The adsorption of hydrogen-bonded and stacked nucleobase pairs on the hexagonal boron nitride (h-BN) surface was studied by density functional theory and molecular dynamics methods. Eight types of nucleobase pairs (i.e., GG, AA, TT, CC, UU, AT, GC, and AU) were chosen as the adsorbates. The adsorption configurations, interaction energies, and electronic properties of the nucleobase pair on the ...

The integrity of the genome relies primarily on the ability of DNA polymerases to efficiently catalyze selective DNA synthesis according to the Watson–Crick rule in a templatedirected manner during DNA replication, repair, and recombination. Remarkably, some DNA polymerases achieve selective information transfer to the offspring in line with the Watson–Crick rule with intrinsic error rates as l...

DNA damage induced via dissociative attachment by low-energy electrons (0 to 20 eV) is well studied in both gas and condensed phases. However, the reactivity of ultrashort-lived prehydrated electrons ([Formula: see text]) with DNA components in a biologically relevant environment has not been fully explored to date. The electron transfer processes of [Formula: see text] to the DNA nucleobases G...

Our cellular genome is continuously exposed to a wide spectrum of exogenous and endogenous DNA damaging agents. These agents can lead to formation of an extensive array of DNA lesions including single- and double-stranded breaks, inter- and intrastrand cross-links, abasic sites, and modification of DNA nucleobases. Persistence of these DNA lesions can be both mutagenic and cytotoxic, and can ca...

Numerous 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with spacious modifications such as dyes and affinity tags like biotin are substrates for DNA polymerases. They are widely employed in many cutting-edge technologies like advanced DNA sequencing approaches, microarrays, and single molecule techniques. Modifications attached to the nucleobase are accepted by many DNA polym...

DNA is under continuous assault by environmental and endogenous reactive oxygen and alkylating species, inducing the formation of mutagenic, toxic and genome destabilizing nucleobase lesions. Due to the implications of such genetic alterations in cell death, aging, inflammation, neurodegenerative diseases and cancer, many efforts have been devoted to developing assays that aim at analyzing DNA ...

So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger fo...

Oligonucleotides incorporating 7-(octa-1,7-diynyl) derivatives of 8-aza-7-deaza-2-deoxyguanosine (2d) were prepared by solid-phase synthesis. The side chain of 2d was introduced by the Sonogashira cross coupling reaction and phosphoramidites (3a, 3b) were synthesized. Duplexes containing 2d are more stabilized compared to those incorporating the non-functionalized 8-aza-7-deaza-2-deoxyguanosine...

The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured ...

The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP-Ag(I)-6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprisi...