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Patent:
Haring Bolivar, P., R. Buettner, et al. (2002). Method for detecting polynucleotide sequences. Int. App. No.: PCT/DE01/02408
The invention relates to a method for detecting a polynucleotide sequence A in a sample containing a plurality of identical or different polynucleotide sequences X in the form of individual strands. The polynucleotide sequence A can be identical to one of the polynucleotide sequences X or can be contained in one of the polynucleotide sequences X in the form of a sequence segment. The method determines the binding status of the polynucleotide sequences X contained in the sample in relation to a known test polynucleotide sequence B which is complementary to polynucleotide sequence A; and comprises the following steps: preparing a test medium which contains test polynucleotide sequences B which are complementary to the polynucleotide sequence A to be detected, in the form of individual strands; and bringing the sample into contact with the test medium by introducing the sample into the test medium or applying the sample to the test medium, so that the individual strands of the polynucleotide sequences X contained in the sample can bind to the complementary test polynucleotide sequences B contained in the test medium. The following step c) is carried out in order to detect the binding of the polynucleotide sequences X to the test polynucleotide sequences B: determining at least one component of the complex index of refraction or an equivalent variable of the sample in contact with the test medium using interaction with incident electromagnetic radiation with a frequency of between 0.1 terahertz (THz) and 20 THz, preferably between 1 THz and 10 THz and then analyzing the properties of the electromagnetic radiation after the interaction, especially in terms of the time or phase delay, absorption, refraction or dispersion of the incident electromagnetic radiation caused by the interaction.
Journal Articles:
Vosseburger, M., M. Brucherseifer, et al. (1998). Propagation effects in electro-optic sampling of terahertz pulses in GaAs. Applied Optics 37(15): 3368-3371.
Freely propagating terahertz pulses are detected in the time domain by electrooptic sampling in bulk GaAs. The authors study the influence of dispersion of the near-IR sampling pulse on the transients by varying the thickness of the GaAs crystal. Pronounced propagation effects are identified that originate from the frequency dependence of the phase-matching condition between the terahertz and the sampling pulse.
Brucherseifer, M., M. Nagel, et al. (2000). Label-free probing of the binding state of DNA by time-domain terahertz sensing. Applied Physics Letters 77(24): 4049-4051.
We present a promising approach for the label-free characterization of genetic material. Time-resolved terahertz (THz) transmission anal. of polynucleotides demonstrate a strong dependence of the complex refractive index on the binding state (hybridized/denatured) of DNA mols. By monitoring THz transients, one can thus infer the binding state of oligo- and polynucleotides, and hence identify polynucleotides by detecting the binding of unknown polynucleotide DNA sequences to known probe mols. A broadband exptl. demonstration in a free-space configuration, as well as a discussion of the potential application for next generation gene chips is presented.
Brucherseifer, M., P. H. Bolivar, et al. (2001). Angle-dependent THz tomography - characterization of thin ceramic oxide films for fuel cell applications. Applied Physics B: Lasers and Optics 72(3): 361-366.
A time-resolved THz tomog. system for the incidence-angle-dependent three-dimensional characterization of layered structures is presented. The capabilities of the developed system are demonstrated on multi-layer ceramic samples used for solid oxide fuel cells (SOFC). Appropriate methods for detg. unknown refractive indexes are discussed. It is shown how the angle of incidence of a THz imaging system has a significant influence on measured signals. This fact can be exploited esp. in Brewster-angle configurations to enhance the capabilities of any THz tomog. system. Data evaluation algorithms are presented.
Nagel, M., T. Dekorsy, et al. (2001). Characterization of polypropylene thin-film microstrip lines at millimeter and submillimeter wavelengths. Microwave and Optical Technology Letters 29(2): 97-100.
We report on the characteristics of thin-film microstrip lines with adhesive polypropylene (PP) tape as dielectric. The attenuation and dispersion have been measured in a frequency range between 30 and 800 GHz by electro-optical sampling. A 31- mu m-wide PP microstrip line exhibits a low attenuation of 0.09 dB/mm and an effective permittivity epsilon /sub r,eff/ of 1.85, both at 30 GHz. Both the excellent dielectric properties as well as the high planarity appear very attractive for future waveguide structures
Brucherseifer, M., P. H. Bolivar, et al. (2002). Combined optical and spatial modulation THz-spectroscopy for the analysis of thin-layered systems. Applied Physics Letters 81(10): 1791-1793.
