Stuart Lindsay

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Name: Lindsay, Stuart

Organization: Arizona State University , USA

Department: Departments of Physics and Chemistry and the Biodesign Institute

Title: (PhD)

Chemicals
References

Recent Progress in Molecular Recognition Imaging Using Atomic Force Microscopy

Co-reporter:Subhadip Senapati and Stuart Lindsay

Accounts of Chemical Research 2016 Volume 49(Issue 3) pp:503

Publication Date(Web):March 2, 2016

DOI:10.1021/acs.accounts.5b00533

Atomic force microscopy (AFM) is an extremely powerful tool in the field of bionanotechnology because of its ability to image single molecules and make measurements of molecular interaction forces with piconewton sensitivity. It works in aqueous media, enabling studies of molecular phenomenon taking place under physiological conditions. Samples can be imaged in their near-native state without any further modifications such as staining or tagging. The combination of AFM imaging with the force measurement added a new feature to the AFM technique, that is, molecular recognition imaging. Molecular recognition imaging enables mapping of specific interactions between two molecules (one attached to the AFM tip and the other to the imaging substrate) by generating simultaneous topography and recognition images (TREC). Since its discovery, the recognition imaging technique has been successfully applied to different systems such as antibody–protein, aptamer–protein, peptide–protein, chromatin, antigen–antibody, cells, and so forth. Because the technique is based on specific binding between the ligand and receptor, it has the ability to detect a particular protein in a mixture of proteins or monitor a biological phenomenon in the native physiological state. One key step for recognition imaging technique is the functionalization of the AFM tips (generally, silicon, silicon nitrides, gold, etc.). Several different functionalization methods have been reported in the literature depending on the molecules of interest and the material of the tip. Polyethylene glycol is routinely used to provide flexibility needed for proper binding as a part of the linker that carries the affinity molecule. Recently, a heterofunctional triarm linker has been synthesized and successfully attached with two different affinity molecules. This novel linker, when attached to AFM tip, helped to detect two different proteins simultaneously from a mixture of proteins using a so-called “two-color” recognition image. Biological phenomena in nature often involve multimolecular interactions, and this new linker could be ideal for studying them using AFM recognition imaging. It also has the potential to be used extensively in the diagnostics technique. This Account includes fundamentals behind AFM recognition imaging, a brief discussion on tip functionalization, recent advancements, and future directions and possibilities.

Universal Readers Based on Hydrogen Bonding or π–π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions

Co-reporter:Sovan Biswas, Suman Sen, JongOne Im, Sudipta Biswas, Predrag Krstic, Brian Ashcroft, Chad Borges, Yanan ZhaoStuart Lindsay, Peiming Zhang

ACS Nano 2016 Volume 10(Issue 12) pp:

Publication Date(Web):November 17, 2016

DOI:10.1021/acsnano.6b06466

A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π–π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π–π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π–π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.Keywords: abasic site; DNA sequencing; hydrogen bonding; recognition tunneling; universal reader; π−π stacking;

A Three-Arm Scaffold Carrying Affinity Molecules for Multiplex Recognition Imaging by Atomic Force Microscopy: The Synthesis, Attachment to Silicon Tips, and Detection of Proteins

Co-reporter:Saikat Manna; Subhadip Senapati; Stuart Lindsay;Peiming Zhang

Journal of the American Chemical Society 2015 Volume 137(Issue 23) pp:7415-7423

Publication Date(Web):May 21, 2015

DOI:10.1021/jacs.5b03079

We have developed a multiplex imaging method for detection of proteins using atomic force microscopy (AFM), which we call multiplex recognition imaging (mRI). AFM has been harnessed to identify protein using a tip functionalized with an affinity molecule at a single molecule level. However, many events in biochemistry require identification of colocated factors simultaneously, and this is not possible with only one type of affinity molecule on an AFM tip. To enable AFM detection of multiple analytes, we designed a recognition head made from conjugating two different affinity molecules to a three-arm linker. When it is attached to an AFM tip, the recognition head would allow the affinity molecules to function in concert. In the present study, we synthesized two recognition heads: one was composed of two nucleic acid aptamers, and the other one composed of an aptamer and a cyclic peptide. They were attached to AFM tips through a catalyst-free click reaction. Our imaging results show that each affinity unit in the recognition head can recognize its respective cognate in an AFM scanning process independently and specifically. The AFM method was sensitive, only requiring 2 to 3 μL of protein solution with a concentration of ∼2 ng/mL for the detection with our current setup. When a mixed sample was deposited on a surface, the ratio of proteins could be determined by counting numbers of the analytes. Thus, this mRI approach has the potential to be used as a label-free system for detection of low-abundance protein biomarkers.

