Sensing DNA through DNA Charge Transport

Zwang, Theodore J.; Tse, Edmund C. M.; Barton, Jacqueline K.

doi:10.1021/acschembio.8b00347

Cited by 58 publications

(48 citation statements)

References 101 publications

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“…In addition, functional self-assembling electronics that move beyond 1D to access the rich space provided by DNA origami and tiled structures promise to further expand the landscape for exploring the phenomena discussed here (133)(134)(135). In the biological context, transport coherence switching on the nanometer-length scale could be recruited by signaling networks, as suggested by Barton and coworkers (23,24,26).…”

Section: Looking Aheadmentioning

confidence: 91%

Why Are DNA and Protein Electron Transfer So Different?

Beratan

2019

Annu. Rev. Phys. Chem.

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The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.

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Section: Looking Aheadmentioning

confidence: 91%

Why Are DNA and Protein Electron Transfer So Different?

Beratan

2019

Annu. Rev. Phys. Chem.

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“…In this regard, asymmetric and catalytic synthesis of chiral compounds have been actively pursued for more than half a century to meet the needs of chemical and biomedical research [7][8][9][10][11][12][13][14][15][16][17][18][19][20]. Among the numerous chiral biomolecules and their complexes, DNA has attracted special attention in the chemistry community because it shows multilayer paired chirality along with their double-or single-strand and i-Motif backbones (Figure 1(a)) [21][22][23]. Proteins also often show multilayer chirality in their folding structures [24].…”

Section: Introductionmentioning

confidence: 99%

Multilayer 3D Chirality and Its Synthetic Assembly

Liu

Yang

et al. 2019

Research

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3D chirality of sandwich type of organic molecules has been discovered. The key element of this chirality is characterized by three layers of structures that are arranged nearly in parallel fashion with one on top and one down from the center plane. Individual enantiomers of these molecules have been fully characterized by spectroscopies with their enantiomeric purity measured by chiral HPLC. The absolute configuration was unambiguously assigned by X-ray diffraction analysis. This is the first multilayer 3D chirality reported and is anticipated to lead to a new research area of asymmetric synthesis and catalysis and to have a broad impact on chemical, medicinal, and material sciences in future.

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“…However, large parts of the picture are still lacking. Indeed, experimental measures are challenging due to the complexity of working at the nanoscale [20, 21], and accurate quantum chemistry calculations are extremely heavy for these systems [22, 23].…”

Section: Introductionmentioning

confidence: 99%

Relation between DNA ionization potentials, single base substitutions and pathogenic variants

Pucci

Rooman

2019

BMC Genomics

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Background It is nowadays clear that single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, despite recent progress, the understanding of these "non-local" effects is still far from being achieved. Results To advance this problem, we analyzed the relationship between the base mutability in specific gene regions and the electron hole transport along the DNA base stacks, as it is one of the mechanisms that have been suggested to contribute to these effects. More precisely, we studied the connection between the normalized frequency of single base substitutions and the vertical ionization potential of the base and its flanking sequence, estimated using MP2/6-31G* ab initio quantum chemistry calculations. We found a statistically significant overall anticorrelation between these two quantities: the lower the vIP value, the more probable the substitution. Moreover, the slope of the regression lines varies. It is larger for introns than for exons and untranslated regions, and for synonymous than for missense substitutions. Interestingly, the correlation appears to be more pronounced when considering the flanking sequence of the substituted base in the 3’ rather than in the 5’ direction, which corresponds to the preferred direction of charge migration. A weaker but still statistically significant correlation is found between the ionization potentials and the pathogenicity of the base substitutions. Moreover, pathogenicity is also preferentially associated with larger changes in ionization potentials upon base substitution. Conclusions With this analysis we gained new insights into the complex biophysical mechanisms that are at the basis of mutagenesis and pathogenicity, and supported the role of electron-hole transport in these matters. Electronic supplementary material The online version of this article (10.1186/s12864-019-5867-y) contains supplementary material, which is available to authorized users.

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Sensing DNA through DNA Charge Transport

Cited by 58 publications

References 101 publications

Why Are DNA and Protein Electron Transfer So Different?

Why Are DNA and Protein Electron Transfer So Different?

Multilayer 3D Chirality and Its Synthetic Assembly

Relation between DNA ionization potentials, single base substitutions and pathogenic variants

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