Here we report on the use of double-nanohole (DNH) optical tweezers as a label-free and free-solution single-molecule probe for protein–DNA interactions. Using this approach, we demonstrate the unzipping of individual 10 base pair DNA-hairpins, and quantify how tumor suppressor p53 protein delays the unzipping. From the Arrhenius behavior, we find the energy barrier to unzipping introduced by p53 to be 2 × 10−20 J, whereas cys135ser mutant p53 does not show suppression of unzipping, which gives clues to its functional inability to suppress tumor growth. This transformative approach to single molecule analysis allows for ultra-sensitive detection and quantification of protein–DNA interactions to revolutionize the fight against genetic diseases.
© 2014 Optical Society of America
Optical tweezers have been used to study protein–DNA interactions, critical for maintaining genetic functionality and integrity, at the single molecule level [1–4]. Although optical tweezers offer forces in the pN-nm range (around kT), relevant for the study of protein–DNA interactions, they mostly use tethering, fluorescent labeling for studying their dynamic behavior and are mostly limited to long DNA strands (~10 kbps) [5–9].Optical tweezers have also been used to study small DNA molecules ranging from 100bp  to few kbps . The present work traps DNA molecules an order of magnitude smaller than found in literature without using tethers. The tether is required because conventional tweezers are not able to hold on to single molecules without using damaging laser powers .Tethering also limits tweezer studies to relatively long DNA strands (~10 kbps) ,where the localization of sites of interest is difficult. Fluorescent labels are used to monitor dynamic processes, such as protein binding  and unzipping . Fluorescence labels change the molecule (except for autofluorescence), heat the molecule, suffer from photo bleaching , have a poor signal-to-noise ratio (SNR)  and are limited to millisecond time-scales . Adding labels and tethers modifies the natural state of the DNA/protein  and restricts free motion, as well as adding cost and complexity. To overcome these limitations of conventional optical tweezers, an ideal approach would be label-free, free-solution and work at the single DNA level with a small number of base-pairs. This approach should also be simple, low-cost, scalable and use low laser power.
Here we demonstrate that the DNH laser tweezer, a nanoplasmonic structure, can overcome the limitations of conventional optical tweezers in the study of protein–DNA interactions for short DNA chains, without the need for tethering and without the need for fluorescent labels. The DNH tweezer approach uses low optical powers and a conductive gold film, so there is negligible heating (estimated to be ~0.1K) . The scattering signal observed in trapping and unzipping is extraordinarily high, with laser transmission changes of around 10% being typical, even for nanoparticles/molecules in the single nanometer range. We demonstrate that the DNH tweezer can easily trap and unzip a 10 bp DNA hairpin. We further show that tumor suppressor protein p53 retards the unzipping, from which we quantify the p53 unzipping suppression energy using Arrhenius scaling. Mutant p53, on the other hand, does not suppress unzipping, which may explain its ineffectiveness in tumor suppression. This shows, we believe for the first time, the direct role of p53 in suppressing DNA unzipping.
2. DNH tweezer set up
The DNH optical tweezer uses simple inverted microscope geometry as shown in Fig. 1. A820 nm laser beam (Sacher Lasertechnik) is focused onto the DNH using a 100 × oil immersion objective (1.25 numerical aperture). The transmission through the DNH is measured using a 50 MHz bandwidth avalanche photodiode (APD) and the transmission is maximized with a half wave plate by aligning the laser polarization along the DNH cusp axis. Even for low laser powers (between 1 and 3 mW at the DNH), an optical density filter (OD 1) is required to prevent saturation of the APD. The DNH focuses the laser power to the nanometric gap between the cusps, favorable for trapping nanoparticles and biomolecules with low incident laser power [18,19]. The increased local electromagnetic field concentration in the DNH aperture provides the necessary optical forces to trap biomolecules like the DNA and protein in the present work. The optical forces are modified by the trapped DNA molecule and scale with the polarizability of the DNA fragment. It should be noted that no static field is applied to the setup. Even for particles at the nanometer scale, the DNH tweezer provides trapping efficiency in the range of pN-nm , which is the regime of the thermal energy at room temperature (kT) relevant to the study of natural biomolecular interactions. The biochip (Fig. 1, zoomed region) consists of DNHs fabricated on commercially available 100 nm thick gold test slides (EMF corp.) using a focused ion beam. For trapping of 10 bp hairpins, the cusp spacing was fabricated to be ~10 nm (Fig. 1 inset). Note that this is significantly smaller than used in past works [21,22],which is a key enabling feature of the present study.
