The authors would like to thank John Grazul (Cornell University), Andre Marziali (The University of British Columbia at Vancouver) and Vincent Tabard-Cossa (The University of Ottawa) for their advice. This work is funded in part by grants from the US National Science Foundation (DMR-0706517 and DMR-1006332) and the National Institutes of Health (R01-GM088403). The nanopore drilling was performed at the Electron Microscopy Facility of the Cornell Center for Materials Research (CCMR) with support from the National Science Foundation - Materials Research Science and Engineering Centers (MRSEC) program (DMR 0520404). The preparation of the silicon nitride membranes was performed at the Cornell NanoScale Facility, a member of the National Nanotechnology Infrastructure Network, which is supported by the National Science Foundation (Grant ECS-0335765).

1. Manufacture of solid-state nanopores in silicon nitride membranes
<ol>
 <li>Bring the FEI Tecnai F20 S/TEM to an acceleration voltage of 200 kV. If using a different S/TEM, the acceleration voltage should be greater than or equal to 200 kV 9</li>
 <li>Load a 20 nm thick SPI silicon nitride window grid into the TEM sample holder and clean with Oxygen plasma for 30 seconds to remove any contaminants from the holder.</li>
 <li>Load the sample into the S/TEM and allow for the vacuum to pump down. Once the S/TEM has pumped down to vacuum, find the nitride window in bright-field TEM mode by looking for a bright square on the Ronchigram. Make sure the TEM is aligned properly, then align and focus the sample.</li>
 <li>Switch the S/TEM into STEM mode. Use the HAADF (or equivalent) detector to image the sample and make sure it is properly aligned.</li>
 <li>Set the Monochromator to a low value. A lower value of the Monochromator allows for a higher current of electrons available for drilling. If the S/TEM does not have a Monochromator, ignore this step.</li>
 <li>Select an appropriate spot size for drilling the nanopore. This corresponds to the diameter of the electron probe. A 3 nm probe works well for drilling 5 nm diameter pores. A larger probe (5 nm) will drill more quickly and create a larger pore. A smaller probe (1 nm) will take longer to drill and create a smaller pore.</li>
 <li>Adjust the STEM alignments, if necessary.</li>
 <li>Focus the nitride membrane and bring it to a magnification of x1.3M. Fine focusing should be done by monitoring the Ronchigram.</li>
 <li>If there is any movement of the sample, then wait for the sample to stabilize. This can take up to an hour. Blank the electron beam while waiting so as not to damage the nitride.</li>
 <li>Place the electron probe on the sample and begin drilling.</li>
 <li>Periodically check the sample by scanning with the HAADF detector, both to make sure the nanopore is being drilled (it will look like a dark spot) and to check that there is no movement of the sample. If the sample drifts slightly, adjust the position of the electron probe to be over the nanopore.</li>
 <li>Watch the Ronchigram to identify when the pore has formed. When in focus, the nitride film has a shimmering appearance. This will disappear when the nanopore forms. Putting the Ronchigram slightly out of focus allows one to see a Fresnel fringe associated with the nanopore.</li>
 <li>Take an image of the nanopore with the HAADF.</li>
 <li>Do an intensity profile of the nanopore image. The diameter of the nanopore can be estimated by the darkest region of the profile.</li>
 <li>Enlargement of the nanopore may be performed by moving the electron probe along the edges of the pore.</li>
 <li>Once the nanopore is of the desired diameter, put the S/TEM into TEM mode.</li>
 <li>Bring the Monochromator to its standard setting and image the nanopore using bright-field TEM to confirm the size (Fig. 1).</li>
</ol>
2. Wetting of the solid-state nanopore
<ol>
 <li>De-gas de-ionized water containing 1 M KCl, 10 mM potassium phosphate, pH 7.4. This can be done by putting the solutions under vacuum and placing them in a bath sonicator for 20 minutes.</li>
 <li>Place the nanopore containing silicon nitride chip into a 10 ml Pyrex beaker. Take care not to break the nitride window as it is very delicate. Place the beaker on a hotplate in a fume hood and set to 100&deg;C.</li>
 <li>Clean the nanopore chip with piranha solution using great care. First add 3 ml sulfuric acid to the container using a glass pipette. Next, carefully add 1 ml hydrogen peroxide to the sulfuric acid to make piranha solution14. Please take all precautions.</li>
 <li>Allow the nanopore chip to soak in piranha solution for 10 minutes.</li>
 <li>Remove the piranha solution from the beaker using a glass pipette. Place it into a proper storage receptacle.</li>
 <li>Fill the beaker with the de-gassed, de-ionized water using a clean glass pipette. Empty beaker of water and repeat at least 5 times.</li>
 <li>Remove the nanopore chip with clean tweezers and dry it by light suction</li>
 <li>Immediately, seal the nanopore chip into the chamber (Fig. 2a, 2b). The chip may be secured in the chamber by O-rings or silicone sealant.</li>
 <li>Fill the chamber with KCl solution</li>
 <li>Connect the Ag/AgCl electrodes to the chamber (Fig. 2b). Electrodes may be made by soaking silver wire in bleach overnight.</li>
 <li>Apply a transmembrane potential across the electrodes and monitor the current response using an Axon 200B patch-clamp amplifier in the voltage-clamp mode.</li>
 <li>Construct an I/V (current-voltage) curve from the measurements. The I/V curve should be highly linear when using 1 M KCl (Fig. 3). The conductance of the nanopore should correspond to its diameter. If the nanopore does not display a linear I/V curve, the conductance is too low, or the open current of the nanopore is not stable (Fig. 4a), it means that the nanopore is not properly wetted and piranha washing should be repeated.</li>
</ol>
3. Monitoring protein adsorption
<ol>
 <li>It is critically important to perform control experiments with a single-nanopore membrane or parallel array of nanopores (see below) to monitor the current with the buffer conditions lacking the protein sample. We recommend the following two steps: (i) the use of a high purity-level buffer (purity &gt; 99.9%; chromatography-grade level), and (ii) the use of a buffer whose interaction with the solid-state nanopore does not produce single-channel events. In addition, we recommend obtaining a high-purity protein sample using standard protein chemistry procedures. The purity of the protein sample should be checked by sodium dodecyl sulfate-polyacrylamide (SDS-PAGE) gel analysis and high-resolution mass spectrometry 15.</li>
 <li>Add a purified sample of the protein to be studied into the grounded bath of the chamber. Allow time for the sample to diffuse throughout the bath. Typical concentrations of protein that can be measured are in the tens of nM to &mu;M range 7,15-21.</li>
 <li>Apply a transmembrane potential voltage bias with polarity opposite to that of the total charge of the protein being studied. For example, BSA has an effective net negative charge at pH 7.4, and therefore a positive voltage bias should be applied. The applied voltage creates potential gradient within the nanopore interior and proteins of opposite charges will be driven by opposite forces. Only voltage polarities that drive the proteins into the nanopore will create measurable signals.</li>
 <li>An applied potential of magnitude of 200 mV should be large enough to observe most protein analytes. Events will appear as transient current deflections from the baseline (Fig. 4b). If no signal is observed, increase the concentration of the protein in the chamber. Higher voltages improve the signal to noise ratio. Nitride nanopores can withstand several volts.</li>
 <li>Protein adsorptions will appear as long-lived changes in the baseline current of the nanopore (Fig. 4c).</li>
</ol>
4. Possibilities for functionalization of the nanopores
There exist several methods for applying functional groups to silicon nitride 22,23. Most nitride films have a thin oxide layer on the outside and exposure to ozone can create an additional oxide layer, if necessary. Different organosilanes can be used and self-assembled onto such layers. Of particular interest is aminosilane, which self-assembles and can be modified further (i.e., carboxylic acid and aldehydes), allowing for the inspection of a range of organic surfaces. After a nanopore has been washed with piranha and secured in the chamber, amine can be added directly to the chamber bath with a supporting electrolyte of 0.5 M TBACl (tetrabutylammonium) and anhydrous MeOH (methanol) used as a solvent. Monolayer formation can be monitored by the application of a 400 mV voltage bias and the measurement of the current drop 23.
5. Determination of the apparent first-order reaction rate constant and the Langmuir adsorption constant using parallel nanopore arrays
5.1 The apparent first-order reaction rate constants for absorption and desorption
We emphasize that the positive aspect of this methodology is its ability to observe individual adsorptions at the single-molecule level. The single-molecule measurements of protein adsorption onto an inorganic surface can be scaled up by employing parallel arrays of solid-state nanopores. The parallel array of nanopores is necessary because of the need to assay many pores to get reliable statistics. To this end, the use of a nanopore array would allow the monitoring of individual adsorptions as well as the measurement of multiple events for further analysis. An array of nanopores in silicon nitride may be formed by the above protocol simply by drilling multiple holes in the sample. Each nanopore should be of similar size. Arrays of nanopores of 6x6 or 7x7 should be adequate. Upon addition of protein analyte in the chamber, the current will decay in an exponential manner with a following expression: 
 
