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Relevant bibliographies by topics / Biomolecular manipulation

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Academic literature on the topic 'Biomolecular manipulation'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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Journal articles on the topic "Biomolecular manipulation"

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Hook, A. L., N. H. Voelcker, and H. Thissen. "Patterned and switchable surfaces for biomolecular manipulation." Acta Biomaterialia 5, no. 7 (September 2009): 2350–70. http://dx.doi.org/10.1016/j.actbio.2009.03.040.

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Mogaki, Rina, P. K. Hashim, Kou Okuro, and Takuzo Aida. "Guanidinium-based “molecular glues” for modulation of biomolecular functions." Chem. Soc. Rev. 46, no. 21 (2017): 6480–91. http://dx.doi.org/10.1039/c7cs00647k.

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Takahashi, Shunsuke, Masahiko Oshige, and Shinji Katsura. "DNA Manipulation and Single-Molecule Imaging." Molecules 26, no. 4 (February 17, 2021): 1050. http://dx.doi.org/10.3390/molecules26041050.

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DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

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Soltani, Mohammad, Jun Lin, Robert A. Forties, James T. Inman, Summer N. Saraf, Robert M. Fulbright, Michal Lipson, and Michelle D. Wang. "Nanophotonic trapping for precise manipulation of biomolecular arrays." Nature Nanotechnology 9, no. 6 (April 28, 2014): 448–52. http://dx.doi.org/10.1038/nnano.2014.79.

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Baker, James E., Ryan P. Badman, and Michelle D. Wang. "Nanophotonic trapping: precise manipulation and measurement of biomolecular arrays." Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 10, no. 1 (April 24, 2017): e1477. http://dx.doi.org/10.1002/wnan.1477.

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Okumura, Shu, Benediktus Nixon Hapsianto, Nicolas Lobato-Dauzier, Yuto Ohno, Seiju Benner, Yosuke Torii, Yuuka Tanabe, et al. "Morphological Manipulation of DNA Gel Microbeads with Biomolecular Stimuli." Nanomaterials 11, no. 2 (January 22, 2021): 293. http://dx.doi.org/10.3390/nano11020293.

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Hydrogels are essential in many fields ranging from tissue engineering and drug delivery to food sciences or cosmetics. Hydrogels that respond to specific biomolecular stimuli such as DNA, mRNA, miRNA and small molecules are highly desirable from the perspective of medical applications, however interfacing classical hydrogels with nucleic acids is still challenging. Here were demonstrate the generation of microbeads of DNA hydrogels with droplet microfluidic, and their morphological actuation with DNA strands. Using strand displacement and the specificity of DNA base pairing, we selectively dissolved gel beads, and reversibly changed their size on-the-fly with controlled swelling and shrinking. Lastly, we performed a complex computing primitive—A Winner-Takes-All competition between two populations of gel beads. Overall, these results show that strand responsive DNA gels have tantalizing potentials to enhance and expand traditional hydrogels, in particular for applications in sequencing and drug delivery.

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Cao, Lizhi, Zhengchun Peng, Wilbur Lam, and Thomas H. Barker. "A combined magnetophoresis/dielectrophoresis based microbead array as high-throughput biomolecular tweezers." TECHNOLOGY 02, no. 01 (March 2014): 23–27. http://dx.doi.org/10.1142/s2339547814500058.

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In this paper we describe a combined magnetophoresis (MAP) and dielectrophoresis (DEP) based platform for high throughput characterization of specific biomolecular interactions. The magnetic manipulation enables parallel loading of individual magnetic beads onto a magnetic pad array, while the combination of tightly controlled opposing magnetic and dielectrophoretic (DEP) forces is employed to produce characteristic out-of-plane (z-axial) bead displacement. We optimized design parameters to evenly load 2.8 μm biomolecule functionalized paramagnetic beads onto magnetic pads, and demonstrate the ability of our tweezers to discriminate between specific antibody-antigen bond from non-specific bond formed between bead and pad surface.