The authors present a combined optical and spatial modulation technique to enhance drastically the resoln. threshold of time-domain THz spectroscopy. By this approach, relative changes of THz transmission can be resolved down to unprecedented values of -90 dB, enabling the broadband anal. of extremely thin layered systems. The system capabilities are demonstrated by characterizing dielec. films, specifically a 1.2 mm thick polymer and a 100. nm thick SiO2 film.
Haring Bolivar, P., M. Brucherseifer, et al. (2002). Label-free probing of genes by time-domain terahertz sensing. Physics in medicine and biology 47(21): 3815-21.
A label-free sensing approach for the label-free characterization of genetic material with terahertz (THz) electromagnetic waves is presented. Time-resolved THz analysis of polynucleotides demonstrates a strong dependence of the complex refractive index of DNA molecules in the THz frequency range on their hybridization state. By monitoring THz signals one can thus infer the binding state (hybridized or denatured) of oligo- and polynucleotides, enabling the label-free determination the genetic composition of unknown DNA sequences. A broadband experimental proof-of-principle in a freespace analytic configuration, as well as a higher-sensitivity approach using integrated THz sensors reaching femtomol detection levels and demonstrating the capability to detect single-base mutations, are presented. The potential application for next generation high-throughput label-free genetic analytic systems is discussed.
Nagel, M., P. H. Bolivar, et al. (2002). Integrated planar terahertz resonators for femtomolar sensitivity label-free detection of DNA hybridization. Applied Optics 41(10): 2074-2078.
A promising label-free approach for the anal. of genetic material by means of detecting the hybridization of polynucleotides with electromagnetic waves at terahertz (THz) frequencies is presented. Using an integrated waveguide approach, incorporating resonant THz structures as sample carriers and transducers for the anal. of the DNA mols., we achieve a sensitivity down to femtomolar levels. The approach is demonstrated with time-domain ultrafast techniques based on femtosecond laser pulses for generating and electro-optically detecting broadband THz signals, although the principle can certainly be transferred to other THz technologies.
Nagel, M., P. Haring Bolivar, et al. (2002). Integrated THz technology for label-free genetic diagnostics. Applied Physics Letters 80(1): 154-156.
We report on a promising approach for the label-free anal. of DNA mols. using direct probing of the binding state of DNA with electromagnetic waves at THz frequencies. Passive THz resonator devices based on planar waveguides are used as sample carriers and transducers for THz transmission anal. In comparison to a formerly used free-space detection scheme, this method provides a drastically enhanced sensitivity enabling anal. down to femtomol levels. We examine the potential of our approach on biol. relevant DNA samples and demonstrate the detection of single base mutations on DNA mols.
Brucherseifer, M., A. Meltzow-Altmeyer, et al. (2003). Low-temperature THz imaging of thin high-temperature superconductor films. Physica C: Superconductivity and Its Applications (Amsterdam, Netherlands) 399(1&2): 53-60.
We demonstrate an imaging system capable of performing spatially resolved anal. in the THz frequency range at temps. down to 10 K. The demonstrated time-resolved THz imaging system is applied for the high-frequency characterization of thin high-temp. superconductor (HTSC) films. It is shown that this low-temp. analytic system enables to quant. assess the quality of growth and structuring processes of such films, and consequently can be applied to support the systematic development and optimization of HTSC based components.
Hadjiloucas, S., R. K. H. Galvao, et al. (2003). Measurement of propagation constant in waveguides with wideband coherent terahertz spectroscopy. Journal of the Optical Society of America B: Optical Physics 20(2): 391-401.
A quasi-optical technique for characterizing micromachined waveguides is demonstrated with wideband time-resolved terahertz spectroscopy. A transfer-function representation is adopted for the description of the relation between the signals in the input and output port of the waveguides. The time-domain responses were discretized, and the waveguide transfer function was obtained through a parametric approach in the z domain after describing the system with an autoregressive with exogenous input model. The a priori assumption of the no. of modes propagating in the structure was inferred from comparisons of the theor. with the measured characteristic impedance as well as with parsimony arguments. Measurements for a precision WR-8 waveguide-adjustable short as well as for G-band reduced-height micromachined waveguides are presented.
Haring Bolivar, P., M. Brucherseifer, et al. (2003). Measurement of the dielectric constant and loss tangent of high dielectric-constant materials at terahertz frequencies. IEEE Transactions on Microwave Theory and Techniques 51(4, Pt. 1): 1062-1066.