It = I&infin; - (I&infin; - I0)exp(-k't)
Here, It, denotes the current at an experimental time t. I0 is the original current passing through the nanopore array. I&infin; indicates the current at saturation level (i.e., infinity). k' is the apparent first-order reaction rate constant, which can be determined from the fit of the experimental curve. A greater k' can be interpreted as a faster adsorption rate. The ratio I&infin;/I0, also called the normalized saturation current, is a dimensionless number between 0 and 1. This parameter is a measure of the occupancy by the adsorbed protein analytes. Therefore, each distinct experimental condition should be associated with two specific output parameters I&infin;/I0 and k'.
It should be noted that the apparent first-order adsorption rate constants and normalized currents are impacted by the effective time spent by proteins within the nanopores. This time is dependent on the concentration of protein analytes in bulk aqueous phase 24. Therefore, additional correction of these numbers needs to be implemented based upon the effective time spent by the proteins within the nanopore interior. We suggest measuring the frequency of fast (translocation) events and multiplying it by the average dwell time of such events. This will give the average time of proteins spent within the nanopore interior per unit time.
The rate constant of desorption can be determined using a parallel array of nanopores as well. As soon as the current level reaches saturation (I&infin;), the voltage should be reversed, so no more proteins are trapped into the nanopores. Desorption of individual proteins will be accompanied by the alteration of the recorded current towards greater values. The rate constant will be then extracted from the rise in the current level.
5.2 The Langmuir adsorption constant
The absorption of protein analytes onto the inorganic surfaces of the nanopores is dependent on the protein concentration in aqueous phase. This phenomenon has already been observed at the single-molecule level 13. If &theta; represents the normalized saturation current (I&infin; / I0), then a typical Langmuir isotherm equation is given by the following expression:
<img alt="Figure 5.2" src="/files/ftp_upload/3560/3560fig5_2.jpg" />
where C is the protein concentration in the aqueous phase. &alpha; is the Langmuir adsorption constant. This constant increases with an increase in the binding energy of adsorption and with a decrease in temperature. The collection of the &theta; data points will employ measurements with parallel arrays carried out at various protein concentrations in aqueous phase. Data should be analyzed in combination with other techniques to verify the magnitude of the fitted Langmuir adsorption constant. In addition, full-atomistic molecular dynamics simulations 25,26 might be also used to help the interpretations of the obtained experimental data.
6. Representative Results
Typical results for solid-state nanopores will be as follows. The open pore current should be highly stable, as seen in Fig. 4a. The I/V characteristics of the nanopore should be highly linear in 1 M KCl, 10 potassium phosphate, pH 7.4, as seen in Fig. 2. The slope of a linear fit to the I/V curve will provide the unitary conductance of the nanopore. The conductance has a direct relationship to the nanopore diameter and should match the equation: <img alt="Figure equation" src="/files/ftp_upload/3560/3560figeqn.jpg" />, where G is the conductance of the nanopore, d is its diameter, l is its length, and &sigma; is the conductivity of the solution in the chamber 14. This value should match to within 30%. If it is too small, your pore is likely not wetted. With addition of protein, rapid events should ensue, as seen in Fig. 4b. Protein adsorption is a long-lived current drop as displayed in Fig. 4c. Some proteins are highly labile and undergo structural transformation within the pore interior. In this case, the long-lived voltage drop will be accompanied by rapid fluctuations.
<img alt="Figure 1" src="/files/ftp_upload/3560/3560fig1.jpg" /> 
Figure 1. Solid-state nanopore fabricated using a Tecnai F20 S/TEM. The pore was drilled in STEM mode to a diameter of 20 nm. The image was taken in bright-field TEM mode. Nitride was 30 nm thick.
<img alt="Figure 2" src="/files/ftp_upload/3560/3560fig2.jpg" /> 
Figure 2. Chamber used for housing a single solid-state nanopore in resistive-pulse measurements. A) Chamber and a silicon chip with free-standing nitride window (TEM grid). The nanopore is drilled into the nitride before loading. Red O-rings are used to form a good seal about the chip, which separates two baths of ionic solution. B) Schematic of the chamber showing placement of solution baths and electrodes with respect to the nanopore.
<img alt="Figure 3" src="/files/ftp_upload/3560/3560fig3.jpg" /> 
Figure 3. Typical I/V traces for solid-state nanopores of different diameters. Single-channel electrical traces were taken in 1 M KCl, 20 mM Tris, pH 8.5. Nanopores were drilled in 30 nm thick silicon nitride. Note nitride thickness will affect the unitary conductance of the nanopore.
<img alt="Figure 4" src="/files/ftp_upload/3560/3560fig4.jpg" /> 
Figure 4. Measured single-channel current traces and the detection of protein adsorption. A) A single-channel electrical trace showing the open current of a 10 nm diameter nanopore. B) Current deflections represent partitioning of bovine serum albumin (BSA) into the interior of the nanopore. C) Adsorption of BSA onto the nitride surface. All traces are from the same nanopore in 1 M KCl, 10 mM potassium phosphate, pH 7.4. The applied transmembrane potential was +40 mV and BSA was added to the grounded chamber bath at a concentration of 120 nM.

<ol>
	<li>Li, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ion-beam+sculpting+at+nanometre+length+scales.">Ion-beam sculpting at nanometre length scales.</a> Nature. 412, 166-169 (2001).</li><li>Li, J., Gershow, M., Stein, D., Brandin, E., Golovchenko, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+molecules+and+configurations+in+a+solid-state+nanopore+microscope.">DNA molecules and configurations in a solid-state nanopore microscope.</a> Nat. Mater. 2, 611-615 (2003).</li><li>Dekker, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solid-state+nanopores.">Solid-state nanopores.</a> Nature. Nanotechnology. 2, 209-215 (2007).</li><li>Branton, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+potential+and+challenges+of+nanopore+sequencing.">The potential and challenges of nanopore sequencing.</a> Nat. Biotechnol. 26, 1146-1153 (2008).</li><li>Wanunu, M., Morrison, W., Rabin, Y., Grosberg, A. Y., Meller, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrostatic+focusing+of+unlabelled+DNA+into+nanoscale+pores+using+a+salt+gradient.">Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient.</a> Nat. Nanotechnol. 5, 160-165 (2010).</li><li>Peng, H., Ling, X. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reverse+DNA+translocation+through+a+solid-state+nanopore+by+magnetic+tweezers.">Reverse DNA translocation through a solid-state nanopore by magnetic tweezers.</a> Nanotechnology. 20, 185101-185101 (2009).</li><li>Talaga, D. S., Li, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+protein+unfolding+in+solid+state+nanopores.">Single-molecule protein unfolding in solid state nanopores.</a> J. Am. Chem. Soc. 131, 9287-9297 (2009).</li><li>Zhao, Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detecting+SNPs+using+a+synthetic+nanopore.">Detecting SNPs using a synthetic nanopore.</a> Nano. Lett. 7, 1680-1685 (2007).</li><li>Storm, A. J., Chen, J. H., Ling, X. S., Zandbergen, H. W., Dekker, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fabrication+of+solid-state+nanopores+with+single-nanometre+precision.">Fabrication of solid-state nanopores with single-nanometre precision.</a> Nat. Mater. 2, 537-540 (2003).</li><li>Sexton, L. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resistive-pulse+studies+of+proteins+and+protein/antibody+complexes+using+a+conical+nanotube+sensor.">Resistive-pulse studies of proteins and protein/antibody complexes using a conical nanotube sensor.</a> J. Am. Chem. Soc. 129, 13144-13152 (2007).</li><li>Martin, C. R., Siwy, Z. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemistry.+Learning+nature's+way:+biosensing+with+synthetic+nanopores.">Chemistry. Learning nature's way: biosensing with synthetic nanopores.</a> Science. 317, 331-332 (2007).</li><li>Sexton, L. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+adsorption-based+model+for+pulse+duration+in+resistive-pulse+protein+sensing.">An adsorption-based model for pulse duration in resistive-pulse protein sensing.</a> J. Am. Chem. Soc. 132, 6755-6763 (2010).</li><li>Niedzwiecki, D. J., Grazul, J., Movileanu, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+observation+of+protein+adsoption+onto+an+inorganic+surface.">Single-molecule observation of protein adsoption onto an inorganic surface.</a> J. Am. Chem. Soc. 132, 10816-10822 (2010).</li><li>Wanunu, M., Meller, A., Selvin, P. R., Ha, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Single-molecule techniques: a laboratory manual. , 395-420 (2008).</li><li>Han, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Label-free+detection+of+single+protein+molecules+and+protein-protein+interactions+using+synthetic+nanopores.">Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores.</a> Anal. Chem. 80, 4651-4658 (2008).</li><li>Han, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensing+protein+molecules+using+nanofabricated+pores.">Sensing protein molecules using nanofabricated pores.</a> Appl. Phys. Lett. 88, (2006).</li><li>Fologea, D., Ledden, B., McNabb, D. S., Li, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrical+characterization+of+protein+molecules+by+a+solid-state+nanopore.">Electrical characterization of protein molecules by a solid-state nanopore.</a> Appl. Phys. Lett. 91, (2007).</li><li>Firnkes, M., Pedone, D., Knezevic, J., Doblinger, M., Rant, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrically+Facilitated+Translocations+of+Proteins+through+Silicon+Nitride+Nanopores:+Conjoint+and+Competitive+Action+of+Diffusion,+Electrophoresis,+and+Electroosmosis.">Electrically Facilitated Translocations of Proteins through Silicon Nitride Nanopores: Conjoint and Competitive Action of Diffusion, Electrophoresis, and Electroosmosis.</a> Nano. Lett. , (2010).</li><li>Pedone, D., Firnkes, M., Rant, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Data+analysis+of+translocation+events+in+nanopore+experiments.">Data analysis of translocation events in nanopore experiments.</a> Anal. Chem. 81, 9689-9694 (2009).</li><li>Oukhaled, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamics+of+Completely+Unfolded+and+Native+Proteins+through+Solid-State+Nanopores+as+a+Function+of+Electric+Driving+Force.">Dynamics of Completely Unfolded and Native Proteins through Solid-State Nanopores as a Function of Electric Driving Force.</a> ACS. Nano.. , (2011).</li><li>Yusko, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlling+protein+translocation+through+nanopores+with+bio-inspired+fluid+walls.">Controlling protein translocation through nanopores with bio-inspired fluid walls.</a> Nat. Nanotechnol. 6, 253-260 (2011).</li><li>Arafat, A., Schroen, K., de Smet, L. C., Sudholter, E. J., Zuilhof, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tailor-made+functionalization+of+silicon+nitride+surfaces.">Tailor-made functionalization of silicon nitride surfaces.</a> J. Am. Chem. Soc. 126, 8600-8601 (2004).