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Iino, Ryota, Tatsuya Iida, Akihiko Nakamura, Ei-ichiro Saita, Huijuan You, and Yasushi Sako. "Single-molecule imaging and manipulation of biomolecular machines and systems." Biochimica et Biophysica Acta (BBA) - General Subjects 1862, no. 2 (February 2018): 241–52. http://dx.doi.org/10.1016/j.bbagen.2017.08.008.

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CHEN, WEI-HUNG, JONATHAN D. WILSON, SITHARA S. WIJERATNE, SARAH A. SOUTHMAYD, KUAN-JIUH LIN, and CHING-HWA KIANG. "PRINCIPLES OF SINGLE-MOLECULE MANIPULATION AND ITS APPLICATION IN BIOLOGICAL PHYSICS." International Journal of Modern Physics B 26, no. 13 (May 5, 2012): 1230006. http://dx.doi.org/10.1142/s021797921230006x.

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Recent advances in nanoscale manipulation and piconewton force detection provide a unique tool for studying the mechanical and thermodynamic properties of biological molecules and complexes at the single-molecule level. Detailed equilibrium and dynamics information on proteins and DNA have been revealed by single-molecule manipulation and force detection techniques. The atomic force microscope (AFM) and optical tweezers have been widely used to quantify the intra- and inter-molecular interactions of many complex biomolecular systems. In this article, we describe the background, analysis, and applications of these novel techniques. Experimental procedures that can serve as a guide for setting up a single-molecule manipulation system using the AFM are also presented.

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Mahajan, Kalpesh D., Gang Ruan, Greg Vieira, Thomas Porter, Jeffrey J. Chalmers, R. Sooryakumar, and Jessica O. Winter. "Biomolecular detection, tracking, and manipulation using a magnetic nanoparticle-quantum dot platform." Journal of Materials Chemistry B 8, no. 16 (2020): 3534–41. http://dx.doi.org/10.1039/c9tb02481f.

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Fluorescent and magnetic materials play a significant role in biosensor technology, enabling sensitive quantification and separations with applications in diagnostics, purification, quality control, and therapeutics.

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Dissertations / Theses on the topic "Biomolecular manipulation"

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Dorcéna, Cassandre Jenny. "Nanoparticles for Biomedical Imaging and Biomolecular Transport and Manipulation." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1408915572.

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Silva, Santisteban Tomas [Verfasser], and Matthias [Akademischer Betreuer] Meier. "Spheroid manipulation on a microfluidic chip platform for biomolecular analysis." Freiburg : Universität, 2017. http://d-nb.info/1144829658/34.

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Hook, Andrew Leslie, and andrew hook@flinders edu au. "Patterned and switchable surfaces for biomaterial applications." Flinders University. Chemistry, Physics and Earth Sciences, 2008. http://catalogue.flinders.edu.au./local/adt/public/adt-SFU20090210.161131.

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The interactions of biomolecules and cells at solid-liquid interfaces play a pivotal role in a range of biomedical applications and have hence been studied in detail. An improved understanding of these interactions results in the ability to manipulate biomolecules and concurrently cells spatially and temporally at surfaces with high precision. Spatial control can be achieved using patterned surface chemistries whilst temporal control is achieved by switchable surfaces. The combination of these two surface properties offers unprecedented control over the behaviour of biomolecules and cells at the solid-liquid interface. This is particularly relevant for cell microarray applications, where a range of biological processes must be duly controlled in order to maximise the efficiency and throughput of these devices. Of particular interest are transfected cell microarrays (TCMs), which significantly widen the scope of microarray genomic analysis by enabling the high-throughput analysis of gene function within living cells Initially, this thesis focuses on the spatially controlled, electro-stimulated adsorption and desorption of DNA. Surface modification of a silicon chip with an allylamine plasma polymer (ALAPP) layer resulted in a surface that supported DNA adsorption and sustained cell attachment. Subsequent high density grafting of poly(ethylene glycol) (PEG) formed a layer resistant to biomolecule adsorption and cell attachment. PEG grafted surfaces also showed significantly reduced attachment of DNA with an equilibrium binding constant of 23 ml/mg as compared with 1600 ml/mg for ALAPP modified surfaces. Moreover, both hydrophobic and electrostatic interactions were shown to contribute to the binding of DNA to ALAPP. Spatial control over the surface chemistry was achieved using excimer laser ablation of the PEG coating which enabled the production of patterns of re-exposed ALAPP with high resolution. Preferential electro-stimulated adsorption of DNA to the ALAPP regions and subsequent desorption by the application of a negative bias was observed. Furthermore, this approach was investigated for TCM applications. Cell culture experiments demonstrated efficient and controlled transfection of cells. Electro-stimulated desorption of DNA was shown to yield enhanced solid phase transfection efficiencies with values of up to 30%. The ability to spatially control DNA adsorption combined with the ability to control the binding and release of DNA by application of a controlled voltage enables an advanced level of control over DNA bioactivity on solid substrates and lends itself to biochip applications. As an alternative approach to surface patterning, the fabrication and characterisation of chemical patterns using a technique that can be readily integrated with methods currently used for the formation of microarrays is also presented. Here, phenylazide modified polymers were printed onto low fouling ALAPP-PEG modified surfaces. UV irradiation of these polymer arrays resulted in the crosslinking of the polymer spots and their covalent attachment to the surface. Cell attachment was shown to follow the patterned surface chemistry. Due to the use of a microarray contact printer it was easily possible to deposit DNA on top of the polymer microarray spots. A transfected cell microarray was generated in this way, demonstrating the ability to limit cell attachment to specific regions and the suitability of this approach for high density cell assays. In order to allow for the high-throughput characterisation of the resultant polymer microarrays, surface plasmon resonance imaging was utilised to study the adsorption and desorption of bovine serum albumin, collagen and fibronectin. This analysis enabled insights into the underlying mechanisms of cell attachment to the polymers studied. For the system analysed here, electrostatic interactions were shown to dominate cellular behaviour.

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Peng, Zhengchun. "Parallel manipulation of individual magnetic microbeads for lab-on-a-chip applications." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/39469.

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Many scientists and engineers are turning to lab-on-a-chip systems for cheaper and high throughput analysis of chemical reactions and biomolecular interactions. In this work, we developed several lab-on-a-chip modules based on novel manipulations of individual microbeads inside microchannels. The first manipulation method employs arrays of soft ferromagnetic patterns fabricated inside a microfluidic channel and subjected to an external rotating magnetic field. We demonstrated that the system can be used to assemble individual beads (1-3µm) from a flow of suspended beads into a regular array on the chip, hence improving the integrated electrochemical detection of biomolecules bound to the bead surface. In addition, the microbeads can follow the external magnet rotating at very high speeds and simultaneously orbit around individual soft magnets on the chip. We employed this manipulation mode for efficient sample mixing in continuous microflow. Furthermore, we discovered a simple but effective way of transporting the microbeads on-chip in the rotating field. Selective transport of microbeads with different size was also realized, providing a platform for effective sample separation on a chip. The second manipulation method integrates magnetic and dielectrophoretic manipulations of the same microbeads. The device combines tapered conducting wires and fingered electrodes to generate desirable magnetic and electric fields, respectively. By externally programming the magnetic attraction and dielectrophoretic repulsion forces, out-of-plane oscillation of the microbeads across the channel height was realized. Furthermore, we demonstrated the tweezing of microbeads in liquid with high spatial resolutions by fine-tuning the net force from magnetic attraction and dielectrophoretic repulsion of the beads. The high-resolution control of the out-of-plane motion of the microbeads has led to the invention of massively parallel biomolecular tweezers.

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Jönsson, Mats. "Microfluidic Devices for Manipulation and Detection of Beads and Biomolecules." Doctoral thesis, Uppsala universitet, Institutionen för teknikvetenskaper, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6746.

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This thesis summarises work towards a Lab-on-Chip (LOC). The request for faster and more efficient chemical and biological analysis is the motivation behind the development of the LOC-concept. Microfluidic devices tend to become increasingly complex in order to include, e.g. sample delivery, manipulation, and detection, in one chip. The urge for smart and simple design of robust and low-cost microdevices is addressed and discussed. Design, fabrication and characterization of such microdevices have been demonstrated using low-cost polymer and glass microfabrication methods. The manufacturing is feasible, to a large extent, to perform outside the clean-room, and has subsequently been the chosen technique for most of the work. Issues of bonding reliability are solved by using polymer adhesive tapes. A planar electrocapture device with LOC-compatibility is demonstrated where beads are immobilised and released in a flowing stream. Retention of nanoparticles by means of electric field-flow fractionation using transparent indium tin oxide electrodes is presented. Moreover, a cast PDMS 4-way crossing is enabling a combination of liquid chromatography and capillary electrophoresis to enhance separation efficiency. Sample transport issues and a new flow-cell design in a quartz crystal microbalance bioanalyzer are also investigated. Fast bacteria counting by impedance measurements, much requested by the pharmaceutical industry for biomass monitoring, is carried out successfully. In conclusion, knowledge in micro system technology to build microdevices have been utilised to manipulate and characterise beads and cells, taking one step further towards viable Lab-on-Chip instruments.

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Jönsson, Mats. "Microfluidic devices for manipulation and detection of beads and biomolecules /." Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6746.

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Jobst, Markus A. [Verfasser], and Hermann [Akademischer Betreuer] Gaub. "Multiplexed single molecule observation and manipulation of engineered biomolecules / Markus A. Jobst ; Betreuer: Hermann Gaub." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/1185978798/34.

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Wu, Di. "Biomolecular Tools for Noninvasive Imaging and Manipulation of Engineered Cells." Thesis, 2021. https://thesis.library.caltech.edu/14174/8/PDF.pdf.

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Today’s most advanced tools for imaging and controlling cellular function are based on fluorescent or light-controlled proteins, which have limited utility in large organisms or engineered living materials due to the scattering of photons. Deeply penetrant forms of energy such as magnetic fields and sound waves, while routinely used to monitor and treat diseases on the tissue and organism level, do not process the equivalent set of biomolecular tools for interfacing with biology on the molecular and cellular level. Emerging technologies discussed in this thesis aim to bridge this gap by harnessing biomolecules that have the appropriate physical properties to interact with sound waves or magnetic fields in such a way that enables the visualization and control of specific cells (Chapter 1). We describe two additions to the expanding toolkit for noninvasive imaging and control. In the first case, we show that gas vesicles, a class of hollow protein nanostructures naturally found in aquatic single-cell organisms, can be used as acoustic actuators to enable the control of cellular forces, movement, and patterning using ultrasound (Chapter 2). In the second case, we show that aquaporins, a class of membrane water channels, can be used to alter cellular permeability and serve as genetic reporters for magnetic resonance imaging (Chapter 3). These tools provide critical capabilities for interfacing with cellular function noninvasively and could open the door to applications in various research, biomedical, and industrial settings.

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Janissen, Richard [Verfasser]. "Biomolecular based nano-manipulation with a combined atomic force microscope and single molecule fluorescence setup / vorgelegt von Richard Janissen." 2008. http://d-nb.info/1000134172/34.

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Nien, Song-Moon, and 粘松木. "Manipulation and Characterization ofNano-Biomolecule." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/94201795314014233179.

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碩士
國立東華大學
應用物理研究所
93
DNA triplex is a kinetic structure in native gene system. In this study, the rupture force and dissociation energy of double strand DNA was measured by a home-made optical tweezer. The magnitude of rupture force of ds-DNA (17 mer) is around 30 pN and the dissociation energy is around 3.1*10-18 J for water environment . Meanwhile, the pair of positional dependent molecular beacon those were labeled on each oligonucleotide strand inducted that both Hoogsteen and Watson strands had same polarity in DNA triplex. Meanwhile, the CW and H can self-assembly and formed triplex structure in an acidic environment. Magnetic properties of metal binding protein, metallothionein (MT), can be engineered by replacing the ratio and species of metal ions containing of MT via an over-critical refolding process. A ferromagnetic MT containing two Mn and five Cd (Mn,Cd-MT-2) has been refolded and its magnetization persists from 277 to 330 K. Meanwhile, the uniform size distribution as tested by dynamic light scattering indicated that each MT molecule is a single molecule magnet. The sizable magnetic moment of Mn,Cd-MT-2 may be attributable to the electrons spin double exchange model among two Mn2+ and one Cd2+ via sulfur bridges of its 　-metal binding cluster, a Zinc Blende structure, of MT. Meanwhile, the peptide backbone of Mn,Cd-MT-2 serves as a bridging ligand to align these magnetic moments near perfection. This magnetic engineering process not only verifies the mechanism of electron double exchange model in single molecular level, and the unique features of its molecular magnetism and bio-compatibility make it a good candidate for biological applications and sensing sources of new nano-devices.

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Books on the topic "Biomolecular manipulation"

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name, No. Manipulation and analysis of biomolecules, cells, and tissues: 28-29 January 2003, San Jose, California, USA. Bellingham, WA: SPIE, 2003.

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Farkas, Daniel L. Imaging, manipulation, and analysis of biomolecules, cells, and tissues VI: 21-23 January 2008, San Jose, California, USA. Edited by Society of Photo-optical Instrumentation Engineers. Bellingham, Wash: SPIE, 2008.

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Farkas, Daniel L. Imaging, manipulation, and analysis of biomolecules, cells, and tissues VII: 26-28 January 2009, San Jose, California, United States. Bellingham, Wash: SPIE, 2009.

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Nicolau, Dan V., Daniel L. Farkas, and Robert C. Leif. Imaging, manipulation, and analysis of biomolecules, cells, and tissues IX: 22-25 January 2011, San Francisco, California, United States. Bellingham, Wash: SPIE, 2011.

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Nicolau, Dan V., Daniel L. Farkas, and Robert C. Leif. Imaging, manipulation, and analysis of biomolecules, cells, and tissues X: 21-23 January 2012, San Francisco, California, United States. Bellingham, Wash: SPIE, 2012.

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Farkas, Daniel L. Imaging, manipulation, and analysis of biomolecules, cells, and tissues VIII: 23-25 January 2010, San Francisco, California, United States. Bellingham, Wash: SPIE, 2010.

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Farkas, Daniel L. Imaging, manipulation, and analysis of biomolecules, cells, and tissues VII: 26-28 January 2009, San Jose, California, United States. Edited by SPIE (Society). Bellingham, Wash: SPIE, 2009.

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Lin, C. W., N. F. Chiu, and C. C. Chang. Modulation design of plasmonics for diagnostic and drug screening. Edited by A. V. Narlikar and Y. Y. Fu. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199533060.013.18.

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This article discusses the modulation design of plasmonics for diagnosis and drug screening applications. It begins with an overview of the advances made in terms of theoretical insights, focusing on the origins of surface plasmon wave and manipulation, admittance loci design method, and surface plasmon grating coupled emission. It then considers how prism coupler, Ge-doped silica waveguide, nanograting and active plasmonics can trigger the excitation of surface plasmon resonance (SPR). It also examines the metallic effect of long-range surface plasmon resonance and conducting metal oxide as adhesive layer before describing three SPR waveguide biosensors that were developed for the realization of a hand-held SPR system. In particular, it presents a lateral-flow microfluidic channel based on a nitrocellulose membrane and integrated with a SPR waveguide biosensor to achieve dynamic detection. Finally, the article evaluates the biomolecular layer effect, with emphasis on kinetics analysis of antibody binding.

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Leif, Robert C. Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XIII. SPIE, 2015.

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Nicolau, Dan, Daniel Farkas, and Robert Leif. Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XV. SPIE, 2018.

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Book chapters on the topic "Biomolecular manipulation"

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Goda, Tatsuro, and Yuji Miyahara*. "Chapter 12. Sensing of Biomolecular Charges at Designer Nanointerfaces." In Manipulation of Nanoscale Materials, 302–17. Cambridge: Royal Society of Chemistry, 2012. http://dx.doi.org/10.1039/9781849735124-00302.

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Greulich, Karl Otto. "Optical trapping and manipulation." In Microsystem Technology: A Powerful Tool for Biomolecular Studies, 453–74. Basel: Birkhäuser Basel, 1999. http://dx.doi.org/10.1007/978-3-0348-8817-2_19.

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Schnelle, Thomas, Torsten Müller, and Günter Fuhr. "Manipulation of particles, cells and liquid droplets by high frequency electric fields." In Microsystem Technology: A Powerful Tool for Biomolecular Studies, 417–52. Basel: Birkhäuser Basel, 1999. http://dx.doi.org/10.1007/978-3-0348-8817-2_18.

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Fritzsche, Wolfgang. "Scanning force microscopy: A microstructured device for imaging, probing, and manipulation of biomolecules at the nanometer scale." In Microsystem Technology: A Powerful Tool for Biomolecular Studies, 353–70. Basel: Birkhäuser Basel, 1999. http://dx.doi.org/10.1007/978-3-0348-8817-2_15.

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Gupta, Shagun, Vijeshwar Verma, and Vipan Kakkar. "Biomolecular and Cellular Manipulation and Detection (Nanofluidics and Micro- and Nanotechnologies in Integrative Biology)." In Nanomaterials and Environmental Biotechnology, 315–32. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-34544-0_17.

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Dragoman, Daniela, and Mircea Dragoman. "Imaging and Manipulation of Biomolecules." In Bionanoelectronics, 107–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-25572-4_3.

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Ishii, Yoshiharu, and Toshio Yanagida. "Single Biomolecule Manipulation for Bioelectronics." In Bioelectronics, 287–307. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/352760376x.ch10.

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Glasgow, Janice, and Evan Steeg. "Motif Discovery in Protein Structure Databases." In Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.003.0011.

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The field of knowledge discovery is concerned with the theory and processes involved in the representation and extraction of patterns or motifs from large databases. Discovered patterns can be used to group data into meaningful classes, to summarize data, or to reveal deviant entries. Motifs stored in a database can be brought to bear on difficult instances of structure prediction or determination from X-ray crystallography or nuclear magnetic resonance (NMR) experiments. Automated discovery techniques are central to understanding and analyzing the rapidly expanding repositories of protein sequence and structure data. This chapter deals with the discovery of protein structure motifs. A motif is an abstraction over a set of recurring patterns observed in a dataset; it captures the essential features shared by a set of similar or related objects. In many domains, such as computer vision and speech recognition, there exist special regularities that permit such motif abstraction. In the protein science domain, the regularities derive from evolutionary and biophysical constraints on amino acid sequences and structures. The identification of a known pattern in a new protein sequence or structure permits the immediate retrieval and application of knowledge obtained from the analysis of other proteins. The discovery and manipulation of motifs—in DNA, RNA, and protein sequences and structures—is thus an important component of computational molecular biology and genome informatics. In particular, identifying protein structure classifications at varying levels of abstraction allows us to organize and increase our understanding of the rapidly growing protein structure datasets. Discovered motifs are also useful for improving the efficiency and effectiveness of X-ray crystallographic studies of proteins, for drug design, for understanding protein evolution, and ultimately for predicting the structure of proteins from sequence data. Motifs may be designed by hand, based on expert knowledge. For example, the Chou-Fasman protein secondary structure prediction program (Chou and Fasman, 1978), which dominated the field for many years, depended on the recognition of predefined, user-encoded sequence motifs for α-helices and β-sheets. Several hundred sequence motifs have been cataloged in PROSITE (Bairoch, 1992); the identification of one of these motifs in a novel protein often allows for immediate function interpretation.

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Thorsen, T. "Manipulation of biomolecules and reactions." In Nanolithography and patterning techniques in microelectronics. CRC Press, 2005. http://dx.doi.org/10.1201/9781439823651.ch11.

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Thorsen, T. "Manipulation of biomolecules and reactions." In Nanolithography and Patterning Techniques in Microelectronics, 320–48. Elsevier, 2005. http://dx.doi.org/10.1533/9781845690908.320.

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Conference papers on the topic "Biomolecular manipulation"

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Craighead, H. G. "Nanodevices for Biomolecular Manipulation and Analysis." In 2006 Sixth IEEE Conference on Nanotechnology. IEEE, 2006. http://dx.doi.org/10.1109/nano.2006.247595.