Click Addition of a DNA Thread to the N-Termini of Peptides for Their Translocation through Solid-State Nanopores

Co-reporter:Sudipta Biswas, Weisi Song, Chad Borges, Stuart Lindsay, and Peiming Zhang

ACS Nano 2015 Volume 9(Issue 10) pp:9652

Publication Date(Web):September 12, 2015

DOI:10.1021/acsnano.5b04984

Foremost among the challenges facing single molecule sequencing of proteins by nanopores is the lack of a universal method for driving proteins or peptides into nanopores. In contrast to nucleic acids, the backbones of which are uniformly negatively charged nucleotides, proteins carry positive, negative and neutral side chains that are randomly distributed. Recombinant proteins carrying a negatively charged oligonucleotide or polypeptide at the C-termini can be translocated through a α-hemolysin (α-HL) nanopore, but the required genetic engineering limits the generality of these approaches. In this present study, we have developed a chemical approach for addition of a charged oligomer to peptides so that they can be translocated through nanopores. As an example, an oligonucleotide PolyT20 was tethered to peptides through first selectively functionalizing their N-termini with azide followed by a click reaction. The data show that the peptide-PolyT20 conjugates translocated through nanopores, whereas the unmodified peptides did not. Surprisingly, the conjugates with their peptides tethered at the 5′-end of PolyT20 passed the nanopores more rapidly than the PolyT20 alone. The PolyT20 also yielded a wider distribution of blockade currents. The same broad distribution was found for a conjugate with its peptide tethered at the 3′-end of PolyT20, suggesting that the larger blockades (and longer translocation times) are associated with events in which the 5′-end of the PolyT20 enters the pore first.Keywords: click addition; DNA thread; nanopore; peptide translocation; peptide-PolyT20 conjugate; protein sequencing;

Fixed-Gap Tunnel Junction for Reading DNA Nucleotides

Co-reporter:Pei Pang, Brian Alan Ashcroft, Weisi Song, Peiming Zhang, Sovan Biswas, Quan Qing, Jialing Yang, Robert J. Nemanich, Jingwei Bai, Joshua T. Smith, Kathleen Reuter, Venkat S. K. Balagurusamy, Yann Astier, Gustavo Stolovitzky, and Stuart Lindsay

ACS Nano 2014 Volume 8(Issue 12) pp:11994

Publication Date(Web):November 7, 2014

DOI:10.1021/nn505356g

Previous measurements of the electronic conductance of DNA nucleotides or amino acids have used tunnel junctions in which the gap is mechanically adjusted, such as scanning tunneling microscopes or mechanically controllable break junctions. Fixed-junction devices have, at best, detected the passage of whole DNA molecules without yielding chemical information. Here, we report on a layered tunnel junction in which the tunnel gap is defined by a dielectric layer, deposited by atomic layer deposition. Reactive ion etching is used to drill a hole through the layers so that the tunnel junction can be exposed to molecules in solution. When the metal electrodes are functionalized with recognition molecules that capture DNA nucleotides via hydrogen bonds, the identities of the individual nucleotides are revealed by characteristic features of the fluctuating tunnel current associated with single-molecule binding events.Keywords: chemical recognition; DNA sequencing; recognition tunneling; tunnel junction;

Combined Effect of Polar Substituents on the Electronic Flows in the Carotenoid Molecular Wires

Co-reporter:Yanan Zhao;Dr. Stuart Lindsay;Sunhwa Jeon;Hyung-Jun Kim;Liang Su;Boram Lim;Dr. Sangho Koo

Chemistry - A European Journal 2013 Volume 19( Issue 33) pp:10832-10835

Publication Date(Web):

DOI:10.1002/chem.201300984

Optical and Electrical Detection of Single-Molecule Translocation through Carbon Nanotubes