</li><li>Wanunu, M., Meller, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemically+modified+solid-state+nanopores.">Chemically modified solid-state nanopores.</a> Nano. Lett. 7, 1580-1585 (2007).</li><li>Movileanu, L., Cheley, S., Bayley, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Partitioning+of+individual+flexible+polymers+into+a+nanoscopic+protein+pore.">Partitioning of individual flexible polymers into a nanoscopic protein pore.</a> Biophys. J. 85, 897-910 (2003).</li><li>Aksimentiev, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deciphering+ionic+current+signatures+of+DNA+transport+through+a+nanopore.">Deciphering ionic current signatures of DNA transport through a nanopore.</a> Nanoscale. 2, 468-483 (2010).</li><li>Timp, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanopore+Sequencing:+Electrical+Measurements+of+the+Code+of+Life.">Nanopore Sequencing: Electrical Measurements of the Code of Life.</a> IEEE Trans. Nanotechnol. 9, 281-294 (2010).</li><li>Roach, P., Farrar, D., Perry, C. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+tailoring+for+controlled+protein+adsorption:+effect+of+topography+at+the+nanometer+scale+and+chemistry.">Surface tailoring for controlled protein adsorption: effect of topography at the nanometer scale and chemistry.</a> J. Am. Chem. Soc. 128, 3939-3945 (2006).</li><li>Roach, P., Farrar, D., Perry, C. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interpretation+of+protein+adsorption:+surface-induced+conformational+changes.">Interpretation of protein adsorption: surface-induced conformational changes.</a> J. Am. Chem. Soc. 127, 8168-8173 (2005).</li><li>Brewer, S. H., Glomm, W. R., Johnson, M. C., Knag, M. K., Franzen, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+BSA+binding+to+citrate-coated+gold+nanoparticles+and+surfaces.">Probing BSA binding to citrate-coated gold nanoparticles and surfaces.</a> Langmuir. 21, 9303-9307 (2005).</li><li>Schon, P., Gorlich, M., Coenen, M. J., Heus, H. A., Speller, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nonspecific+protein+adsorption+at+the+single+molecule+level+studied+by+atomic+force+microscopy.">Nonspecific protein adsorption at the single molecule level studied by atomic force microscopy.</a> Langmuir. 23, 9921-9923 (2007).</li><li>Rabe, M., Verdes, D., Zimmermann, J., Seeger, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+organization+and+cooperativity+during+nonspecific+protein+adsorption+events.">Surface organization and cooperativity during nonspecific protein adsorption events.</a> J. Phys. Chem. B. 112, 13971-13980 (2008).</li><li>Rabe, M., Verdes, D., Rankl, M., Artus, G. R., Seeger, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comprehensive+study+of+concepts+and+phenomena+of+the+nonspecific+adsorption+of+beta-lactoglobulin.">A comprehensive study of concepts and phenomena of the nonspecific adsorption of beta-lactoglobulin.</a> Chemphyschem. 8, 862-872 (2007).</li><li>Micic, M., Chen, A., Leblanc, R. M., Moy, V. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scanning+Electron+Microscopy+Studies+of+Protein-Functionalized+Atomic+Force+Microscopy+Cantilever+Tips.">Scanning Electron Microscopy Studies of Protein-Functionalized Atomic Force Microscopy Cantilever Tips.</a> Scanning. 21, 394-397 (1999).</li><li>Grant, A. W., Hu, Q. H., Kasemo, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transmission+electron+microscopy+'windows'+for+nanofabricated+structures.">Transmission electron microscopy 'windows' for nanofabricated structures.</a> Nanotechnology. 15, 1175-1181 (2004).</li><li>Giannoulis, C. S., Desai, T. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+proteins+and+fibroblasts+on+thin+inorganic+films.">Characterization of proteins and fibroblasts on thin inorganic films.</a> J. Mater. Sci: Mater. Med. 13, 75-80 (2002).</li><li>Gustavsson, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+modifications+of+silicon+nitride+for+cellular+biosensors+applications.">Surface modifications of silicon nitride for cellular biosensors applications.</a> J. Mater. Sci: Mater. Med. 19, 1839-1850 (2008).</li><li>Shirshov, Y. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+the+response+of+planar+polarization+interferometer+to+molecular+layer+formation:+fibrinogen+adsorption+on+silicon+nitride+surface.">Analysis of the response of planar polarization interferometer to molecular layer formation: fibrinogen adsorption on silicon nitride surface.</a> Biosens. Bioelectron. 16, 381-390 (2001).</li><li>Chen, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+layer+deposition+to+fine-tune+the+surface+properties+and+diamters+of+fabricated+nanopores.">Atomic layer deposition to fine-tune the surface properties and diamters of fabricated nanopores.</a> Nano. Lett. 4, 1333-1337 (2004).</li><li>Siwy, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+biosensors+based+on+biofunctionalized+conical+gold+nanotubes.">Protein biosensors based on biofunctionalized conical gold nanotubes.</a> J. Am. Chem. Soc. 127, 5000-5001 (2005).</li><li>Ding, S., Gao, C., Gu, L. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capturing+Single+Molecules+of+Immunoglobulin+and+Ricin+with+an+Aptamer-Encoded+Glass+Nanopore.">Capturing Single Molecules of Immunoglobulin and Ricin with an Aptamer-Encoded Glass Nanopore.</a> Anal. Chem. , (2009).</li><li>Kim, M. -. J., Wanunu, M., Bell, C. D., Meller, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+Fabrication+of+Uniform+Size+Nanopores+and+Nanopore+Arrays+for+Parallel+DNA+Analysis.">Rapid Fabrication of Uniform Size Nanopores and Nanopore Arrays for Parallel DNA Analysis.</a> Adv. Mater. 18, 3149-3153 (2006).</li><li>Bezrukov, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ion+channels+as+molecular+Coulter+counters+to+probe+metabolite+transport.">Ion channels as molecular Coulter counters to probe metabolite transport.</a> J. Membr. Biol. 174, 1-13 (2000).</li></ol>

