The nucleobase guanine in DNA (dG) and RNA (rG) has the lowest standard reduction potential of the bases, rendering it a major site of oxidative damage in these polymers. Mapping the sites at which oxidation occurs in an oligomer via chemical reagents utilizes hot piperidine for cleaving oxidized DNA and aniline (pH 4.5) for cleaving oxidized RNA. In the present studies, a series of time-depend...

Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstei...

Hydroxyl radical reacts at numerous sites within nucleic acids to form a wide range of derivatives yet the conformational specificity of only one of these processes, direct strand fragmentation, has received much attention to date. Since the deleterious effects of this radical are not likely limited to strand fragmentation in vivo, this report examined the conformational specificity expressed i...

This work concerns a dithymine tetrapeptide, which can be seen as a new analogue of a dinucleoside monophosphate, made of both unfunctionalized and thymine-containing L-serine units alternated in the sequence. The new nucleopeptide was obtained on the solid phase by two different synthetic strategies. The first one is suitable to easily realize nucleopeptides with homonucleobase sequences, obta...

RNA editing from adenosine to inosine (A-to-I editing) is one of the mechanisms that regulate and diversify the transcriptome. Here, a triplex-forming peptide nucleic acid (PNA) modified with a 2-aminopyridine nucleobase was applied for the recognition of the A-to-I editing event in double-stranded RNAs. The triplex-forming PNA enabled sequence-specific detection of single nucleobase editing at...

Guanosine analogs assemble to unusual nucleobase tetrads, restricting possible conformations of four-stranded DNAs.

In this Article, we failed to indicate that the term ENBT1 was previously used as the name of a putative transporter involved in the dipyridamole-insensitive, purine-selective nucleobase transport system in primary human cardiac microvascular endothelial cells (ref. 11). More recently, the term has also been used to indicate the cellular function of a dipyridamole-insensitive, sodium-independen...

DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study ...

A new series of nucleobase adenine (A) functionalized naphthalene diimide (NDI) derivatives to form a donor-acceptor conjugate has been designed, synthesized and characterized. The photoinduced electron transfer from to...