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Mokkapati, V. R. S. S., V. Di Virgilio, J. Mollinger, J. Bastemeijer, and A. Bossche. "Nanochannels Fabrication, Filling and DNA Manipulation." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13281.

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Fabrication of nanochannels is drawing considerable interest due to its broad applications in nanobiotechnology (e.g. biomolecular sensing and single DNA manipulation). Nanochannels offer distinct advantages in allowing a slower translocation and multiple sensing spots along the channel both of which improve the read-out resolution. However, implementing electrodes inside nanochannel has rarely been demonstrated to our knowledge. Therefore, we are highly motivated to do this research. The device described in this work is a Si-Glass anodically bonded Lab-on-a-Chip (LOC) device of a few millimeters in size using femtoliters in volume capable of performing DNA manipulation. The LOC structure is based on two mainstream microchannels interconnected by nanochannels. Organic samples as DNA will be released in the microfluidic mainstream and then, once confined in the nanochannels, are observed, manipulated and analyzed. We expect the general folded shape of DNA evolves to the unfolded linear shape due to the confinement in narrow channels. This shape is especially suitable for advanced manipulation and analysis.

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Zhao, Wei, Kangmin Xu, Xiaoping Qian, and Rong Wang. "Tip Based Nano Manipulation Through Successive Directional Push." In ASME 2010 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/detc2010-28578.

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Nano manipulation refers to the process of transporting nanoscale components. It has found applications in nano device prototyping and biomolecular and cellular investigation. In this paper, we present an atomic force microscope (AFM) based approach for automated manipulation of nano particles to form designed patterns. The automated manipulation is based on a novel method, successive directional push. This method keeps pushing along a fixed forward direction until the particle reaches the baseline of the target position, and it then repeats the pushing process along the base line direction. This process is iterated until the particle reaches its target position. By examining the topography of several local parallel scan lines, this method can determine the lateral coordinate of the particle. The novelty of this method lies in the fact that further pushing along the same pushing direction can be conducted without precise information about the forward position. The successive directional push method has been successfully implemented into an AFM system. We demonstrate that complex designed patterns including over one hundred latex particles of 50 nm diameter can be fabricated with this method.

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Pishkenari, H. Nejat, S. H. Mahboobi, M. A. Mahjour, and A. Meghdari. "Simulation of Biomanipulation Using Molecular Dynamics." In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-86804.

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In this paper, the simulation of biomolecules manipulation using molecular dynamics (MD) is studied. In order to investigate the manipulation behavior, we have used the ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a two-layer graphene sheet as substrate. Along this line, a series of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between the tip and substrate, initial orientation of protein, and the tip position with respect to the biomolecule.

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Majumdar, Arun. "Integrated Nanofluidic Devices and Circuits." In ASME 4th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2006. http://dx.doi.org/10.1115/icnmm2006-96070.

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The fundamental length scales related to ions and molecules in liquids fall in the range of 1–100 nm. These involves the range of intermolecular forces due to steric interactions, electrostatic forces between charged species, and van der Waals interactions. This talk will focus on how confinement of aqueous solutions in the range of Debye screening length (1–50 nm) in nanochannels can lead to formation of unipolar ionic solutions. The ionic current in such nanochannels is found to several orders of magnitude higher than that predicted by macroscopic theories, and is extremely sensitive to surface charge, which can be used to study surface biomolecular reactions. Furthermore, this phenomenon can be exploited to develop nanofluidic transistors, diodes, and integrated circuits, which is now forming the basis for manipulating and analyzing complex mixtures of biomolecules in ultrasmall volumes.

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Berlin, Andrew A., and Xing Su. "Ultrasensitive detection and manipulation of biomolecules." In Optics East, edited by Linda A. Smith and Daniel Sobek. SPIE, 2004. http://dx.doi.org/10.1117/12.581957.

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Bustamante, Carlos. "Recent advances on the manipulation of single biomolecules." In the eighth annual international conference. New York, New York, USA: ACM Press, 2004. http://dx.doi.org/10.1145/974614.974661.

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Daiguji, Hirofumi, Peidong Yang, Andrew Szeri, and Arun Majumdar. "Transport Phenomena in Nanofluidic Channels." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46036.

