. The amount of the DNA adsorbed is roughly half that
mixed with 10 µL of 0.005 munit/µL SVP and heated to 40 °C for adsorbed to PL-coated diamonds at the corresponding pH.
8 min. Centrifuged diamonds were then mixed with 3 µL of Mass Analysis of Dilute DNA Solutions with Contami-
ammonium hydroxide and 3 µL of matrix solution sequentially in nants. Figure 2a displays the mass spectrum acquired directly
the same tube. A 1-µL aliquot of the mixture was deposited on for d(ATCGGCTAATCGGCTA) from a 1-µL solution at 50 nM
the probe for final MALDI-TOF mass analysis. prepared with deionized water. Both singly and doubly charged
ions of the oligonucleotides can be identified at m/z 4880 and
RESULTS AND DISCUSSION
Adsorption of DNA to PL-Coated Diamond Surfaces. (30) Kong, X. L.; Huang, L. C. L.; Hsu. C.-M.; Chen, W.-H.; Han, C.-C.; Chang,
Figure 1 shows the maximal amount of d(ATCGGCTAATCG- H.-C. Anal. Chem. 2005, 77, 259-265.
GCTA) adsorbed to PL-coated diamonds as a function of solution (31) Measured with a surface area analyzer (Gemini V, Micrometrics) by
nitrogen adsorption at -196 °C.
pH. The quantities decrease nearly monotonically with solution (32) Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry; Freeman: San
pH from 3 to 9. This behavior is in marked contrast to the Francisco, 1980.
CONCLUSION
We have developed a method to improve the performance of
MALDI-TOF MS for DNA oligonucleotides in highly diluted and
contaminated solutions based on microextraction using poly(L-
lysine)-coated diamond nanocrystals as the solid supports. The
method integrates isolation, concentration, purification, digestion,
and analysis of DNA in one microcentrifuge tube (in the sense
that target molecules are always retained on the diamond substrate
and interfering molecules are always left in the solution and can
thereupon easily disposed of), and it performs exceptionally well
for mass analysis of oligonucleotides in solution containing an
excessive amount of proteins such as ubiquitin. The method is
general and is expected to be applicable to mass analysis of DNA
in more complex protein solutions and even cell lysates. The
Figure 5. MALDI-TOF mass spectra of enzymatic d(ATCG-
simplicity of the method makes automation feasible.
GCTAATCGGCTA) digests. The digestion was conducted in solution
and analyzed (a) without preconcentration and (b) with preconcen-
tration using PL-coated diamonds. The corresponding on-particle ACKNOWLEDGMENT
digestion result is shown in (c). Asterisks denote doubly charged DNA The research was supported by Academia Sinica and the
fragment ions. National Science Council (Grant NSC 92-3112-B-001-012-Y under
the National Research Program for Genomic Medicine) of Taiwan,
Republic of China.
MALDI-TOF MS. It should be noted that the oligonucleotide
concentration used in this experiment is 200 nM, which is lower
SUPPORTING INFORMATION AVAILABLE
than the concentration typically used in exonuclease digestion for
Additional information as noted in text. This material is
base sequencing24-26 by 2 orders of magnitude.
available free of charge via the Internet at http://pubs.acs.org.
A potentially important application of the presently developed
method is to conduct the enzymatic digestion directly on particle.
We demonstrate the feasibility of this approach with SVP at pH Received for review February 3, 2005. Accepted March 7,
close to 8. In this pH range, a large fraction of the oligonucleotides 2005.
remains attached to the surface for digestion (Figure 1) and the AC050213C