3. DNA hairpin unzipping
Figure 2 shows the detected laser transmission at the APD for the DNH tweezer trapping events for 20 base DNA strands. Figure 2(a) shows the trapping event, seen with a discrete jump in the APD voltage, for a single-stranded DNA that does not hairpin. The discrete jump in transmission is due to dielectric loading of the DNH . Figure 2(b) shows the trapping event for a single-strand that forms a hairpin. It is clearly seen that there is a double-step in Fig. 2(b). We attribute the double step to the unzipping of the 20 base (10 bp) hairpin. (Note that the unzipped single stranded DNA is only ~7 nm long). This was observed consistently for hairpin structures, but never for single-stranded DNAs that do not hairpin. The DNH tweezer energetically favors unzipping of the hairpin because the elongated DNA has a larger polarizability than one that is zipped up, and the polarizability determines the interaction energy with the laser field.. Thus we have shown the ability of the DNH tweezers to trap 20 base DNA and unzip the hairpin structure over a typical timescale of 0.1 s. Figure 2(c) shows a simple energy reaction diagram showing the trapping and unzipping of the hairpin DNA. The hairpin DNA is initially trapped with energy of ~10 kT, as suggested by Ashkin for stable trapping  and followed by unzipping requiring approximately the same energy. We estimate the energy change by the size of the transmission change through the aperture. The initial change in transmission is due to dielectric loading of the aperture by the DNA molecule and is associated with the polarizability of the molecule and its dielectric constant. We associate the initial jump in transmission to the potential well necessary for trapping a molecule of given polarizability. The second transition of the transmission signal is due to unzipping, which increases the polarizability of the molecule due to its elongation. Since the optical trapping potential scales with the intensity, we can estimate that the change in transmission intensity is proportional to the change in energy potential from trapping. This is evident from the similar change in the transmission intensity during trapping and unzipping. Figure 3 shows the trapping event for a 12bp DNA. The time to unzip shows no significant difference compared to 10bp DNA strand and is of the order of 0.01s. The time to unzip is not simply related to the length of the DNA base pair since the optical forces also increase with the length of DNA due to increased polarizability. It may be noted that a 12bp DNA molecule shows a relatively larger change in transmission after unzipping as expected.
4. p53 protein–DNA interactions
4.1 Wildtype p53–DNA interactions
DNA binding proteins can stabilize or destabilize the DNA structure, which can impact unzipping . In the present case, we study the tumor suppressor p53 protein–DNA interaction, for which the suppression of unzipping has not been established, but fluorescence anisotropy works have shown the binding strength .
Figure 4(a) shows the trapping signal of the p53 wild type protein– DNA complex with a long unzipping time (∆t). The increased unzipping time is associated with the strong binding of p53 with the consensus DNA hairpin structure , critical for the biological activity of p53 . The 20 base DNA fragment has a strong binding affinity for p53 DNA binding domain with a value of logKd = −7.38 . Due to strong binding affinity Koff (unbinding coefficient) is very small and hence binding is almost irreversible. The DNA fragment binds to the DNA binding domain of p53 and thus affects the unzipping of the DNA. The unzipping time (∆t) can be used to quantify the unzipping suppression energy of p53 protein–DNA interaction . The cumulative probability plot shown in Fig. 4(b) shows the unzipping time ∆t always greater than 1s for wild type p53–DNA complex as compared to that of DNA for a given probability range.
The energy reaction diagram for the protein–DNA complex, as shown Figure 4(c) is similar to that of hairpin DNA except for an increase in the energy barrier (∆U) between the trapped and unzipped state. The increase in energy barrier ∆U results in longer unzipping time (∆t) and is a measure of the unzipping suppression energy ∆U. Therefore using the Arrhenius behavior ∆U is given by
Using the above values we find the energy of unzipping suppression ∆U = 2 × 10−20J. While p53 is well-known to suppress tumors, as far as we can tell no works have suggested that p53 suppresses DNA unzipping, let alone quantified the energy for this suppression [28,29]. Recent electron microscopy studies have presented a tetramer structure for p53 that encapsulates the DNA; however, the function with respect to DNA unzipping of this structure has not been addressed [30,31]. The energy of unzipping suppression is expected to be less than, but of the same order of magnitude as the maximal binding energy for p53, which is found to be 6.9 × 10−20J by fluorescence anisotropy studies .For the particular DNA sequence we are using, there is a 2 bp mismatch from the optimal p53 binding structure, and so the binding energy is expected to be 6.7 × 10−20J, using a previously proposed formulation for binding energy .
