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Tunnelling readout of hydrogen-bonding-based recognition.

Chang S, He J, Kibel A, Lee M, Sankey O, Zhang P, Lindsay S - Nat Nanotechnol (2009)

Bottom Line: Junctions that are held together by three hydrogen bonds per base pair (for example, guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per base pair (for example, adenine-thymine interactions).Similar, but less pronounced effects are observed on the approach of the tunnelling probe, implying that attractive forces that depend on hydrogen bonds also have a role in determining the rise of current.These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.

ABSTRACT
Hydrogen bonding has a ubiquitous role in electron transport and in molecular recognition, with DNA base pairing being the best-known example. Scanning tunnelling microscope images and measurements of the decay of tunnel current as a molecular junction is pulled apart by the scanning tunnelling microscope tip are sensitive to hydrogen-bonded interactions. Here, we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA base pairs. Junctions that are held together by three hydrogen bonds per base pair (for example, guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per base pair (for example, adenine-thymine interactions). Similar, but less pronounced effects are observed on the approach of the tunnelling probe, implying that attractive forces that depend on hydrogen bonds also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal.

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Determination of elastic-interaction parameters and prediction of the tunnel decay curves. a, Conducting AFM measurements of interaction force (blue points) and simultaneously acquired tunnel current (red points) for A-thymidine with a cantilever of spring constant 0.35 N/m. The inset shows how the extent of the current-distance curves is controlled by the stiffness of the cantilever (black curves, K=2 N/m, red curves, K=0.35 N/m). b, Adhesion force plotted vs. set-point current for a 2-amino-8-mercaptoadenine functionalized probe interacting with a thymidine monlayer (red points) and a 8-mercaptoadenine probe interacting with a thymidine monolayer (blue points). The black dots are control data obtained with thio-phenol functionalized probes. The solid lines are fits to Fad ∝ NHB ln(BISP + 1) + FNS (assuming all bonds are of equal strength) with B set to 2.83 nA−1. The coefficient of the log terms are 1.97±0.3 (AA-T) and 1.0±0.16 (A-T), so their ratio is 1.96 (+0.7, −0.5) a range that spans the expected value of 1.5 (NHB (2AA −T)/NHB (A − T) = 3/2). Representative STM decay curves (red) for an 8-mercaptoguanine probe interacting with a deoxycytidine monolayer (c) and an 8-mercaptoadenine probe interacting with a thymidine monolayer (d) for several set-points (each curve is the average of 26 raw data curves). The blue dashed-lines show how the current should decay from each set point if it follows the form of the 3nA data. The green lines are predicted by the elastic distortion model described in the text where the same two parameters are used to fit both the G-C and A-T data.
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Figure 4: Determination of elastic-interaction parameters and prediction of the tunnel decay curves. a, Conducting AFM measurements of interaction force (blue points) and simultaneously acquired tunnel current (red points) for A-thymidine with a cantilever of spring constant 0.35 N/m. The inset shows how the extent of the current-distance curves is controlled by the stiffness of the cantilever (black curves, K=2 N/m, red curves, K=0.35 N/m). b, Adhesion force plotted vs. set-point current for a 2-amino-8-mercaptoadenine functionalized probe interacting with a thymidine monlayer (red points) and a 8-mercaptoadenine probe interacting with a thymidine monolayer (blue points). The black dots are control data obtained with thio-phenol functionalized probes. The solid lines are fits to Fad ∝ NHB ln(BISP + 1) + FNS (assuming all bonds are of equal strength) with B set to 2.83 nA−1. The coefficient of the log terms are 1.97±0.3 (AA-T) and 1.0±0.16 (A-T), so their ratio is 1.96 (+0.7, −0.5) a range that spans the expected value of 1.5 (NHB (2AA −T)/NHB (A − T) = 3/2). Representative STM decay curves (red) for an 8-mercaptoguanine probe interacting with a deoxycytidine monolayer (c) and an 8-mercaptoadenine probe interacting with a thymidine monolayer (d) for several set-points (each curve is the average of 26 raw data curves). The blue dashed-lines show how the current should decay from each set point if it follows the form of the 3nA data. The green lines are predicted by the elastic distortion model described in the text where the same two parameters are used to fit both the G-C and A-T data.

Mentions: Several factors indicate that the signals are not purely electronic in origin: Firstly, the decay distance is much too long to correspond to an electronic process5 where tunneling decay lengths are typically Å not nm.12,13 Secondly, the change in shape of the decay curves with ISP is not consistent with a simple tunneling process. We illustrate this in Figure 4c with a set of averaged curves (red lines) for each ISP for the G-C interaction. If the decay at lower set-point currents had the same shape as the ISP = 3nA curve, the curves would lie on the blue dashed lines. They clearly do not. Thirdly, there is considerable hysteresis in the data. On approach, the probe must be brought closer to the surface to restore a signal (supporting information) and its growth is more rapid than the decay was on withdrawal. Fourthly, a theoretical simulation (see below) indicates that the electronic conductance of a base-nucleoside pair is not particularly sensitive to hydrogen-bonding, being dominated by the low conductance across the sugar ring.


