Coherent optical spectroscopy in a biological semiconductor quantum dot-DNA hybrid system
© Li and Zhu; licensee Springer. 2012
Received: 24 September 2011
Accepted: 16 February 2012
Published: 16 February 2012
We theoretically investigate coherent optical spectroscopy of a biological semiconductor quantum dot (QD) coupled to DNA molecules. Coupling with DNAs, the linear optical responses of the peptide QDs will be enhanced significantly in the simultaneous presence of two optical fields. Based on this technique, we propose a scheme to measure the vibrational frequency of DNA and the coupling strength between peptide QD and DNA in all-optical domain. Distinct with metallic quantum dot, biological QD is non-toxic and pollution-free to environment, which will contribute to clinical medicine experiments. This article leads people to know more about the optical behaviors of DNAs-quantum dot system, with the currently popular pump-probe technique.
Rapid and highly sensitive detection of DNA molecules contributes to ultrasensitive and automated biological assays such as sensing, imaging, immunoassay, and other diagnostics applications [1–3]. Conventional approaches have focused on inorganic/organic hybrid DNA biomedicine sensors for biological labels, cell tracking, and monitoring response to therapeutic agents [4–6]. Among numerical hybrid components, the unique size-dependent, narrow, symmetric, bright, and stable fluorescence of quantum dots (QDs) have made themselves powerful tools for investigating a wide range of biological problems . This is a difficult task with standard fluorophores because their relatively narrow excitation and broad emission spectra often result in spectra overlap. Besides, the optical behaviors of quantum dots are typically unaffected while they are conjugating to bio-molecules, which make them highly stable and bright probes, especially suitable for photon-limited in vivo studies and continuous tracking experiments over extended time periods . Recently, the coherent optical spectroscopy of a strongly driven quantum dot has been experimentally investigated by Xu et al. [8, 9]. They have shown that, like single atom two- and three-level quantum systems, single QD can also exhibit interference phenomena including Autler-Townes splitting and gain without population inversion when driven simultaneously by two optical fields. In this case, researchers are indulged in quantum dots and DNA conjugates to study biological activities and medical diagnosis [10, 11], which have applications in biomolecule targets exploitation [12, 13]. But for the research of coherent optical spectrum in such coupled DNAs-QD, no study has ever been undertaken, neither in experiment nor in theory.
Furthermore, there is another question. The metallic quantum dots used in biological assays always have toxicity, which may limit the capabilities of biomedicine assays and bring in some unnecessary troubles. So the search for cadmium-free quantum dots has therefore becomes another major research area. Most recently, Amdursky et al. [14, 15] have experimentally demonstrated that the peptide quantum dots represent one of the simplest forms of quantum dot and the most important feature of these quantum dots is the nontoxicity to the environment and to human body. These quantum dots will become new labeling materials in biological and biomedical assays. However, the coherent optical properties of such QDs coupled to DNAs are still lacking.
In the present study, we theoretically investigate the coherent optical spectroscopy for a peptide quantum dot (QD) coupled to DNA molecules, with pump-probe technique. Recently, this two-laser technique has been realized by several groups [16–20] while investigating the optomechanical system. Here we show that this hybrid peptide QD-DNA system will become transparent due to the DNA's vibrations when applying a strong control laser. Under some conditions the output signal laser even be enhanced significantly. Furthermore, the vibrational frequency of DNA molecule and the coupling strength between peptide QD and DNA can be measured due to the absorption splitting peaks in all-optical domain.
2 Model and theory
where ω ex is the exciton frequency of peptide quantum dot.
where m i and ω i are the mass and vibrational frequency of DNA molecule, respectively.
where M i is the coupling strength between the peptide QD and the i th DNA. It is should be noted that due to the dilute aqueous solution of DNA molecules, here we do not consider the effect of the coupling between the DNA molecules although it may be significant in the dense aqueous solutions .
where Δ c = ω ex - ω c , , Ω c is the Rabi frequency of the control field, and δ = ω s - ω c is the detuning between the signal field and the control field.