Low-loss high dielec.-const. materials are analyzed in the terahertz frequency range using time-domain spectroscopy. The dielec. const. and loss tangent for steatite, Al2O3, TiO2-loaded polystyrene, and Zr-Sn titanate are presented and compared to measurements on high-resistivity Si. For these materials, the real part of the dielec. const. ranges from 6-90. All of the samples were found to have reasonable low-loss tangents. Applications as photonic crystal substrates for terahertz frequency antenna are envisaged.
Haring Bolivar, P., M. Nagel, et al. (2004). Label-free THz sensing of genetic sequences: towards 'THz biochips'. Philosophical Transactions of the Royal Society of London, Series A: Mathematical, Physical and Engineering Sciences 362(1815): 323-335
A review. THz-wave-based approaches for the label-free characterization of genetic material are described. Time-resolved THz spectroscopic anal. of genetic sequences (polynucleotides) demonstrate a distinct complex refractive index in the THz frequency range as a function of the binding state of the analyzed DNA sequences. By monitoring THz signals, one can thus infer the binding state of oligo- and polynucleotides, enabling the label-free detn. of the genetic compn. of target polynucleotides by sensing their binding to known probe mols. Here we review integrated THz sensing array developments exhibiting high sensitivity and single-base mutation detection capabilities. Recent achievements using functionalized biosensing arrays of high-Q resonators are illustrated.
Conferences:
Brucherseifer, M., P. H. Bolivar, et al. (1999). THz imaging in a Brewster-angle configuration: characterization of thin oxide coatings for fuel cell applications. Proceedings of SPIE-The International Society for Optical Engineering.
Time-resolved THz imaging for the incidence-angle dependent 3D tomog. characterization of layered structures is presented. We illustrate the capabilities of the developed system on multi-layer ceramic samples used for solid oxide fuel cells. Diverse methods for detg. unknown refractive indexes are discussed. The significant influence of the angle of incidence of a THz imaging system on the measured signal is demonstrated, which can be exploited esp. in Brewster-angle configurations to enhance the capabilities of any THz tomog. system.
Brucherseifer, M., R. Martini, et al. (1999). Angle dependent THz-tomography - characterization of thin ceramic oxide films for fuel cell applications. Proceedings of the International Conference on Lasers.
A time-resolved THz imaging system for incidence angle dependent three-dimensional tomog. anal. of layered structures is presented. The capabilities of the developed setup are demonstrated on multilayer ceramic samples used for high-temp. solid oxide fuel cells. Methods for measuring unknown refractive indexes are discussed. It is shown that the angle of incidence of a THz imaging system has a significant influence on measured signals. This fact can be exploited esp. in Brewster-angle configurations to enhance the capabilities of any THz tomog. system.
Brucherseifer, M., H. P. M. Pellemans, et al. (2000). THz spectroscopy with ultrahigh sensitivity. Conference on Lasers and Electro-Optics (CLEO 2000). Technical Digest. Postconference Edition. TOPS Vol.39, 7-12 May 2000, San Francisco, CA, USA, Opt. Soc. America.
Although THz radiation has been used successfully for several applications the signal-to-noise ratio is mostly restricted to 10/sup 4/ to 10/sup 6/ in intensity. Especially for thin films of material the absorption and time delay of a THz pulse are mostly too low to be detected. We show a new method to enhance the sensitivity of THz spectroscopy to relative changes of 10/sup -10/ in intensity by shaking a sample through the focus of a THz beam and using lock-in detection on the shaking frequency
Haring Bolivar, P., M. Brucherseifer, et al. (2000). Label-free probing of the binding state of DNA by time-domain THz sensing. Twelfth International Conference on Ultrafast Phenomena Vol.43. Technical Digest. Postconference Edition, 9-13 July 2000, Charleston, SC, USA, Opt. Soc. America.
We present a new approach for the label-free characterization of genetic material. Time-resolved THz transmission analysis of polynucleotides demonstrates a strong dependence of the complex refractive index on the binding state (hybridized/denatured) of DNA molecules. By monitoring THz transients one can thus infer the binding state of oligo- and polynucleotides. A broadband experimental demonstration in a free-space configuration is presented. The integration into higher-sensitivity approaches in planar structures, as well as the potential application for next generation gene chips are discussed
Pellemans, H. P. M., P. H. Bolivar, et al. (2000). Characterization techniques for passive devices from 150 GHz to 3 THz using THz-transient spectroscopy. Conference on Lasers and Electro-Optics (CLEO 2000). Technical Digest. Postconference Edition. TOPS Vol.39, 7-12 May 2000, San Francisco, CA, USA, Opt. Soc. America.