Co-reporter:Weisi Song, Pei Pang, Jin He, and Stuart Lindsay

ACS Nano 2013 Volume 7(Issue 1) pp:689

Publication Date(Web):December 18, 2012

DOI:10.1021/nn3050598

Ion current through a single-walled carbon nanotube (SWCNT) was monitored at the same time as fluorescence was recorded from charged dye molecules translocating through the SWCNT. Fluorescence bursts generally follow ion current peaks with a delay time consistent with diffusion from the end of the SWCNT to the fluorescence collection point. The fluorescence amplitude distribution of the bursts is consistent with single-molecule signals. Thus each peak in the ion current flowing through the SWCNT is associated with the translocation of a single molecule. Ion current peaks (as opposed to blockades) were produced by both positively (Rhodamine 6G) and negatively (Alexa 546) charged molecules, showing that the charge filtering responsible for the current bursts is caused by the molecules themselves.Keywords: carbon nanotubes; dye translocation; nanopore ion current; nanopores; single-molecule fluorescence

Slowing DNA Translocation through a Nanopore Using a Functionalized Electrode

Co-reporter:Padmini Krishnakumar, Brett Gyarfas, Weisi Song, Suman Sen, Peiming Zhang, Predrag Krstić, and Stuart Lindsay

ACS Nano 2013 Volume 7(Issue 11) pp:10319

Publication Date(Web):October 28, 2013

DOI:10.1021/nn404743f

Nanopores were fabricated with an integrated microscale Pd electrode coated with either a hydrogen-bonding or hydrophobic monolayer. Bare pores, or those coated with octanethiol, translocated single-stranded DNA with times of a few microseconds per base. Pores functionalized with 4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide slowed average translocation times, calculated as the duration of the event divided by the number of bases translocated, to about 100 μs per base at biases in the range of 50 to 80 mV.Keywords: DNA sequencing; DNA translocation; nanopore; recognition tunneling; slowing translocation

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson–Crick base pairs for DNA sequencing by electron tunneling

Co-reporter:Feng Liang, Stuart Lindsay and Peiming Zhang

Organic & Biomolecular Chemistry 2012 vol. 10(Issue 43) pp:8654-8659

Publication Date(Web):13 Sep 2012

DOI:10.1039/C2OB26529J

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

Synthesis, Physicochemical Properties, and Hydrogen Bonding of 4(5)-Substituted 1-H-Imidazole-2-carboxamide, a Potential Universal Reader for DNA Sequencing by Recognition Tunneling

Co-reporter:Dr. Feng Liang;Dr. Shengqing Li; Stuart Lindsay; Peiming Zhang

Chemistry - A European Journal 2012 Volume 18( Issue 19) pp:5998-6007

Publication Date(Web):

DOI:10.1002/chem.201103306

Abstract

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores.1 The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6–10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.

Gap Distance and Interactions in a Molecular Tunnel Junction

Co-reporter:Shuai Chang, Jin He, Peiming Zhang, Brett Gyarfas, and Stuart Lindsay

Journal of the American Chemical Society 2011 Volume 133(Issue 36) pp:14267-14269

Publication Date(Web):August 12, 2011

DOI:10.1021/ja2067737

The distance between electrodes in a tunnel junction cannot be determined from the external movement applied to the electrodes because of interfacial forces that distort the electrode geometry at the nanoscale. These distortions become particularly complex when molecules are present in the junction, as demonstrated here by measurements of the AC response of a molecular junction over a range of conductivities from microsiemens to picosiemens. Specific chemical interactions within the junction lead to distinct features in break-junction data, and these have been used to determine the electrode separation in a junction functionalized with 4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide, a reagent developed for reading DNA sequences.

