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• W2156685874 abstract "Nano-telegraph: It is shown quantum chemically how the hydrogen-bond strength of a DNA base pair can be remotely switched (across several nanometers) between three states (weak, intermediate, and strong) through a π-conjugated “organic wire”. Hydrogen bonding plays an important role in the formation of DNA base pairs1 and has been the subject of many theoretical studies.2, 3 Previously, we have provided a proof of principle for a chemically controlled nanoswitch based on the guanine–cytosine (GC) Watson–Crick pair.4, 5 This supramolecular complex can be switched in terms of bond strength and shape, by stepwise protonation of a substituent X at guanine C8, from: a) strong and “bent up”, via b) medium and “not bent”, to c) weak and “bent down”, as illustrated in Scheme 1 (X−, X, X+ correspond, for example, to O−, OH, OH2+, respectively). The origin of this switching behavior is that an anionic substituent, O−, reduces the hydrogen-bond donating and increases the hydrogen-bond accepting capabilities of a DNA base (and vice versa for a cationic substituent, OH2+) in combination with the fact that guanine is a double hydrogen-bond donor but only a single hydrogen-bond acceptor.4, 5 Nanoswitch based on substituted GC pair. In this work, we want to show that it is possible to control such a molecular switch remotely. To this end, the substituent X is connected to the C8 of guanine through a π-conjugated linker of acetylene units, -(CC)n-. Previously, Chao et al.6–8 have shown that depending on the linker that is used the signal from the substituent to the hydrogen bond between, in their case, the pyrole molecule and ammonia, can be either reduced or amplified. They used an imine group as substituent, which can be protonated. Here, we employ the hydroxy group as our substituent (X=OH), which can be protonated or deprotonated. In our model systems, we have elongated the -(CC)n- linker stepwise from n=0 to 10, which corresponds to a length of about two and a half nanometers (25.7 Å; see also Figure 1 a). Our computations are carried out with the ADF program at BP86/TZ2P.9 Our results are collected in Figure 1 and 2. Further details and Cartesian coordinates of all stationary points are provided in Tables S1–S6 in the Supporting Information. a) Substituted GC base pair with: b) bond energy ΔE of X-(CC)n-G + C with X=O−, OH, H, OH2+; c) difference in bond energies ΔΔE of O−-(CC)n-G + C relative to HO-(CC)n-G + C (red: deprotonation of OH) and of H2O+-(CC)n-G + C relative to HO-(CC)n-G + C (blue: protonation of OH); d) hydrogen bond lengths in X-(CC)n-GC with X=OH2+, e) with X=OH, and f) with X=O−. It appears that the hydrogen bonding of our substituted GC pair can indeed be switched between three states, namely weak, intermediate, and strong, by respectively having a deprotonated hydroxy group (O−), the neutral hydroxy group (OH), or the protonated hydroxy group (OH2+) as a substituent (see Figure 1 b and 1c). Interestingly, this is so not only without a linker, but also with a -(CC)n- linker in between guanine and the substituent X. Without a linker (n=0), the hydrogen bond energy switches from −22.0 to −25.9 to −34.6 kcal mol−1 along the series X=O−, OH, and OH2+. Introducing the linker -(CC)n- slightly weakens the hydrogen bonds for X=OH2+ and strengthens the hydrogen bonds for X=OH and especially O− (see Figure 1 b). But the switching pattern remains unaltered. Thus, with one -CC- unit as a linker (n=1), the hydrogen bond energy switches from −24.4 to −26.4 to −32.9 kcal mol−1 along the series X=O−, OH, and OH2+. And for our longest linker, -(CC)10- (n=10), the hydrogen bond strength still varies between −25.8, −28.0, and −31.8 kcal mol−1, respectively. We conclude that the switching effect as a function of the extent of protonation of the substituent X persists and does not fade out up to our longest linker (n=10). In the case of X=OH or OH2+, the hydrogen bond lengths change only slightly, that is, by ±0.04 Å or less, as a function of the linker length n=0 to 10 (see Figure 1 d and e). But in the