In recent years, new micromachining techniques have been developed for the easy and cheap fabrication of three-dimensional waveguide and antenna components in the GHz- and THz frequency range. We are developing characterization techniques for such devices, of which we present two examples: antenna-coupled waveguides and horn antenna patterns
Pellemans, H. P. M., M. Nagel, et al. (2000). Near-field antenna pattern measurements at 94 GHz using synchronized photoconductive sampling. Conference on Lasers and Electro-Optics (CLEO 2000). Technical Digest. Postconference Edition. TOPS Vol.39, 7-12 May 2000, San Francisco, CA, USA, Opt. Soc. America.
Coherent detection of free-space GHz- and THz radiation is important for the characterization of free-radiating systems. Most methods reported to date have relied on coherent generation, for instance through photomixing of two laser frequencies, to ensure a fixed phase between detector and source. At this time, such systems cannot provide the power levels required to measure spatially large systems. Here, we use an alternative method, developed by Loffler et al., which uses photoconductive sampling to coherently detect a signal generated by a free-running source. We demonstrate this in a real-life application, namely the measurement of the near-field radiation pattern of a large-aperture antenna at 94 GHz
Haring Bolivar, P., M. Brucherseifer, et al. (2001). Time-domain terahertz spectroscopy and sensing. Terahertz Sources and Systems. Proceedings of the NATO Advanced Research Workshop, 22-27 June 2000, Chateau de Bonas, France, Kluwer Academic.
Spectroscopy in the terahertz (THz) region of the electromagnetic spectrum is an important and growing field of research with a broad range of applications. The characteristic properties of THz radiation, localised between the infrared and the microwave frequencies, suggest many applications in the spectroscopy of gases, liquids and condensed matter. This chapter briefly recapitulates the general advantages of time-domain THz spectroscopy, before going on to discuss examples of recent progress. The paper is structured as follows: the initial part focuses on simple examples of linear THz spectroscopy, before going into non-linear (optical pump-THz probe) THz experiments, modulation THz spectroscopy, and spatially resolved measurements which demonstrate the wide flexibility of THz sensing for the characterisation of THz devices. We show how glass-fibre-integrated and synchronised THz techniques are especially powerful means of characterising THz systems and components
Brucherseifer, M., A. Meltzow-Altmeyer, et al. (2002). Low-density optical pump - THz probe analysis of high-temperature superconductors. 13th International Meeting on Ultrafast Phenomena, 12-17 May 2002, Vancouver, BC, Canada, Opt. Soc. America.
Using time-resolved THz probing we analyze the dynamics of low-density optically excited, optimally doped YBa/sub 2/Cu/sub 3/O/sub 7- delta /. A previously unknown additional relaxation component is found, tentatively indicating the separate relaxation of charge and spin excitations
Brucherseifer, M., A. Meltzow-Altmeyer, et al. (2002). Low-temperature THz imaging for high-temperature superconductor thin-film analysis. Technical Digest. Summaries of papers presented at the Quantum Electronics and Laser Science Conference. Conference Edition, 19-24 May 2002, Long Beach, CA, USA, Opt. Soc. America.
We present the experimental demonstration of THz imaging performed at low-temperatures. The experimental setup allows the spatially resolved analysis of THz properties at temperatures down to 10 K. The setup is used for analyzing high- temperature superconductor thin films where THz spectroscopy has been demonstrated provide fundamental and technological information
Brucherseifer, M., M. Nagel, et al. (2002). Label-free sensing of genetic sequences with integrated terahertz systems. Conference Proceedings. Second Joint EMBS-BMES Conference 2002 24th Annual International Conference of the Engineering in Medicine and Biology Society. Annual Fall Meeting of the Biomedical Engineering Society, 23-26 Oct. 2002, Houston, TX, USA, IEEE.