Electronic Sensitivity of Carbon Nanotubes to Internal Water Wetting

Co-reporter:Di Cao, Pei Pang, Jin He, Tao Luo, Jae Hyun Park, Predrag Krstic, Colin Nuckolls, Jinyao Tang, and Stuart Lindsay

ACS Nano 2011 Volume 5(Issue 4) pp:3113

Publication Date(Web):March 31, 2011

DOI:10.1021/nn200251z

We have constructed devices in which the interior of a single-walled carbon nanotube (SWCNT) field-effect transistor acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. These observations are consistent with theoretical simulations that show that internal water both generates a large dipole electric field, causing charge polarization of the tube and metal electrodes, and shifts the valence band of the SWCNT, while external water has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT simultaneously functions as a concentrator, nanopore, and extremely sensitive electronic detector, exploiting the enhanced sensitivity of the interior surface.Keywords: biosensor; carbon nanotube; nanoconfinement; nanofluidics; nanopore; water in nanoscale channels

Origin of Giant Ionic Currents in Carbon Nanotube Channels

Co-reporter:Pei Pang, Jin He, Jae Hyun Park, Predrag S. Krstić, and Stuart Lindsay

ACS Nano 2011 Volume 5(Issue 9) pp:7277

Publication Date(Web):September 2, 2011

DOI:10.1021/nn202115s

Fluid flow inside carbon nanotubes is remarkable: transport of water and gases is nearly frictionless, and the small channel size results in selective transport of ions. Very recently, devices have been fabricated in which one narrow single-walled carbon nanotube spans a barrier separating electrolyte reservoirs. Ion current through these devices is about 2 orders of magnitude larger than predicted from the bulk resistivity of the electrolyte. Electroosmosis can drive these large excess currents if the tube both is charged and transports anions or cations preferentially. By building a nanofluidic field-effect transistor with a gate electrode embedded in the fluid barrier, we show that the tube carries a negative charge and the excess current is carried by cations. The magnitude of the excess current and its control by a gate electrode are correctly predicted by the Poisson–Nernst–Planck–Stokes equations.Keywords: carbon nanotube; electroosmosis; ionic field effect transistor; nanochannel; nanofluidics; nanopore

Electronic Signatures of all Four DNA Nucleosides in a Tunneling Gap

Co-reporter:Shuai Chang, Shuo Huang, Jin He, Feng Liang, Peiming Zhang, Shengqing Li, Xiang Chen, Otto Sankey and Stuart Lindsay

Nano Letters 2010 Volume 10(Issue 3) pp:1070-1075

Publication Date(Web):February 8, 2010

DOI:10.1021/nl1001185

Nucleosides diffusing through a 2 nm electron-tunneling junction generate current spikes of sub-millisecond duration with a broad distribution of peak currents. This distribution narrows 10-fold when one of the electrodes is functionalized with a reagent that traps nucleosides in a specific orientation with hydrogen bonds. Functionalizing the second electrode reduces contact resistance to the nucleosides, allowing them to be identified via their peak currents according to deoxyadenosine > deoxycytidine > deoxyguanosine > thymidine, in agreement with the order predicted by a density functional calculation.

Recognition Tunneling Measurement of the Conductance of DNA Bases Embedded in Self-Assembled Monolayers†

Co-reporter:Shuo Huang ; Shuai Chang ; Jin He ; Peiming Zhang ; Feng Liang ; Michael Tuchband ; Shengqing Li

The Journal of Physical Chemistry C 2010 Volume 114(Issue 48) pp:20443-20448

Publication Date(Web):July 22, 2010

DOI:10.1021/jp104792s

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson−Crick base pairs. When bases are embedded in a self-assembled alkanethiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

Translocation of Single-Stranded DNA Through Single-Walled Carbon Nanotubes

Co-reporter:Haitao Liu;Jin He;Jinyao Tang;Hao Liu;Pei Pang;Di Cao;Predrag Krstic;Sony Joseph;Colin Nuckolls

Science 2010 Volume 327(Issue 5961) pp:64-67

Publication Date(Web):01 Jan 2010

DOI:10.1126/science.1181799

Response to comment by Di Ventra on Molecular Junctions: Clearing Mists

Co-reporter:Stuart. M. Lindsay;Mark A. Ratner

Advanced Materials 2009 Volume 21( Issue 16) pp:

Publication Date(Web):

DOI:10.1002/adma.200803718

No abstract is available for this article.