We have nothing to disclose.

Spontaneous adsorption of proteins onto solid-state surfaces 27-29 is fundamentally important in a number of areas, such as biochip applications and design of a new class of functional hybrid biomaterials. Previous studies have shown that proteins adsorbed to solid-state surfaces do not show lateral mobility or significant desorption rates, and therefore protein adsorption is generally considered an irreversible and nonspecific process 30-32. Protein adsorption onto solid state surfaces is thought t...

<table><tbody><tr><td>Tecnai F20 S/TEM</td><td>FEI</td><td></td><td>S/TEM requires acceleration voltage &amp;#8805;200kV and field-emission source. </td></tr><tr><td>20 nm thick silicon nitride membrane window for TEM</td><td>SPI Supplies</td><td>4163SN-BA</td><td></td></tr><tr><td>Axon Axopatch 200B patch-clamp amplifier</td><td>Molecular Devices</td><td></td><td></td></tr><tr><td>Axon Digidata 1440A</td><td>Molecular Devices</td><td></td><td></td></tr><tr><td>pCLAMP 10 software</td><td>Molecular Devices</td><td></td><td>Electrophysiology Data Acquisition and Analysis Software</td></tr><tr><td>Sulfuric Acid</td><td>Fisher Scientific</td><td>A300</td><td></td></tr><tr><td>hydrogen peroxide</td><td>Fisher Scientific</td><td>H325</td><td></td></tr><tr><td>silicone O-rings</td><td>McMaster-Carr</td><td>003 S70</td><td>Alternatively use PDMS </td></tr><tr><td>silver wire</td><td>Sigma-Aldrich</td><td>348759</td><td>For electrodes</td></tr><tr><td>SPC Technology, D sub contact, pin</td><td>Newark Inc</td><td>9K4978</td><td>For electrodes</td></tr><tr><td>potassium chloride</td><td>Sigma-Aldrich</td><td>P9541</td><td></td></tr><tr><td>potassium phosphate dibasic</td><td>Sigma-Aldrich</td><td>P2222</td><td></td></tr><tr><td>potassium phosphate monobasic</td><td>Sigma-Aldrich</td><td>P5379</td><td></td></tr><tr><td>PDMS</td><td>Dow Corning</td><td></td><td>Sylgar 184 Elastomer set. For making chamber.</td></tr><tr><td>Kwik-Cast Sealant</td><td>World Precision Instruments, Inc.</td><td>KWIK-CAST</td><td>Fast acting silicone sealant</td></tr><tr><td>hot plate</td><td>Fisher Scientific</td><td></td><td></td></tr><tr><td>Faraday cage</td><td></td><td></td><td></td></tr></tbody></table>

monitoring protein adsorption with solid-state nanopores

Solid-state nanopores have been used to perform measurements at the single-molecule level to examine the local structure and flexibility of nucleic acids 1-6, the unfolding of proteins 7, and binding affinity of different ligands 8. By coupling these nanopores to the resistive-pulse technique 9-12, such measurements can be done under a wide variety of conditions and without the need for labeling 3. In the resistive-pulse technique, an ionic salt solution is introduced on both sides of the nanopore. Therefore, ions are driven from one side of the chamber to the other by an applied transmembrane potential, resulting in a steady current. The partitioning of an analyte into the nanopore causes a well-defined deflection in this current, which can be analyzed to extract single-molecule information. Using this technique, the adsorption of single proteins to the nanopore walls can be monitored under a wide range of conditions 13. Protein adsorption is growing in importance, because as microfluidic devices shrink in size, the interaction of these systems with single proteins becomes a concern. This protocol describes a rapid assay for protein binding to nitride films, which can readily be extended to other thin films amenable to nanopore drilling, or to functionalized nitride surfaces. A variety of proteins may be explored under a wide range of solutions and denaturing conditions. Additionally, this protocol may be used to explore more basic problems using nanopore spectroscopy.