Furthermore, we may consider the decoherence and relaxation of exciton and DNA mode in combination with their interaction to external environments into the Hamiltonian [25–28]. In general, the environments can be described as independent ensembles of harmonic oscillators with spectral densities. We also assume that DNA molecules interact bilinearly with external environment via its position, and the exciton interacts with the environment through S x operator and S z operator. The S x coupling to the environment models the relaxation process of the exciton, while the S z coupling to the environment models the pure dephasing process of the exciton [25–28]. On the other hand, because ω ex is much larger than ω i , it is reasonable to use the rotating-wave approximation to the exciton-environment coupling term, but not to the DNA-environment coupling term in the system-environment coupling Hamiltonian.
where the coefficients A, B, E, D, G, and L correspond to the characteristics of the coupling, and to the structure and properties of the environments. Their explicit form can be written as , , , , , , where γ1 = 2π J x ( ω ex ), γ2 = 2π J z (0), γ3 = 2 π J c (ω i ) . is the Boltzman-Einstein distribution of the thermal equilibrium environments. J x , J z , and J c describe the spectral densities of the respective environments coupled through S x and S z to the exciton, and through Q to the DNA molecule, respectively. denotes the principal value of the argument.
where e1 = i + Δc 0-λ0/(2w0), e2 = i-Δc 0+ λ0/(2w0), δ0 = δ/Γ2, Ωc 0= Ω c /Γ2, λ0 = λ/Γ2 ωD 0= ω D /Γ2, τD 0= τ D Γ2, Δc 0= Δ c /Γ2, , and Γ1 = 2Γ2.
3 Results and discussions
For illustration of the numerical results, we choose the realistic coupled system of a peptide QD linked to the DNA molecules in the simultaneous presence of a strong control beam and a weak signal beam as shown in Figure 1. In such coupled system, many DNA molecules linked with one QD. These DNA molecules in solution form may be distorted in mess, but one can extend these molecules into linear form by applying electromagnetic field or fluid force . In addition, the longitudinal vibrational frequency can be determined by the length of DNA molecules. In the theoretical calculation, we select the vibrational frequency and the lifetime of DNA molecule are ω D = 32 GHz and τ D = 3 ns, respectively [24, 32–34]. The decay time of peptide quantum dot is 6 fs , which corresponds to Γ1 = 160 THz.
3.1 Vibrational frequency measurement of DNA molecule
3.2 Coupling strength determination between peptide quantum dot and DNA molecule
Furthermore, in conventional QD-linked biomedicine sensors, excited by single optical field, the fluorescence emission efficiencies still remain challenge due to the coated chemicals, the autofluorescence of background and the copy number of the target to each QD . However, the emission efficiency would be largely enhanced in coherent optical driven by double optical fields, described in this article. From Figure 4, we find that the amplified signal field comes from the quantum interference between the hybrid components and external lasers, which has no relevant with spontaneous fluorescence lifetime of quantum dot. In this case, we anticipate that DNA-linked peptide QD system excited by control-signal technique can be applied to biological imaging, which are nontoxic to environment and human body. For example, once the peptide quantum dot is attached to abnormal DNA molecules, we first apply a strong control field to the peptide QD, provided by Δ c = -ωD, then the hybrid system is transparent to other optical fields. Thereafter, we apply a second weak signal beam across the exciton frequency, then the output signal beam can be amplified at Δ s = 0, which means the peptide quantum dot can be luminant in all-optical domain. Meanwhile, different vibrational frequencies of DNA molecule and the coupling strengths between quantum dot and DNA result in different amplitudes of amplification, which are shown in Figures 4 and 5. This is the DNA enhanced signal spectroscopy of peptide quantum dot, which will have a potential applications in cellular imaging, immunoassays, and clinical diagnosis.
In this article, we theoretically investigated the coherent optical spectroscopy in a coupled DNA-peptide quantum dot system in the presence of two optical fields. Theoretical analysis shows that the vibrational frequency of DNA and the coupling strength between peptide QD and DNA can be measured effectively and precisely in all-optical domain. Finally, we hope that our predictions in the present study can be testified by experiments in the near future.