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Ion transport in nanoscale channels has recently received increasing attention. Much of that has resulted from experiments that report modulation of ion transport through the protein ion channel, α-hemolysin, due to passage of single biomolecules of DNA or proteins [1]. This has prompted research towards fabricating synthetic nanopores out of inorganic materials and studying biomolecular transport through them [2]. Recently, the synthesis of arrays of silica nanotubes with internal diameters in the range of 5–100 nm and with lengths 1–20 μm was reported [3]. These tubes could potentially allow new ways of detecting and manipulating single biomolecules and new types of devices to control ion transport. Theoretical modeling of ionic distribution and transport in silica nanotubes, 30 nm in diameter and 5 μm long, suggest that when the diameter is smaller than the Debye length, a unipolar solution of counterions is created within the nanotube and the coions are electrostatically repelled [4]. We proposed two different types of devices to use this unipolar nature of solution, i.e. ‘transistor’ and ‘battery’. When the electric potential bias is applied at two ends of a nanotube, ionic current is generated. By locally modifying the surface charge density through a gate electrode, the concentration of counterions can be depleted under the gate and the ionic current can be significantly suppressed. This could form the basis of a unipolar ionic field-effect transistor. By applying the pressure bias instead of electric potential bias, the fluid flow is generated. Because only the counterions are located inside the channel, the streaming current and streaming potential are generated. This could form the basis of an electro-chemo-mechanical battery. In the present study, transport phenomena in nanofluidic channels were investigated and the performance characteristics were evaluated using continuum dynamics.

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Sinha, Ashok, Ranjan Ganguly, and Ishwar K. Puri. "Magnetic Micromanipulation of a Single Magnetic Microsphere in a Microchannel." In ASME 4th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2006. http://dx.doi.org/10.1115/icnmm2006-96202.

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Magnetic microspheres are well known for their ability to provide high surface-to-volume ratio mobile reaction surfaces for chemical and biochemical reactions. Their use in microfluidic devices opens up novel avenues for uses in ‘lab-on-a-chip’ applications, e.g., as magnetic tweezers. Cantilevers and optical tweezers are widely used for micromanipulating cells or biomolecules in order to measure their mechanical properties, or for biosensor applications. However, they do not allow for ease of rotary motion and can sometimes damage the handled material. We present herein a system of magnetic tweezers that uses functionalized magnetic microspheres as mobile substrates for biological and biochemical reactions and offers better manipulation of the cells or organic molecules. The predominant transport issue for these magnetic tweezers is the precise magnetic manipulations of the microbeads so that the chemical/biological reactions at the bead surface are controlled. The best way to obtain unambiguous information about the behavior of particles is to begin with the study of a single isolated particle in a microchannel flow. We have conducted a fundamental study to manipulate an isolated magnetic microparticle using the concept of ‘action-at-a-distance’. An external magnetic field is used to direct and steer the particle across a microchannel. Such a study is directly pertinent to practical applications where usually a small number of such microspheres are utilized, such as DNA sequencing and separation, cell manipulation and separation, exploration of complex biomolecules by specific binding enabling folding and stretching, etc. Numerical simulation of the microchannel flow and particle manipulation is performed using a finite-volume transient CFD code and Lagrangian tracking of magnetic microspheres in the flow under an imposed magnetic field gradient. Experimental validation of the numerical results is then performed. The effects of varying viscosity and flowrate using two different particle sizes are investigated. Parametric study is performed to tune the external magnetic field so as to obtain a desired particle trajectory. Finally, the proof of concept demonstration of the magnetic tweezing is reported. We conclude that magnetic tweezers are viable and can be fabricated as part of a biocompatible setup that could become a suitable alternative to the other available micromanipulators.

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Nick, Christoph, Christina Hock, Florian Emmerich, Stefan Belle, Christiane Thielemann, Tim Asmus, Thomas Loose, and Karl-Heinz Wienand. "Ultrathin gold as sensor platform for biomolecules." In 2015 International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale (3M-NANO). IEEE, 2015. http://dx.doi.org/10.1109/3m-nano.2015.7425462.

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