Watch this Scientific Journal Video about Monitoring Protein Adsorption with Solid-state Nanopores at JoVE.com

Monitoring Protein Adsorption with Solid-state Nanopores

A method of using solid-state nanopores to monitor the non-specific adsorption of proteins onto an inorganic surface is described. The method employs the resistive-pulse principle, allowing for the adsorption to be probed in real-time and at the single-molecule level. Because the process of single protein adsorption is far from equilibrium, we propose the employment of parallel arrays of synthetic nanopores, enabling for the quantitative determination of the apparent first-order reaction rate constant of protein adsorption as well as and the Langmuir adsorption constant.

Solid-state nanopores have been used to perform measurements at the single-molecule level to examine the local structure and flexibility of nucleic acids ...

monitoring-protein-adsorption-with-solid-state-nanopores

Universidad de Cartagena UDEC

Research

JoVE Journal

Bioengineering

13.5K Views.  Syracuse University. A method of using solid-state nanopores to monitor the non-specific adsorption of proteins onto an inorganic surface is described. The method employs the resistive-pulse principle, allowing for the adsorption to be probed in real-time and at the single-molecule level. Because the process of single protein adsorption is far from equilibrium, we propose the employment of parallel arrays of synthetic nanopores, enabling for the quantitative determination of the apparent firs...

Video: Monitoring Protein Adsorption with Solid-state Nanopores

Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores

Solid-state nanopores have emerged as a versatile tool for the characterization of single biomolecules such as nucleic acids and proteins1. However, the creation of a nanopore in a thin insulating membrane remains challenging. Fabrication methods involving specialized focused electron beam systems can produce well-defined nanopores, but yield of reliable and low-noise nanopores in commercially available membranes remains low2,3 and size control is nontrivial4,5. Here, the application of high electric fields to fine-tune the size of the nanopore while ensuring optimal low-noise performance is demonstrated. These short pulses of high electric field are used to produce a pristine electrical signal and allow for enlarging of nanopores with subnanometer precision upon prolonged exposure. This method is performed in situ in an aqueous environment using standard laboratory equipment, improving the yield and reproducibility of solid-state nanopore fabrication.

A methodology for preparing solid-state nanopores in solution for biomolecular translocation experiments is presented. By applying short pulses of high electric fields, the nanopore diameter can be controllably enlarged with subnanometer precision and its electrical noise characteristics significantly improved. This procedure is performed in situ using standard laboratory equipment under experimental conditions.

Solid-state nanopores have emerged as a versatile tool for the characterization of single biomolecules such as nucleic acids and proteins1. However, the ...

Engineering

Plasmonic Trapping and Release of Nanoparticles in a Monitoring Environment

Plasmonic tweezers use surface plasmon polaritons to confine polarizable nanoscale objects. Among the various designs of plasmonic tweezers, only a few can observe immobilized particles. Moreover, a limited number of studies have experimentally measured the exertable forces on the particles. The designs can be classified as the protruding nanodisk type or the suppressed nanohole type. For the latter, microscopic observation is extremely challenging. In this paper, a new plasmonic tweezer system is introduced to monitor particles, both in directions parallel and orthogonal to the symmetric axis of a plasmonic nanohole structure. This feature enables us to observe the movement of each particle near the rim of the nanohole. Furthermore, we can quantitatively estimate the maximal trapping forces using a new fluidic channel.

A microchip fabrication process that incorporates plasmonic tweezers is presented here. The microchip enables the imaging of a trapped particle to measure maximal trapping forces.

Plasmonic tweezers use surface plasmon polaritons to confine polarizable nanoscale objects. Among the various designs of plasmonic tweezers, only a few ...

Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis

In current protocol, a combinatorial approach has been developed to simplify the design and production of sensing materials for the construction of electronic tongues (eT) for protein analysis. By mixing a small number of simple and easily accessible molecules with different physicochemical properties, used as building blocks (BBs), in varying and controlled proportions and allowing the mixtures to self-assemble on the gold surface of a prism, an array of combinatorial surfaces featuring appropriate properties for protein sensing was created. In this way, a great number of cross-reactive receptors can be rapidly and efficiently obtained. By combining such an array of combinatorial cross-reactive receptors (CoCRRs) with an optical detection system such as surface plasmon resonance imaging (SPRi), the obtained eT can monitor the binding events in real-time and generate continuous recognition patterns including 2D continuous evolution profile (CEP) and 3D continuous evolution landscape (CEL) for samples in liquid. Such an eT system is efficient for discrimination of common purified proteins.

A novel approach is described for construction of electronic tongue (eT), which greatly simplifies the design and production of sensing materials, and allows the eT to generate continuous evolution profiles and landscapes for samples in liquid. The obtained eT is efficient for common protein analysis such as discrimination.

In current protocol, a combinatorial approach has been developed to simplify the design and production of sensing materials for the construction of ...