4.2 p53 mutant (cys135ser) DNA interaction
To understand the interaction of the hairpin DNA with a p53 mutant we also trap the p53 mutant-DNA complex. Figure 5(a) shows the trapping signal for p53 mutant–DNA complex, showing no appreciable difference in the unzipping time ∆t. This is interesting because the single point mutation of cys135ser results in only partial loss of DNA binding  but here we show that it completely loses the ability to suppress the unzipping of the hairpin DNA. The cumulative probability distribution of the unzipping time ∆t shows an overlap with that of DNA as shown in Fig. 5(b). Thus the DNH tweezers also shows the ability to distinguish between the interactive behaviour of the p53 wild type and its mutant protein with hairpin DNA; that is, it shows the specificity required for a good sensor/detector.
5. p53 wildtype and mutant trapping
To ensure that we were not trapping p53 alone in the above measurements, we trapped p53 wild type and its mutant individually without the DNA. Typical events are shown in Fig. 6(a) and 6(b). Both the trapping events look almost identical with small optical scattering and unstable behavior. These events have a much smaller step than from the protein – DNA complex and from the DNA alone due to lower scattering of the signal by the p53 molecule which has a spherical conformation with less polarizability compared to protein-DNA complex and DNA. Also, a lower refractive index of p53 molecule as compared to DNA may cause a smaller change in transmission signal. The nearly identical behavior for the mutant and the wild-type is because of minimal structural difference between the two proteins as has been illustrated for single point cy238ser mutant numerically .
In summary a label-free, free solution, sensitive and low cost DNH optical tweezer was used to show the unzipping of the hairpin DNA structure and its interaction with the tumor suppressor p53 protein. We showed the suppression of unzipping by wild type p53 protein due to strong binding with the consensus hairpin DNA and evaluate the unzipping suppression energy based on Arrhenius behavior to be ∆U = 2 × 10−20J. The mutant (cys135ser) shows negligible impact on the unzipping of the DNA even though there is only partial loss in the binding activity, which may explain its ineffectiveness in suppression tumor development. Thus DNH tweezers show the ability to understand the dynamics of small DNA fragments and the capability to distinguish the impact of a normal protein from its mutant on their behavior. The experiment shows the ability of the nanoplasmonic tweezer to study protein-DNA interaction in real time and provide aid to researchers in understanding of the biomolecular interactions. It should be emphasized that it is not the goal of this limited work to present definitive results on the biological relevance of the p53 blocking DNA unzipping.
We believe that this capability will have a transformative impact on biosensors. For example, we can distinguish mutant from wild-type species. It also shows great promise for drug discovery; for example, for the p53 case shown, the influence of small molecules that allow the mutant form to function normally would be of great interest. Finally, our work represents an almost ideal research tool to better understand how protein – DNA interactions (and other similarly sized molecules) in real time, at the single molecule level, in free-solution and in a label-free way.
7.1 Preparation of DNA solution
The 20 base hairpin DNA sequence, 5′- AGG CAT GCC TAG GCA TGC CT −3′ and a single strand DNA sequence, 5′-GGG CGG GGA GGG GGA AGG GA −3′ were used (Integrated DNA Technologies). The DNA fragments were re-suspended in the phosphate buffer solution (PBS) of pH 7.5 to 0.02% w/v concentration. The p53 human recombinant full length protein (Cedarlane Labs, CLPRO742) and its mutant cys135ser (Cedarlane Labs, CLPRO301) are produced in E.coli. The protein – DNA complex solution was prepared with 1:1 ratio of protein and DNA by volume. This was done for both p53 wild type and its mutant.
7.2 Nanofabrication of the DNH
The DNH with separation of ~10 nm between the cusps were fabricated using Hitachi FB-2100 focused ion beam system. The DNH were fabricated on gold test slides (EMF Corporation) with 100nm thick gold layer with a 5 nm Ti adhesion layer on a glass substrate. A gallium ion beam of accelerating voltage 40kV and current 0.001nA was used to mill the gold at a magnification of 80K. The beam of dwell time 10μs with 30 passes fabricates the DNH with ~10 nm cusp separation.
The authors acknowledge support from the Natural Sciences and Engineering Research Council (Canada) Discovery Grant Program.