The part of this study was supported by the National Natural Science Foundation of China (Nos. 10774101 and 10974133).
- Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Komiyama M: Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy. Nat Commun 2011, 2: 449.View ArticleGoogle Scholar
- Finkelstein IJ, Visnapuu ML, Greene EC: Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase. Nat Commun 2010, 468: 983.View ArticleGoogle Scholar
- Boukany PE, Hemminger O, Wang SQ, Lee LJ: Molecular imaging of slip in entangled DNA solution. Phys Rev Lett 2010, 105: 027802.View ArticleGoogle Scholar
- Kamiya K, Okada S: Energetics and electronic structure of encapsulated single-stranded DNA in carbon nanotubes. Phys Rev B 2011, 83: 155444.View ArticleGoogle Scholar
- Cherepinsky V, Hashmi G, Mishra B: Competitive hybridization models. Phys Rev E 2010, 82: 051914.View ArticleGoogle Scholar
- Tikhomirov G, Hoogland S, Lee PE, Fischer A, Sargent EH, Kelley SO: DNA-based programming of quantum dot valency, self-assembly and luminescence. Nat Nanotechnol 2011, 6: 485. 10.1038/nnano.2011.100View ArticleGoogle Scholar
- Fu A, Gu WW, Larabell C, Alivisatos AP: Semiconductor nanocrystals for biological imaging. Curr Opin Neurobiol 2005, 15: 568. 10.1016/j.conb.2005.08.004View ArticleGoogle Scholar
- Xu XD, Sun B, Berman PR, Steel DG, Bracker AS, Gammon D, Sham LJ: Coherence optical spectroscopy of a strongly driven quantum dot. Science 2007, 317: 929. 10.1126/science.1142979View ArticleGoogle Scholar
- Xu XD, Sun B, Kim ED, Smirl K, Berman PR, Steel DG, Bracker AS, Gammon D, Sham LJ: Single charged quantum dot in a strong optical field: absorption, gain, and the ac-Stark effect. Phys Rev Lett 2008, 101: 227401.View ArticleGoogle Scholar
- Medintz IL, Uyeda HT, Goldman ER, Mattoussi H: Quantum dot bio-conjugates for imaging labelling and sensing. Nat Mater 2005, 4: 435. 10.1038/nmat1390View ArticleGoogle Scholar
- Medintz IL, Clapp AR, Mattoussi H, Goldman ER, Fisher B, Mauro JM: Self-assembled nanoscale biosensors based on quantum dot FRET donors. Nat Mater 2003, 2: 630. 10.1038/nmat961View ArticleGoogle Scholar
- Gao XH, Cui YY, Levenson RM, Chung LWK, Nie S: In vivo cancer targeting and imaging with semiconductor quantum dots. Nat Biotech-nol 2004, 22: 969.View ArticleGoogle Scholar
- Cai WB, Chen XY: Preparation of peptide-conjugated quantum dots for tumor vasculature-targeted imaging. Nat Protocol 2008, 3: 89. 10.1038/nprot.2007.478View ArticleGoogle Scholar
- Amdursky N, Molotskii M, Gazit E, Rosenman G: Self-assembled bioin-spired quantum dots: optical properties. Appl Phys Lett 2009, 94: 261907. 10.1063/1.3167354View ArticleGoogle Scholar
- Amdursky N, Molotskii M, Gazit E, Rosenman G: Elementary building blocks of self-assembled peptide nanotubes. J Am Chem Soc 2010, 132: 15632. 10.1021/ja104373eView ArticleGoogle Scholar
- Weis S, Rivièere R, Deléeglise S, Gavartin E, Arcizet O, Schliesser A, Kip-perberg TJ: Optomechanically induced transparency. Science 2010, 330: 1520. 10.1126/science.1195596View ArticleGoogle Scholar
- Teufel JD, Li D, Allman MS, Cicak K, Sirois AJ, Whittaker JD, Simmonds RW: Circuit cavity electromechanics in the strong-coupling regime. Nature 2011, 471: 204. 10.1038/nature09898View ArticleGoogle Scholar