High Resolution Physical Characterization of Single Metallic Nanoparticles

Individual molecules can be detected and characterized by measuring the degree by which they reduce the ionic current flowing through a single nanometer-scale pore. The signal is characteristic of the molecule&#39;s physicochemical properties and its interactions with the pore. We demonstrate that the nanopore formed by the bacterial protein exotoxin Staphylococcus aureus alpha hemolysin (&#945;HL) can detect polyoxometalates (POMs, anionic metal oxygen clusters), at the single molecule limit. Moreover, multiple degradation products of 12-phosphotungstic acid POM (PTA, H3PW12O40) in solution are simultaneously measured. The single molecule sensitivity of the nanopore method allows for POMs to be characterized at significantly lower concentrations than required for nuclear magnetic resonance (NMR) spectroscopy. This technique could serve as a new tool for chemists to study the molecular properties of polyoxometalates or other metallic clusters, to better understand POM synthetic processes, and possibly improve their yield. Hypothetically, the location of a given atom, or the rotation of a fragment in the molecule, and the metal oxidation state could be investigated with this method. In addition, this new technique has the advantage of allowing the real-time monitoring of molecules in solution.&#160;

Here, we present a protocol to detect discrete metal oxygen clusters, polyoxometalates (POMs), at the single molecule limit using a biological nanopore-based electronic platform. The method provides a complementary approach to traditional analytical chemistry tools used in the study of these molecules.

Individual molecules can be detected and characterized by measuring the degree by which they reduce the ionic current flowing through a single ...

Chemistry

A Closed-Type Wireless Nanopore Electrode for Analyzing Single Nanoparticles

Measuring the intrinsic features of single nanoparticles by nanoelectrochemistry holds deep fundamental importance and has potential impacts in nanoscience. However, electrochemically analyzing single nanoparticles is challenging, as the sensing nanointerface is uncontrollable. To address this challenge, we describe here the fabrication and characterization of a closed-type wireless nanopore electrode (WNE) that exhibits a highly controllable morphology and outstanding reproducibility. The facile fabrication of WNE enables the preparation of well-defined nanoelectrodes in a general chemistry laboratory without the use of a clean room and expensive equipment. One application of a 30 nm closed-type WNE in analysis of single gold nanoparticles in the mixture is also highlighted, which shows a high current resolution of 0.6 pA and high temporal resolution of 0.01 ms. Accompanied by their excellent morphology and small diameters, more potential applications of closed-type WNEs can be expanded from nanoparticle characterization to single molecule/ion detection and single-cell probing.

Here, we present a protocol for fabrication of a closed-type wireless nanopore electrode and subsequent electrochemical measurement of single nanoparticle collisions.

Measuring the intrinsic features of single nanoparticles by nanoelectrochemistry holds deep fundamental importance and has potential impacts in ...

Study of Short Peptide Adsorption on Solution Dispersed Inorganic Nanoparticles Using Depletion Method

Fundamentals of inorganic-organic interactions are critically important in the discovery and development of novel biointerfaces amenable for utilization in biotechnology and medicine. Recent studies indicate that proteins interact with surfaces through limited adsorption sites. Protein fragments such as amino acids and peptides can be used for interaction modeling between complex biological macromolecules and inorganic surfaces. During the last three decades, many valid and sensitive methods have been developed to measure the physical chemistry fundamentals of those interactions: isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), quartz crystal microbalance (QCM), total internal reflection fluorescence (TIRF), and attenuated total reflectance spectroscopy (ATR).
The simplest and most affordable technique for the measurement of adsorption is the depletion method, where the change in sorbate concentration (depletion) after contact with solution-dispersed sorbent is calculated and assumed to be adsorbed. Adsorption isotherms based on depletion data provide all basic physicochemical data. However, adsorption from solutions requires longer equilibration times due to kinetic restrictions and sorbents with a high specific surface area, making it almost inapplicable to macroscopic fixed plane surfaces. Moreover, factors such as the instability of sols, nanoparticle aggregates, sorbent crystallinity, nanoparticle size distribution, pH of the solution, and competition for adsorption, should be considered while studying adsorbing peptides. Depletion data isotherm construction provides comprehensive physical chemistry data for literally every soluble sorbate yet remains the most accessible methodology, as it does not require expensive setups. This article describes a basic protocol for the experimental study of peptide adsorption on inorganic oxide and covers all critical points that affect the process.

The first step in comprehending biomolecule-inorganic solid phase interaction is revealing fundamental physicochemical constants that may be evaluated by establishing adsorption isotherms. Adsorption from the liquid phase is restricted by kinetics, surface capacity, pH, and competitive adsorption, which all should be cautiously considered before setting an adsorption experiment.

Fundamentals of inorganic-organic interactions are critically important in the discovery and development of novel biointerfaces amenable for utilization ...

Determination of Zeta Potential via Nanoparticle Translocation Velocities through a Tunable Nanopore: Using DNA-modified Particles as an Example

Nanopore technologies, known collectively as Resistive Pulse Sensors (RPS), are being used to detect, quantify and characterize proteins, molecules and nanoparticles. Tunable resistive pulse sensing (TRPS) is a relatively recent adaptation to RPS that incorporates a tunable pore that can be altered in real time. Here, we use TRPS to monitor the translocation times of DNA-modified nanoparticles as they traverse the tunable pore membrane as a function of DNA concentration and structure (i.e., single-stranded to double-stranded DNA).
TRPS is based on two Ag/AgCl electrodes, separated by an elastomeric pore membrane that establishes a stable ionic current upon an applied electric field. Unlike various optical-based particle characterization technologies, TRPS can characterize individual particles amongst a sample population, allowing for multimodal samples to be analyzed with ease. Here, we demonstrate zeta potential measurements via particle translocation velocities of known standards and apply these to sample analyte translocation times, thus resulting in measuring the zeta potential of those analytes.
As well as acquiring mean zeta potential values, the samples are all measured using a particle-by-particle perspective exhibiting more information on a given sample through sample population distributions, for example. Of such, this method demonstrates potential within sensing applications for both medical and environmental fields.