Tunnelling readout of hydrogen-bonding-based recognition.

Chang S, He J, Kibel A, Lee M, Sankey O, Zhang P, Lindsay S - Nat Nanotechnol (2009)

Determination of elastic-interaction parameters and prediction of the tunnel decay curves. a, Conducting AFM measurements of interaction force (blue points) and simultaneously acquired tunnel current (red points) for A-thymidine with a cantilever of spring constant 0.35 N/m. The inset shows how the extent of the current-distance curves is controlled by the stiffness of the cantilever (black curves, K=2 N/m, red curves, K=0.35 N/m). b, Adhesion force plotted vs. set-point current for a 2-amino-8-mercaptoadenine functionalized probe interacting with a thymidine monlayer (red points) and a 8-mercaptoadenine probe interacting with a thymidine monolayer (blue points). The black dots are control data obtained with thio-phenol functionalized probes. The solid lines are fits to Fad ∝ NHB ln(BISP + 1) + FNS (assuming all bonds are of equal strength) with B set to 2.83 nA−1. The coefficient of the log terms are 1.97±0.3 (AA-T) and 1.0±0.16 (A-T), so their ratio is 1.96 (+0.7, −0.5) a range that spans the expected value of 1.5 (NHB (2AA −T)/NHB (A − T) = 3/2). Representative STM decay curves (red) for an 8-mercaptoguanine probe interacting with a deoxycytidine monolayer (c) and an 8-mercaptoadenine probe interacting with a thymidine monolayer (d) for several set-points (each curve is the average of 26 raw data curves). The blue dashed-lines show how the current should decay from each set point if it follows the form of the 3nA data. The green lines are predicted by the elastic distortion model described in the text where the same two parameters are used to fit both the G-C and A-T data.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2698135&req=5

Figure 4: Determination of elastic-interaction parameters and prediction of the tunnel decay curves. a, Conducting AFM measurements of interaction force (blue points) and simultaneously acquired tunnel current (red points) for A-thymidine with a cantilever of spring constant 0.35 N/m. The inset shows how the extent of the current-distance curves is controlled by the stiffness of the cantilever (black curves, K=2 N/m, red curves, K=0.35 N/m). b, Adhesion force plotted vs. set-point current for a 2-amino-8-mercaptoadenine functionalized probe interacting with a thymidine monlayer (red points) and a 8-mercaptoadenine probe interacting with a thymidine monolayer (blue points). The black dots are control data obtained with thio-phenol functionalized probes. The solid lines are fits to Fad ∝ NHB ln(BISP + 1) + FNS (assuming all bonds are of equal strength) with B set to 2.83 nA−1. The coefficient of the log terms are 1.97±0.3 (AA-T) and 1.0±0.16 (A-T), so their ratio is 1.96 (+0.7, −0.5) a range that spans the expected value of 1.5 (NHB (2AA −T)/NHB (A − T) = 3/2). Representative STM decay curves (red) for an 8-mercaptoguanine probe interacting with a deoxycytidine monolayer (c) and an 8-mercaptoadenine probe interacting with a thymidine monolayer (d) for several set-points (each curve is the average of 26 raw data curves). The blue dashed-lines show how the current should decay from each set point if it follows the form of the 3nA data. The green lines are predicted by the elastic distortion model described in the text where the same two parameters are used to fit both the G-C and A-T data.
Mentions: Several factors indicate that the signals are not purely electronic in origin: Firstly, the decay distance is much too long to correspond to an electronic process5 where tunneling decay lengths are typically Å not nm.12,13 Secondly, the change in shape of the decay curves with ISP is not consistent with a simple tunneling process. We illustrate this in Figure 4c with a set of averaged curves (red lines) for each ISP for the G-C interaction. If the decay at lower set-point currents had the same shape as the ISP = 3nA curve, the curves would lie on the blue dashed lines. They clearly do not. Thirdly, there is considerable hysteresis in the data. On approach, the probe must be brought closer to the surface to restore a signal (supporting information) and its growth is more rapid than the decay was on withdrawal. Fourthly, a theoretical simulation (see below) indicates that the electronic conductance of a base-nucleoside pair is not particularly sensitive to hydrogen-bonding, being dominated by the low conductance across the sugar ring.

Bottom Line: Junctions that are held together by three hydrogen bonds per base pair (for example, guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per base pair (for example, adenine-thymine interactions).Similar, but less pronounced effects are observed on the approach of the tunnelling probe, implying that attractive forces that depend on hydrogen bonds also have a role in determining the rise of current.These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.

ABSTRACT
Hydrogen bonding has a ubiquitous role in electron transport and in molecular recognition, with DNA base pairing being the best-known example. Scanning tunnelling microscope images and measurements of the decay of tunnel current as a molecular junction is pulled apart by the scanning tunnelling microscope tip are sensitive to hydrogen-bonded interactions. Here, we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA base pairs. Junctions that are held together by three hydrogen bonds per base pair (for example, guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per base pair (for example, adenine-thymine interactions). Similar, but less pronounced effects are observed on the approach of the tunnelling probe, implying that attractive forces that depend on hydrogen bonds also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal.

Show MeSH
Related in: MedlinePlus