Solution Stucture of the d(T-C-G-A) Duplex at Acidic pH

The poly dA helix: a new structural motif for high performance DNA-based molecular switches

“…Furthermore, 2D NOESY of dTA 6 showed a set of eleven H8–H1′ NOEs (Figure 3B) characteristic of six A–A base pairs found in A-containing duplexes that form a parallel-stranded Π-DNA helix (29). Importantly the absence of NOEs between Adenine NH 2 protons and the Adenine H2 protons are consistent with the reverse Hoogsteen base-pairing scheme seen in the d A containing parallel duplex (30).

Figure 2.( A ) Schematic showing poly d A 15 changing between single helix to duplex conformations induced by alternate addition of acid and base respectively.

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“…One millimolar dTA 6 in 10% D 2 O/H 2 O at 10°C on a Bruker 800 MHz NMR spectrometer showed exactly six Adenine H8 protons and only one type of Thymine CH 3 and H6 protons (see Supplementary Data and Figure 3A) confirming that this sequence forms a single population of dimer in bulk, precluding any slipped structures for at least six contiguous adenine tracts. Importantly, the 1D spectrum of dTA 6 showed hydrogen-bonded N6 aminos that were downfield shifted to 8.4–9 δppm from the usual 6–7 δppm for these protons (see Figure 3A), characteristic of hydrogen bonding seen in A–A base pairing (Figure 2B) (30). These were not seen in either the D 2 O exchanged spectrum at pH 4 or the single helical, monomeric structure at pH 8 in 5% D 2 O [Figure 3A (2 and 3)].…”

Genetically Unstable CXG Repeats are Structurally Dynamic and Have a High Propensity for Folding. An NMR and UV Spectroscopic Study

“…A limited number of structural studies of TR oligonucleotides exist (Robinson et al, 1992;Fry & Loeb, 1994;Chen et al, 1995;Gacy et al, 1995;Gao et al, 1995;Nadel et al, 1995;Smith et al, 1995), which focus on a subset of TR sequences, such as (GAC) n and (CGG) n (n = number of repeats; for simplicity deoxyribose nomenclature will be omitted throughout the text). NMR studies by Wang, Patel and co-workers imply that CGA (a permutation of GAC) is a parallel duplex motif under acidic conditions (Robinson et al, 1992;Wang & Patel, 1994). In these studies, mismatch base-pairs G·G, A·A and C·C have been characterized in detail.…”

What Do γ-Ray Bursts Look Like?

“…This model could also give an explanation for the observed steepening. Recently, Wang et al (1999c) proved that the dense environment model can also explain well the radio afterglow of GRB 980519 (Frail et al 1999). Thus, we should study the break appearing in the light curve further to take both beaming and dense environment effects into account.…”

“…If its radiation is isotropic, the radiation energy only in γ-rays is already as high as E γ ∼ 3.4 × 10 54 ergs, closely equals two solar rest energy (E γ ≈ 2M ⊙ c 2 )! As the typical mass of the stellar object is in the order of ∼ 1M ⊙ , while the radiation efficiency for the total energy converting into the γ-ray emission is usually very low, such a high emission energy is very difficult to understand (Wang, Dai & Lu 1999a).…”