Here we use a polyurethane tunable nanopore integrated into a resistive pulse sensing technique to characterize nanoparticles surface chemistry via the measurement of particle translocation velocities, which can be used to determine the zeta potential of individual nanoparticles.

Nanopore technologies, known collectively as Resistive Pulse Sensors (RPS), are being used to detect, quantify and characterize proteins, molecules and ...

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Current single-molecule techniques to characterize proteins typically require labels, tethers, or the use of non-native solution conditions. Such changes can alter protein biophysics and reduce the usefulness of the data acquired. Plasmonic nanotweezers is a technique that uses localized surface plasmon resonance (LSPR) on gold nanostructures to enhance the electric field within a confined hotspot region. This field enhancement allows for the use of low laser powers to trap single nanoparticles far smaller than conventional optical tweezers, down to only a few nanometers in diameter, such as single proteins. Trapping of single protein molecules within the hotspot region induces a shift in the local refractive index (nprotein &#62; nwater), altering light scattering as a product of the molecule&#39;s polarisability, which is affected by its volume, shape anisotropy, and refractive index. An avalanche photodiode (APD) collects the subsequent changes in light scattering. These alterations can then be analyzed to determine changes in the trapped molecule, including its size, global conformation, and dynamics of conformational change over time. The incorporation of microfluidics within the system allows for controlled environmental changes and real-time monitoring of their subsequent effects on the molecule. In this protocol, we demonstrate the steps to trap single protein molecules, alter their environmental solution conditions, and monitor their corresponding conformational changes using a plasmonic nanotweezers system.

Plasmonic nanotweezers use localized surface plasmon resonance in gold nanostructures to trap single nanoparticles, including proteins, within a nanometer-scale optical field. Changes in the scattered signal reveal protein presence and conformational dynamics, enabling monitoring without fluorophore modifications or surface tethering.

Current single-molecule techniques to characterize proteins typically require labels, tethers, or the use of non-native solution conditions. Such changes ...

Real Time Measurements of Membrane Protein:Receptor Interactions Using Surface Plasmon Resonance (SPR)

Protein-protein interactions are pivotal to most, if not all, physiological processes, and understanding the nature of such interactions is a central step in biological research. Surface Plasmon Resonance (SPR) is a sensitive detection technique for label-free study of bio-molecular interactions in real time. In a typical SPR experiment, one component (usually a protein, termed 'ligand') is immobilized onto a sensor chip surface, while the other (the 'analyte') is free in solution and is injected over the surface. Association and dissociation of the analyte from the ligand are measured and plotted in real time on a graph called a sensogram, from which pre-equilibrium and equilibrium data is derived. Being label-free, consuming low amounts of material, and providing pre-equilibrium kinetic data, often makes SPR the method of choice when studying dynamics of protein interactions. However, one has to keep in mind that due to the method's high sensitivity, the data obtained needs to be carefully analyzed, and supported by other biochemical methods. 
SPR is particularly suitable for studying membrane proteins since it consumes small amounts of purified material, and is compatible with lipids and detergents. This protocol describes an SPR experiment characterizing the kinetic properties of the interaction between a membrane protein (an ABC transporter) and a soluble protein (the transporter's cognate substrate binding protein).

Real Time Measurements of Membrane Protein:Receptor Interactions Using Surface Plasmon Resonance SPR

Surface Plasmon Resonance (SPR) is a label-free method for detecting bio-molecular interactions in real time. Herein, a protocol for a membrane protein:receptor interaction experiment is described, while discussing the pros and cons of the technique.

Protein-protein interactions are pivotal to most, if not all, physiological processes, and  understanding the nature of such interactions is a central ...

Biology

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Membrane protein transport on the single protein level still evades detailed analysis, if the substrate translocated is non-electrogenic. Considerable efforts have been made in this field, but techniques enabling automated high-throughput transport analysis in combination with solvent-free lipid bilayer techniques required for the analysis of membrane transporters are rare. This class of transporters however is crucial in cell homeostasis and therefore a key target in drug development and methodologies to gain new insights desperately needed.
The here presented manuscript describes the establishment and handling of a novel biochip for the analysis of membrane protein mediated transport processes at single transporter resolution. The biochip is composed of microcavities enclosed by nanopores that is highly parallel in its design and can be produced in industrial grade and quantity. Protein-harboring liposomes can directly be applied to the chip surface forming self-assembled pore-spanning lipid bilayers using SSM-techniques (solid supported lipid membranes). Pore-spanning parts of the membrane are freestanding, providing the interface for substrate translocation into or out of the cavity space, which can be followed by multi-spectral fluorescent readout in real-time. The establishment of standard operating procedures (SOPs) allows the straightforward establishment of protein-harboring lipid bilayers on the chip surface of virtually every membrane protein that can be reconstituted functionally. The sole prerequisite is the establishment of a fluorescent read-out system for non-electrogenic transport substrates.
High-content screening applications are accomplishable by the use of automated inverted fluorescent microscopes recording multiple chips in parallel. Large data sets can be analyzed using the freely available custom-designed analysis software. Three-color multi spectral fluorescent read-out furthermore allows for unbiased data discrimination into different event classes, eliminating false positive results.
The chip technology is currently based on SiO2 surfaces, but further functionalization using gold-coated chip surfaces is also possible.

The presented protocol describes the analysis of membrane protein mediated transport on the single transporter level using pore-spanning solvent-free lipid bilayers. This is achieved by the creation of bulk produced nanopore array chips, combined with highly parallel data acquisition and analysis, enabling the future establishment of membrane protein effector screenings.

Membrane protein transport on the single protein level still evades detailed analysis, if the substrate translocated is non-electrogenic. Considerable ...