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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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Charge transfer, obtained from integration of the tunnel current decay curves, plotted as a function of set-point current for different molecular junctions. The junctions plotted are non-hydrogen bonding controls (triangles), 2AA-deoxycytidine (black dots), A-thymidine (green dots), 2AA-Thymidine (red dots) and G-deoxycytidine (blue dots). The two sets of controls correspond to a bare probe and a thio-phenol functionalized probe interacting with a thymidine monolayer. The withdraw speed was 100 nm/s and the error bars are ±1sd. The solid lines are calculated according to equation 2 for NHB = 0, 1, 2 and 3 using the values of B and CK1/K2 obtained from fits to the G-C data in Figure 4c.
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Figure 5: Charge transfer, obtained from integration of the tunnel current decay curves, plotted as a function of set-point current for different molecular junctions. The junctions plotted are non-hydrogen bonding controls (triangles), 2AA-deoxycytidine (black dots), A-thymidine (green dots), 2AA-Thymidine (red dots) and G-deoxycytidine (blue dots). The two sets of controls correspond to a bare probe and a thio-phenol functionalized probe interacting with a thymidine monolayer. The withdraw speed was 100 nm/s and the error bars are ±1sd. The solid lines are calculated according to equation 2 for NHB = 0, 1, 2 and 3 using the values of B and CK1/K2 obtained from fits to the G-C data in Figure 4c.

Mentions: Fits to the current decay data are complicated by factors that affect I(X1) and that are not incorporated into this simple mechanical model. The model is better-tested by integrating the current decay curves to obtain the charge transferred in each interaction (when the x axis is converted to time using the known retraction speed of the probe). This removes the explicit dependence on I(X1). The mean charge transferred, Q, as a function of initial set-point is plotted for a number of types molecular junctions in Figure 5. The error bars are ± 1 sd of the distributions for each point. The mechanical model of gap distortion yields the following result for Q: (2)Q=ISPβv(1+CK1K2NHBln(BISP+1)). Here is the retraction speed of the STM probe (100 nm/s) and β is the intrinsic decay constant (taken to be the 6 nm−1 measured in solvent - supporting information) and B and are the parameters introduced in Equation 1. Calculated values of Q are shown by the solid lines in Figure 5 for NHB = 0, 1, 2 and 3. The experimental data fall close to the corresponding lines, with the exception of the data for 2AA-C which falls on the NHB =1 line, presumably because the two H-bonds in this complex are significantly less stiff. It is interesting to note that the data for G-C (9 kcal/mol for each H-bond17) lies above the line while the data for 2AA-T (5 kcal/mole for each H-bond17) are closer to the prediction.


Tunnelling readout of hydrogen-bonding-based recognition.

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

Charge transfer, obtained from integration of the tunnel current decay curves, plotted as a function of set-point current for different molecular junctions. The junctions plotted are non-hydrogen bonding controls (triangles), 2AA-deoxycytidine (black dots), A-thymidine (green dots), 2AA-Thymidine (red dots) and G-deoxycytidine (blue dots). The two sets of controls correspond to a bare probe and a thio-phenol functionalized probe interacting with a thymidine monolayer. The withdraw speed was 100 nm/s and the error bars are ±1sd. The solid lines are calculated according to equation 2 for NHB = 0, 1, 2 and 3 using the values of B and CK1/K2 obtained from fits to the G-C data in Figure 4c.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Charge transfer, obtained from integration of the tunnel current decay curves, plotted as a function of set-point current for different molecular junctions. The junctions plotted are non-hydrogen bonding controls (triangles), 2AA-deoxycytidine (black dots), A-thymidine (green dots), 2AA-Thymidine (red dots) and G-deoxycytidine (blue dots). The two sets of controls correspond to a bare probe and a thio-phenol functionalized probe interacting with a thymidine monolayer. The withdraw speed was 100 nm/s and the error bars are ±1sd. The solid lines are calculated according to equation 2 for NHB = 0, 1, 2 and 3 using the values of B and CK1/K2 obtained from fits to the G-C data in Figure 4c.
Mentions: Fits to the current decay data are complicated by factors that affect I(X1) and that are not incorporated into this simple mechanical model. The model is better-tested by integrating the current decay curves to obtain the charge transferred in each interaction (when the x axis is converted to time using the known retraction speed of the probe). This removes the explicit dependence on I(X1). The mean charge transferred, Q, as a function of initial set-point is plotted for a number of types molecular junctions in Figure 5. The error bars are ± 1 sd of the distributions for each point. The mechanical model of gap distortion yields the following result for Q: (2)Q=ISPβv(1+CK1K2NHBln(BISP+1)). Here is the retraction speed of the STM probe (100 nm/s) and β is the intrinsic decay constant (taken to be the 6 nm−1 measured in solvent - supporting information) and B and are the parameters introduced in Equation 1. Calculated values of Q are shown by the solid lines in Figure 5 for NHB = 0, 1, 2 and 3. The experimental data fall close to the corresponding lines, with the exception of the data for 2AA-C which falls on the NHB =1 line, presumably because the two H-bonds in this complex are significantly less stiff. It is interesting to note that the data for G-C (9 kcal/mol for each H-bond17) lies above the line while the data for 2AA-T (5 kcal/mole for each H-bond17) are closer to the prediction.

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