Transverse Tunneling through DNA Hydrogen Bonded to an Electrode

Co-reporter:Jin He, Lisha Lin, Peiming Zhang, Quinn Spadola, Zhiqun Xi, Qiang Fu and Stuart Lindsay

Nano Letters 2008 Volume 8(Issue 8) pp:2530-2534

Publication Date(Web):July 29, 2008

DOI:10.1021/nl801646y

Guanidinium ions tethered to an electrode form electrical contacts to DNA via hydrogen bonding with the backbone phosphates, thus providing a sequence-independent electrical connector for native DNA submerged in an aqueous electrolyte. DNA adlayers on a guanidinium modified electrode can be imaged by scanning tunneling microscopy with tens of pS gap conductance. The image resolution suggests that multiatom contacts contribute to the tunnel conductance, so we estimate that the single-nucleotide pair conductance may be on the order of 1 pS.

Molecular Transport Junctions: Clearing Mists

Co-reporter:M. A. Ratner;S. M. Lindsay

Advanced Materials 2007 Volume 19(Issue 1) pp:23-31

Publication Date(Web):4 JAN 2007

DOI:10.1002/adma.200601140

Recent progress in the measurement and modeling of transport in molecular junctions has been very significant. Tunnel transport in the Landauer–Imry regime is now broadly understood for several systems, although a detailed understanding of the role of contact geometry is still required. We overview some clear indications from recent research and note the quite reasonable agreement between measured and calculated conductance in metal–molecule–metal junctions. The next challenge lies in obtaining a microscopic understanding of charge transport that involves reduction or oxidation of molecules.

In situ measurements of oligoaniline conductance: Linking electrochemistry and molecular electronics

Co-reporter:Fan Chen, Colin Nuckolls, Stuart Lindsay

Chemical Physics 2006 Volume 324(Issue 1) pp:236-243

Publication Date(Web):9 May 2006

DOI:10.1016/j.chemphys.2005.08.052

Abstract

The single-molecule conductance of a dithiolated aniline trimer has been measured under potential control and also under an inert solvent. In each experiment, two sets of currents are found, differing by a factor 4, and these are tentatively assigned to differing connections to the electrodes (e.g., on-top vs. hollow sites). The conductances peak (to 17 ± 1.6 and 5.8 ± 0.85 nS) between the first and second oxidations of the molecule and change smoothly with surface potential. There is no evidence for a coexistence of oxidized and reduced molecules. Measurements made at a fixed surface potential as a function of tip to substrate bias show a peak current at 0.1 V followed by a region of negative differential resistance. This is accounted for semi-quantitatively by modification of the local potential by the applied bias altering the oxidation state of the molecule under the probe. Measurements made in toluene are Ohmic, indicating that the tip does not alter the oxidation state of the molecule in the absence of screening ions. We discuss the role of gap geometry and bonding in these processes.

Comparison of Electronic Transport Measurements on Organic Molecules (Adv. Mater. 2003, 15, 1883.)

Co-reporter:A. Salomon;D. Cahen;S. Lindsay;J. Tomfohr;V.B. Engelkes;C.D. Frisbie

Advanced Materials 2004 Volume 16(Issue 6) pp:

Publication Date(Web):22 MAR 2004

DOI:10.1002/adma.200490020

Single-molecule recognition imaging microscopy

Co-reporter:C. Stroh;R. Bash;H. Wang;J. Nelson;B. Ashcroft;H. Gruber;D. Lohr;S. M. Lindsay;P. Hinterdorfer

PNAS 2004 Volume 101 (Issue 34 ) pp:12503-12507

Publication Date(Web):2004-08-24

DOI:10.1073/pnas.0403538101

Atomic force microscopy is a powerful and widely used imaging technique that can visualize single molecules and follow processes at the single-molecule level both in air and in solution. For maximum usefulness in biological applications, atomic force microscopy needs to be able to identify specific types of molecules in an image, much as fluorescent tags do for optical microscopy. The results presented here demonstrate that the highly specific antibody–antigen interaction can be used to generate single-molecule maps of specific types of molecules in a compositionally complex sample while simultaneously carrying out high-resolution topographic imaging. Because it can identify specific components, the technique can be used to map composition over an image and to detect compositional changes occurring during a process.

