Limits...
The self-assembled behavior of DNA bases on the interface.

Liu L, Xia D, Klausen LH, Dong M - Int J Mol Sci (2014)

Bottom Line: A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases.The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures.The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

View Article: PubMed Central - PubMed

Affiliation: Institute for Advanced Materials, Jiangsu University, 301 Xuefu Road, Jiangsu 212013, China. liu@ujs.edu.cn.

ABSTRACT
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

Show MeSH
Co-adsorption of guanine and cytosine at the 1-octanol/HOPG interface. (a) Typical STM image presenting three domains, marked with I, II and III. Scan size: 50 nm × 50 nm; (b) Correlation averaged magnified image of the structure in domain I, 5 nm × 5 nm, a unit cell is indicated. There is a line profile on the bottom of (b) along the blue line in the top of the STM image; and (c) Correlation averaged magnified image of the structure in domain III, 5 nm × 5 nm, a unit cell is indicated. Bottom: height profile along the blue line in the top of panel. The structural model is superimposed on the STM image. Iset = 549 pA, Vbias = 750 mV. (Reproduced with the permission from [25]. Copyright 2006 American Chemistry Society.).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3958828&req=5

f4-ijms-15-01901: Co-adsorption of guanine and cytosine at the 1-octanol/HOPG interface. (a) Typical STM image presenting three domains, marked with I, II and III. Scan size: 50 nm × 50 nm; (b) Correlation averaged magnified image of the structure in domain I, 5 nm × 5 nm, a unit cell is indicated. There is a line profile on the bottom of (b) along the blue line in the top of the STM image; and (c) Correlation averaged magnified image of the structure in domain III, 5 nm × 5 nm, a unit cell is indicated. Bottom: height profile along the blue line in the top of panel. The structural model is superimposed on the STM image. Iset = 549 pA, Vbias = 750 mV. (Reproduced with the permission from [25]. Copyright 2006 American Chemistry Society.).

Mentions: The hydrogen bond between guanine and cytosine is one kind of NA base complementary pairing. Guanine and cytosine are able to assembly into G-dimers and C-dimers, further forming G and C chains based on intermolecular hydrogen bonds between themselves. The co-adsorption of G and C on the surface will result in the co-assembly formed by G–C complementary pairing. The well-ordered adlayer is presented in the STM image (Figure 4 [25]). The formation of a distinct double row structure is clearly observed, and expected to be ascribed to aligned GC pairs. The co-assemblies of G and C on the surface are different from the structures assembled by pure G or C molecules. In the co-adsorption of G and C on the surface, three distinct domains of self-assembled structures can be identified, marked I, II and III (Figure 4a). The correlation averaging processing can improve the quality of high-resolution structures with molecular contrast. Domains I and II are composed of assembled bases with the feature aligned into straight and parallel rows. The periodicity of domain I/II is presented in Table 2. The parameter of the unit cell of domain I/II is determined to be a = 0.87 ± 0.09 nm, b = 0.45 ± 0.05 nm and θ = 77.3° ± 2.3°. The structure of domain I/II is in agreement with the structure formed by pure cytosine (Figure 3b). The lattice parameters of domain I/II are mostly similar to the ones of pure C assembling structures. It is therefore concluded that domain I and II are formed by cytosine molecule alone. Domain III, however, is in comparison, distinct from the previous STM images of pure C and G assemblies; it is indeed a mixed phase consisting of both C and G molecules. The periodic molecular arrangement alternates between rows of high and low protrusions within domain III (Figure 4c). G and C form heterodimers aligned into rows. The lattice parameters are determined to be a = 1.71 ± 0.18 nm, b = 0.69 ± 0.07 nm and θ = 84.1° ± 2.4°. To obtain an insight into the underlying molecule-molecule interaction, theoretical modeling based on the self-consistent charge density functional-based tight binding method was performed. It was determined that the planar structures for homodimers of G and C are the lowest energy configuration with binding energies of 0.4 (CC) and 0.5 eV (GG), presented in Figure 5a,b, respectively. The optimum heterodimer is definitely a Watson-Crisk GC pair (Figure 5c), which is found to have the considerably higher binding energy of 0.9 eV. It is therefore plausible that a GC dimer is the most preferential complex to form. GC dimers could also arrange into a row with an optimized model (Figure 5d). The periodicity along the model structure is 0.74 nm, consistent with the 0.69 ± 0.07 nm determined from the experiment, thus experiment and theoretical model are in good agreement. The row structure of GC dimers was stabilized in fact through the intermolecular hydrogen bonds. The dimer-dimer interaction energy values were obtained by calculating the binding energy per GC dimer. The binding energy for row segments with n GC dimers increase monotonically toward the limit for an infinite chain. It is the main reason explaining why the GC dimer could further assemble into the structures. It is also found that the so-called GCGC quartet was formed in four-stranded DNA quadruplexes due to the interaction between G and C [26]. The quartet structure can be realized from the model of Figure 5d, and by rotating the GC dimer by 180° around the surface normal each second, which results in the optimized structures shown in Figure 5e. The quartet row structure (G and C molecules alternate along the row direction) found from the calculation is slightly (0.1 eV per dimer) more stable than the dimer row observed by STM (Figure 4c), which appears to be inconsistent with the experiment. It is true that STM could not capture the configuration of GC pairs with the lowest binding energies, however, it also shows the possible assembling structures of G and C.


The self-assembled behavior of DNA bases on the interface.

Liu L, Xia D, Klausen LH, Dong M - Int J Mol Sci (2014)

Co-adsorption of guanine and cytosine at the 1-octanol/HOPG interface. (a) Typical STM image presenting three domains, marked with I, II and III. Scan size: 50 nm × 50 nm; (b) Correlation averaged magnified image of the structure in domain I, 5 nm × 5 nm, a unit cell is indicated. There is a line profile on the bottom of (b) along the blue line in the top of the STM image; and (c) Correlation averaged magnified image of the structure in domain III, 5 nm × 5 nm, a unit cell is indicated. Bottom: height profile along the blue line in the top of panel. The structural model is superimposed on the STM image. Iset = 549 pA, Vbias = 750 mV. (Reproduced with the permission from [25]. Copyright 2006 American Chemistry Society.).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3958828&req=5

f4-ijms-15-01901: Co-adsorption of guanine and cytosine at the 1-octanol/HOPG interface. (a) Typical STM image presenting three domains, marked with I, II and III. Scan size: 50 nm × 50 nm; (b) Correlation averaged magnified image of the structure in domain I, 5 nm × 5 nm, a unit cell is indicated. There is a line profile on the bottom of (b) along the blue line in the top of the STM image; and (c) Correlation averaged magnified image of the structure in domain III, 5 nm × 5 nm, a unit cell is indicated. Bottom: height profile along the blue line in the top of panel. The structural model is superimposed on the STM image. Iset = 549 pA, Vbias = 750 mV. (Reproduced with the permission from [25]. Copyright 2006 American Chemistry Society.).
Mentions: The hydrogen bond between guanine and cytosine is one kind of NA base complementary pairing. Guanine and cytosine are able to assembly into G-dimers and C-dimers, further forming G and C chains based on intermolecular hydrogen bonds between themselves. The co-adsorption of G and C on the surface will result in the co-assembly formed by G–C complementary pairing. The well-ordered adlayer is presented in the STM image (Figure 4 [25]). The formation of a distinct double row structure is clearly observed, and expected to be ascribed to aligned GC pairs. The co-assemblies of G and C on the surface are different from the structures assembled by pure G or C molecules. In the co-adsorption of G and C on the surface, three distinct domains of self-assembled structures can be identified, marked I, II and III (Figure 4a). The correlation averaging processing can improve the quality of high-resolution structures with molecular contrast. Domains I and II are composed of assembled bases with the feature aligned into straight and parallel rows. The periodicity of domain I/II is presented in Table 2. The parameter of the unit cell of domain I/II is determined to be a = 0.87 ± 0.09 nm, b = 0.45 ± 0.05 nm and θ = 77.3° ± 2.3°. The structure of domain I/II is in agreement with the structure formed by pure cytosine (Figure 3b). The lattice parameters of domain I/II are mostly similar to the ones of pure C assembling structures. It is therefore concluded that domain I and II are formed by cytosine molecule alone. Domain III, however, is in comparison, distinct from the previous STM images of pure C and G assemblies; it is indeed a mixed phase consisting of both C and G molecules. The periodic molecular arrangement alternates between rows of high and low protrusions within domain III (Figure 4c). G and C form heterodimers aligned into rows. The lattice parameters are determined to be a = 1.71 ± 0.18 nm, b = 0.69 ± 0.07 nm and θ = 84.1° ± 2.4°. To obtain an insight into the underlying molecule-molecule interaction, theoretical modeling based on the self-consistent charge density functional-based tight binding method was performed. It was determined that the planar structures for homodimers of G and C are the lowest energy configuration with binding energies of 0.4 (CC) and 0.5 eV (GG), presented in Figure 5a,b, respectively. The optimum heterodimer is definitely a Watson-Crisk GC pair (Figure 5c), which is found to have the considerably higher binding energy of 0.9 eV. It is therefore plausible that a GC dimer is the most preferential complex to form. GC dimers could also arrange into a row with an optimized model (Figure 5d). The periodicity along the model structure is 0.74 nm, consistent with the 0.69 ± 0.07 nm determined from the experiment, thus experiment and theoretical model are in good agreement. The row structure of GC dimers was stabilized in fact through the intermolecular hydrogen bonds. The dimer-dimer interaction energy values were obtained by calculating the binding energy per GC dimer. The binding energy for row segments with n GC dimers increase monotonically toward the limit for an infinite chain. It is the main reason explaining why the GC dimer could further assemble into the structures. It is also found that the so-called GCGC quartet was formed in four-stranded DNA quadruplexes due to the interaction between G and C [26]. The quartet structure can be realized from the model of Figure 5d, and by rotating the GC dimer by 180° around the surface normal each second, which results in the optimized structures shown in Figure 5e. The quartet row structure (G and C molecules alternate along the row direction) found from the calculation is slightly (0.1 eV per dimer) more stable than the dimer row observed by STM (Figure 4c), which appears to be inconsistent with the experiment. It is true that STM could not capture the configuration of GC pairs with the lowest binding energies, however, it also shows the possible assembling structures of G and C.

Bottom Line: A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases.The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures.The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

View Article: PubMed Central - PubMed

Affiliation: Institute for Advanced Materials, Jiangsu University, 301 Xuefu Road, Jiangsu 212013, China. liu@ujs.edu.cn.

ABSTRACT
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

Show MeSH