A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases S1 A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases

The effect of interactions of various Ia and IIa cations with two positions of the adenine-thymine (A−T) and guanine-cytosine (G−C) base pairs on the geometries and individual hydrogen bond (HB) energies have been investigated by using the atoms in molecules (AIM) method at the B3LYP/6-311++G(d,p) level of theory. The cations that possess higher charge/radius (q/rad) ratio make higher changes o...

The synthesis, structure, and electronic spectra of a series of DNA hairpins possessing two perylenediimide (PDI) base pair surrogates are reported. The PDI chromophores are located in opposite strands of the hairpin base pair domain opposite abasic sites and are either adjacent to each other or separated by a variable number of AT or GC base pairs. Molecular modeling of the conjugate having ad...

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of ...

Hydroxypyridone and pyridopurine homo- and hetero-base pairs have been investigated in the context of duplex GNA (glycol nucleic acid). Phosphoramidites for automated GNA solid phase synthesis were synthesized economically in a few steps starting from commercially available enantiopure glycidol. Similar to their behavior in DNA, the hydroxypyridone and pyridopurine homo-base pairs display a met...

The base pairs in double helical nucleic acids have been compared to see how they can be recognized by proteins. We conclude that a single hydrogen bond is inadequate for uniquely identifying any particular base pair, as this leads to numerous degeneracies. However, using two hydrogen bonds, fidelity of base pair recognition may be achieved. We propose specific amino-acid side chain interaction...

The BPS (http://bps.rutgers.edu) is a database of RNA base-pair structures, higher-order base interactions and isosteric pairs (base pairs with similar shape). The main functions of the BPS are to find and annotate the structural and chemical features of the Watson-Crick and non-Watson-Crick (noncanonical) base pairs in high-resolution RNA structures, and to provide a user-friendly interface to...

For many tRNAs, the discriminator base preceding the CCA sequence at the 3' end is important for aminoacylation. We show that the discriminator base influences the stability of the 1.72 base pair onto which it is stacked. Mutations of the discriminator base from adenosine to cytidine or uridine make the cytidine residue in the C1-G72 base pair of mutant Escherichia coli initiator tRNAs more rea...

Efficiency of 6-ethynylpyridone (E), a potential thymine (T) analogue, which forms high-fidelity base pairs with adenine (A) and gives rise to stabler DNA duplexes, with stability comparable to those containing canonical cytosine(C):guanine(G) base pairs, has been reported recently. Estimates of the interaction energies, involving geometry optimization at the DFT level (including middle range d...