We present a THz wave based approach for the label-free characterization of genetic material. Time-resolved THz spectroscopic analysis of genetic sequences (polynucleotides) demonstrate a clearly distinct complex refractive index in the THz frequency range as a function of the hybridization state (hybridized/denatured) of the analysed DNA sequences. By monitoring THz signals one can thus infer the binding state of oligo- and polynucleotides, enabling the label-free determination of the genetic composition of polynucleotides. A broadband experimental proof-of-principle in a free-space configuration, as well as a first demonstration of a high-sensitivity integrated approach reaching femtomol detection levels and single base mutation detection capabilities, are presented
Hadjiloucas, S., R. K. H. Galvao, et al. (2002). Wavelet filtered modelling applied to measurements of a waveguide's THz time domain response. THz 2002. 2002 IEEE Tenth International Conference on Terahertz Electronics Proceedings, 9-10 Sept. 2002, Cambridge, UK, IEEE.
A quasi-optical de-embedding technique for characterizing waveguides is demonstrated using wideband time-resolved terahertz spectroscopy. A transfer function representation is adopted for the description of the signal in the input and output port of the waveguides. The time domain responses were discretised and the waveguide transfer function was obtained through a parametric approach in the z-domain after describing the system with an ARX as well as with a state space model. Prior to the identification procedure, filtering was performed in the wavelet domain to minimize signal distortion and the noise propagating in the ARX and subspace models. The model identification procedure requires isolation of the phase delay in the structure and therefore the time-domain signatures must be firstly aligned with respect to each other before they are compared. An initial estimate of the number of propagating modes was provided by comparing the measured phase delay in the structure with theoretical calculations that take into account the physical dimensions of the waveguide. Models derived from measurements of THz transients in a precision WR-8 waveguide adjustable short will be presented
Haring Bolivar, P., M. Brucherseifer, et al. (2002). Label-free probing of the binding state of DNA by time-domain terahertz sensing. 11th International Symposium on Ultrafast Phenomena in Semiconductors (11-UFPS), 27-29 Aug. 2001, Vilnius, Lithuania.
We present a new approach for the label-free characterization of genetic material. Time-resolved THz transmission analysis of polynucleotides demonstrate a strong dependence of the complex refractive index of DNA molecules on their hybridization state (hybridized/denatured). By monitoring THz signals one can thus infer the binding state of oligo- and polynucleotides, enabling the label-free determination the genetic composition of unknown DNA sequences. A broadband experimental proof-of-principle in a free-space configuration, as well as a first demonstration of a higher-sensitivity integrated approach using planar THz resonator sensors, are elucidated. The potential application for next generation high-throughput label-free genetic analytic systems is discussed
Nagel, M., M. Brucherseifer, et al. (2002). Integrated THz technologies for femtomol sensitivity label-free detection of DNA. 13th International Meeting on Ultrafast Phenomena, 12-17 May 2002, Vancouver, BC, Canada, Opt. Soc. America.
An integrated label-free approach for genetic analysis using time-domain femtosecond techniques for generating and electrooptically detecting THz signals is presented. Using planar THz resonators a femtomol sensitivity for DNA molecule detection is reached
Nagel, M., F. Richter, et al. (2002). THz technology for label-free genetic diagnostics. LEOS 2002. 2002 IEEE/LEOS Annual Meeting Conference Proceedings. 15th Annual Meeting of the IEEE Lasers and Electro-Optics Society, 10-14 Nov. 2002, Glasgow, UK, IEEE.
THz-wave based approaches for the label-free characterization of genetic material are presented. Time-resolved THz spectroscopic analysis of genetic sequences (polynucleotides) demonstrate a clearly distinct complex refractive index in the THz frequency range as a function of the hybridization state (hybridized/denatured) of the analysed DNA sequences. By monitoring THz signals one can thus infer the binding state of oligo- and polynucleotides, enabling the label-free determination of the genetic composition of polynucleotides. A broadband experimental proof-of-principle in a free-space configuration, as well as a first demonstration of a high-sensitivity integrated approach reaching femtomol detection levels and single base mutation detection capabilities, are presented
Brucherseifer, M., C. Kranz, et al. (2005). Combination of AFM with IR-ATR Spectroscopy for Measurements in Liquid Environment Conference on Lasers and Electro-Optics (CLEO 2005). Technical Digest. 22-27 May 2005, Baltimore, MA, USA, Opt. Soc. America.
We present the instrumental combination of atomic force microscopy with infrared attenuated total reflectance spectroscopy. This is the first time to demonstrate AFM scanning while recording IR-spectra in a liquid environment.
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