References and links
4. J. W. Shaevitz, E. A. Abbondanzieri, R. Landick, and S. M. Block, “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution,” Nature 426(6967), 684–687 (2003). [CrossRef] [PubMed]
6. G. Farge, N. Laurens, O. D. Broekmans, S. M. van den Wildenberg, L. C. Dekker, M. Gaspari, C. M. Gustafsson, E. J. Peterman, M. Falkenberg, and G. J. Wuite, “Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A,” Nat.Commun. 3, 1013 (2012). [CrossRef] [PubMed]
7. P. R. Bianco, L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin, “Processive translocation and DNA unwinding by individual RecBCD enzyme molecules,” Nature 409(6818), 374–378 (2001). [CrossRef] [PubMed]
9. K. R. Chaurasiya, T. Paramanathan, M. J. McCauley, and M. C. Williams, “Biophysical characterization of DNA binding from single molecule force measurements,” Phys. Life Rev. 7(3), 299–341 (2010). [CrossRef] [PubMed]
10. K. Raghunathan, J. N. Milstein, and J. Meiners, “Stretching short sequences of DNA with constant force axial optical tweezers,” J. Vis. Exper. 56, 3405 (2011).
13. I. Heller, G. Sitters, O. D. Broekmans, G. Farge, C. Menges, W. Wende, S. W. Hell, E. J. G. Peterman, and G. J. L. Wuite, “STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA,” Nat. Methods 10(9), 910–916 (2013). [CrossRef] [PubMed]
14. M. A. Dijk, L. C. Kapitein, J. Mameren, C. F. Schmidt, and E. J. Peterman, “Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores,” J. Phys. Chem. B 108(20), 6479–6484 (2004). [CrossRef] [PubMed]
16. S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha, “Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction,” Science 318(5848), 279–283 (2007). [CrossRef] [PubMed]
17. P. N. Melentiev, A. E. Afanasiev, A. A. Kuzin, A. S. Baturin, and V. I. Balykin, “Giant optical nonlinearity of a single plasmonic nanostructure,” Opt. Express 21(12), 13896–13905 (2013). [CrossRef] [PubMed]
19. M. L. Juan, M. Righini, and R. Quidant, “Plasmon nano-optical tweezers,” Nat. Photonics 5(6), 349–356 (2011). [CrossRef]
21. M. L. Juan, R. Gordon, Y. Pang, F. Eftekhari, and R. Quidant, “Self-induced back-action optical trapping of dielectric nanoparticles,” Nat. Phys. 5(12), 915–919 (2009). [CrossRef]
25. T. Göhler, M. Reimann, D. Cherny, K. Walter, G. Warnecke, E. Kim, and W. Deppert, “Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain,” J. Biol. Chem. 277(43), 41192–41203 (2002). [CrossRef] [PubMed]
26. J. Buzek, L. Latonen, S. Kurki, K. Peltonen, and M. Laiho, “Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277,” Nucleic Acids Res. 30(11), 2340–2348 (2002). [CrossRef] [PubMed]
27. M. A. Hall, A. Shundrovsky, L. Bai, R. M. Fulbright, J. T. Lis, and M. D. Wang, “High-resolution dynamic mapping of histone-DNA interactions in a nucleosome,” Nat. Struct. Mol. Biol. 16(2), 124–129 (2009). [CrossRef] [PubMed]
28. Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, and L. Chen, “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion,” Nucleic Acids Res. 41(17), 8368–8376 (2013). [CrossRef] [PubMed]
29. S. Lukman, D. P. Lane, and C. S. Verma, “Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics,” PLoS ONE 8(11), e80221 (2013). [CrossRef] [PubMed]
30. R. Melero, S. Rajagopalan, M. Lázaro, A. C. Joerger, T. Brandt, D. B. Veprintsev, G. Lasso, D. Gil, S. H. Scheres, J. M. Carazo, A. R. Fersht, and M. Valle, “Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA,” Proc. Natl. Acad. Sci. U.S.A. 108(2), 557–562 (2011). [CrossRef] [PubMed]
31. D. I. Cherny, G. Striker, V. Subramaniam, S. D. Jett, E. Palecek, and T. M. Jovin, “DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy,” J. Mol. Biol. 294(4), 1015–1026 (1999). [CrossRef] [PubMed]
32. M. Ferrone, F. Perrone, E. Tamborini, M. S. Paneni, M. Fermeglia, S. Suardi, E. Pastore, D. Delia, M. A. Pierotti, S. Pricl, and S. Pilotti, “Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y),” Mol. Cancer Ther. 5(6), 1467–1473 (2006). [CrossRef] [PubMed]