Comparison of Electronic Transport Measurements on Organic Molecules

Co-reporter:A. Salomon;D. Cahen;S. Lindsay;J. Tomfohr;V.B. Engelkes;C.D. Frisbie

Advanced Materials 2003 Volume 15(Issue 22) pp:

Publication Date(Web):20 NOV 2003

DOI:10.1002/adma.200306091

We compile, compare, and discuss experimental results on low-bias, room-temperature currents through organic molecules obtained in different electrode–molecule–electrode test-beds. Currents are normalized to single-molecule values for comparison and are quoted at 0.2 and 0.5 V junction bias. Emphasis is on currents through saturated alkane chains where many comparable measurements have been reported, but comparison to conjugated molecules is also made. We discuss factors that affect the magnitude of the measured current, such as tunneling attenuation factor, molecular energy gap and conformation, molecule/electrode contacts, and electrode material.

Antibody-Unfolding and Metastable-State Binding in Force Spectroscopy and Recognition Imaging

Co-reporter:Parminder Kaur, Qiang-Fu, Alexander Fuhrmann, Robert Ros, Linda Obenauer Kutner, Lumelle A. Schneeweis, Ryman Navoa, Kirby Steger, Lei Xie, Christopher Yonan, Ralph Abraham, Michael J. Grace, Stuart Lindsay

Biophysical Journal (5 January 2011) Volume 100(Issue 1) pp:

Publication Date(Web):5 January 2011

DOI:10.1016/j.bpj.2010.11.050

Force spectroscopy and recognition imaging are important techniques for characterizing and mapping molecular interactions. In both cases, an antibody is pulled away from its target in times that are much less than the normal residence time of the antibody on its target. The distribution of pulling lengths in force spectroscopy shows the development of additional peaks at high loading rates, indicating that part of the antibody frequently unfolds. This propensity to unfold is reversible, indicating that exposure to high loading rates induces a structural transition to a metastable state. Weakened interactions of the antibody in this metastable state could account for reduced specificity in recognition imaging where the loading rates are always high. The much weaker interaction between the partially unfolded antibody and target, while still specific (as shown by control experiments), results in unbinding on millisecond timescales, giving rise to rapid switching noise in the recognition images. At the lower loading rates used in force spectroscopy, we still find discrepancies between the binding kinetics determined by force spectroscopy and those determined by surface plasmon resonance—possibly a consequence of the short tethers used in recognition imaging. Recognition imaging is nonetheless a powerful tool for interpreting complex atomic force microscopy images, so long as specificity is calibrated in situ, and not inferred from equilibrium binding kinetics.

Recognition Imaging of Acetylated Chromatin Using a DNA Aptamer

Co-reporter:Liyun Lin, Qiang Fu, Berea A.R. Williams, Abdelhamid M. Azzaz, Michael A. Shogren-Knaak, John C. Chaput, Stuart Lindsay

Biophysical Journal (16 September 2009) Volume 97(Issue 6) pp:

Publication Date(Web):16 September 2009

DOI:10.1016/j.bpj.2009.06.045

Histone acetylation plays an important role in the regulation of gene expression. A DNA aptamer generated by in vitro selection to be highly specific for histone H4 protein acetylated at lysine 16 was used as a recognition element for atomic force microscopy-based recognition imaging of synthetic nucleosomal arrays with precisely controlled acetylation. The aptamer proved to be reasonably specific at recognizing acetylated histones, with recognition efficiencies of 60% on-target and 12% off-target. Though this selectivity is much poorer than the >2000:1 equilibrium specificity of the aptamer, it is a large improvement on the performance of a ChIP-quality antibody, which is not selective at all in this application, and it should permit high-fidelity recognition with repeated imaging. The ability to image the precise location of posttranslational modifications may permit nanometer-scale investigation of their effect on chromatin structure.

Chromatin Control of Gene Expression: The Simplest Model

Co-reporter:Stuart Lindsay

Biophysical Journal (15 February 2007) Volume 92(Issue 4) pp:

Publication Date(Web):15 February 2007

DOI:10.1529/biophysj.106.098699

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson–Crick base pairs for DNA sequencing by electron tunneling

Co-reporter:Feng Liang, Stuart Lindsay and Peiming Zhang

Organic & Biomolecular Chemistry 2012 - vol. 10(Issue 43) pp:NaN8659-8659

Publication Date(Web):2012/09/13

DOI:10.1039/C2OB26529J