- Safavi-Naeini AH, Mayer Alegre TP, Chan J, Eichenfield M, Winger M, Lin Q, Hill JT, Chang DE, Painter O: Electromagnetically induced transparency and slow light with optomechanics. Nature 2011, 472: 69. 10.1038/nature09933View ArticleGoogle Scholar
- Li JJ, Zhu KD: A scheme for measuring vibrational frequency and coupling strength in a coupled annomechancial resonator-quantum dto system. Appl Phys Lett 2009, 94: 063116. 94:249903 94:249903 10.1063/1.3072599View ArticleGoogle Scholar
- He W, Li JJ, Zhu KD: Coupling-rate determination based on radiation-pressure-inducd normal mode splitting in cavity optomechanical systems. Opt Lett 2010, 35: 339. 10.1364/OL.35.000339View ArticleGoogle Scholar
- Van Zandt LL: Resonant microwave absorption by dissolved DNA. Phys Rev Lett 1986, 57: 2085. 10.1103/PhysRevLett.57.2085View ArticleGoogle Scholar
- Dorfman BH: The effects of viscous water on the normal mode vibrations of DNA. Dissert Abstr Int 1984, 45: 2213.Google Scholar
- Edwards GS, Davis CC, Saffer JD, Swicord ML: Resonant microwave absorption of selected DNA molecules. Phys Rev Lett 1984, 53: 1284. 10.1103/PhysRevLett.53.1284View ArticleGoogle Scholar
- Edwards GS, Davis CC, Saffer JD, Swicord ML: Microwave-field-driven acoustic modes in DNA. Biophys J 1985, 47: 799. 10.1016/S0006-3495(85)83984-9View ArticleGoogle Scholar
- Gardiner CW, Zoller P: Quantum Noise. 2nd edition. Berlin: Springer; 2000:425.View ArticleGoogle Scholar
- Walls DF, Milburn GJ: Quantum Optics. Berlin: Springer; 1994:245.View ArticleGoogle Scholar
- Carmichael H: Statistical Methods in Quantum Optics I. Berlin: Springer; 1999:261.View ArticleGoogle Scholar
- Breuer HP, Petruccione F: The Theory of Open Quantum Systems. Oxford: Oxford University Press; 2002:441.Google Scholar
- de M Donega C, Bode M, Meijerink A: Size-and temperature-dependence of exciton lifetimes in CdSe quantum dots. Phys Rev B 2006, 74: 085320.View ArticleGoogle Scholar
- Boyd RW: Nonlinear Optics. Amsterdam: Academic Press; 2008:313.Google Scholar
- Marko JF, Siggia ED: Stretching DNA. Macromolecules 1995, 28: 8759. 10.1021/ma00130a008View ArticleGoogle Scholar
- Yuan CL, Chen HM, Lou XW, Archer LA: DNA bending stiffness on small length scales. Phys Rev Lett 2008, 100: 018102.View ArticleGoogle Scholar
- Gill R, Willner I, Shweky I, Banin U: Fluorescence resonance energy transfer in CdSe/ZnS-DNA conjugates: probing hybridization and DNA cleavage. J Phy Chem B 2005, 109: 23715. 10.1021/jp054874pView ArticleGoogle Scholar
- Adair BK: Vibrational resonances in biological systems at microwave. Biophys J 2002, 82: 1147. 10.1016/S0006-3495(02)75473-8View ArticleGoogle Scholar
- Khitrova G, Gibbs HM, Kira M, Koch SW, Scherer A: Vacuum Rabi splitting in semiconductors. Nat Phys 2006, 2: 81. 10.1038/nphys227View ArticleGoogle Scholar
- Zhou DJ, Ying LM, Hong X, Hall EA, Abell C, Klenerman D: A compact functional quantum dot-DNA conjugate: preparation, hybridization, and specific label-free DNA detection. Langmuir 2008, 24: 1659. 10.1021/la703583uView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.