A DNA pentaplex incorporating nucleobase quintets

Silicene-based DNA Nucleobase Sensing

We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the current-voltage relation in the presence of nucleobases with various orientations. We demonstrate that when nucleobases pass through a pore, even after sampling...

Quintets of uracil and thymine: a novel structure of nucleobase self-assembly studied by electrospray ionization mass spectrometry.

ESI-MS and molecular dynamic calculations reveal that in the presence of K(+), Rb(+) and Cs(+), uracil, thymine and their homologues form self-assembled quintet structures that are stabilized by hydrogen bonding and ion dipole interactions.

Asymmetric Recognition of Nucleobase Features by DNA Polymerases

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing.

We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulat...

Long-wavelength fluorescence from 2-aminopurine-nucleobase dimers in DNA.

When 2-aminopurine (2AP) is substituted for adenine in DNA, it is widely accepted that its fluorescence spectrum is essentially unchanged from that of the free fluorophore. We show that 2AP in DNA exhibits long-wavelength emission and excitation bands, in addition to the familiar short-wavelength spectra, as a result of formation of a ground-state heterodimer with an adjacent, pi-stacked, natur...