case of X=O− hydrogen bond lengths vary significantly as the linker is elongated (see Figure 1 f). Thus, the upper hydrogen bond of guanine, O6N4 expands by 0.13 Å, the middle hydrogen bond N1N3 contracts by 0.03 Å, and the lower hydrogen bond N2O2 contracts by 0.12 Å. To understand the above findings, we have analyzed how the substituent X in guanine affects the hydrogen-bonding mechanism using Kohn–Sham molecular orbital (MO) theory10 and Voronoi deformation density (VDD) atomic charges11 (see Figure 2; see also Table S2 in the Supporting Information). The major trend, that is, the switching of the GC hydrogen bonds from strong (X=OH2+), via medium (X=OH, H) to weak (X=O−) is based on exactly the same mechanism as found before in the absence of a linker.4, 5 The substituent X is still conjugated with the π system of guanine through the π orbitals of the linker and accepts charge from the base (X=OH2+), has little effect on the base (X=OH, H), or donates charge into the base (X=O−; see Figure 2). The slightly positive, approximately neutral, and slightly negative net charge, respectively, on guanine has the well-known consequence of a) strengthening the two hydrogen bonds N1N3 and N2O2 for X=OH2+, b) little effect for X=OH, H, and c) strengthening of the O6N4 hydrogen bond for X=O−. a) Charge Q(G) of guanine, b) charge Q(X) of substituent X, and c) charge Q[(CC)n] of linker (CC)n in X-(CC)n-G with X=O−, OH, H, OH2+. d) Orbital energies in H-(CC)n-H. e) O6 atomic charge, f) H1 atomic charge, and g) H2 atomic charge in X-(CC)n-G with X=O−, OH, OH2+. h) Orbital energy of HOMO in X-(CC)n-G with X=O−, OH, OH2+. Superimposed on the main trend (i.e., the switching), we have found that the magnitude of the switching effect is slightly diminished if the -(CC)n- linker is introduced and if the latter becomes longer (see Figure 1 b and 1c). This can be understood on the basis of the π-orbital electronic structure of the linking unit. To this end, we examined the electronic structure of the isolated linker terminated with hydrogen atoms, that is, H-(CC)n-H. The π HOMO of the isolated linker monotonically rises in energy and the π* LUMO pronouncedly drops in energy as the number of -(CC)- units increases from n=1 to 10 (see Figure 2 d). This means that, the longer it is, the -(CC)n- linker becomes both a better π-electron donor and acceptor. In line with this, it accepts part of the excess negative charge of the negative substituent X=O−. It also donates some of its π electrons into the positive substituent X=OH2+, but this effect is not very pronounced (see Figure 2). Finally, in the case of the neutral substituents X=OH or H, an even more subtle effect can be observed. Now, the dominant role of the linker is to act through its π* LUMO as an acceptor of charge from guanine (see Figure 2 a, 2 c, 2 d–g). This leads to the observed (slight) strengthening of the Watson–Crick hydrogen bonds as the linker becomes longer (see Figure 1 b). In conclusion, we have shown that a DNA-based nanoswitch, that is, a guanine C8-substituted GC pair, can in principle also be switched (by protonation or deprotonation of the substituent X=OH) if this substituent is separated from guanine through a -(CC)n- linker. This linker is π conjugated with both, and electronically connects the DNA base and the substituent. This enables a remote communication between substituent and DNA base over a distance of up to nearly 3 nm. We thank the National Research School Combination for Catalysis (NRSC-C), the Netherlands organization for Scientific Research (NWO-CW and NWO-NCF) and the HPC-Europa program of the European Union for financial support. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article." @default.
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• W2156685874 date "2011-07-05" @default.
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• W2156685874 title "Remote Communication in a DNA-Based Nanoswitch" @default.
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• W2156685874 doi "https://doi.org/10.1002/chem.201101335" @default.
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