Determinants of DNA Quadruplex Structural Type:  Sequence and Potassium Binding

Abstract

There are DNA sequences which adopt the same quadruplex structural type in the presence of sodium as in the presence of sodium and potassium. There are also sequences that appear to have a requirement for the presence of potassium for the adoption of a particular quadruplex structural type. Information about the basis for these potassium effects has been obtained by examining the structures of a set of DNAs with differing numbers of loop residues and different lengths of runs of dG residues in the presence of sodium alone and in the presence of potassium and sodium. On the basis of the results, obtained primarily via solution-state NMR, it appears that very small loops favor parallel stranded quartet structures which do not require the presence of potassium. DNAs with loops of two to four residues and runs of two dG residues can form quadruplex structures of the "edge" or "chair" type in the presence of potassium but not in the presence of sodium alone. When all of the loops contain four residues, a "crossover" or "basket" type structure can be formed in the presence of sodium as well as in the presence of sodium and potassium. Structures with runs of three or four dG residues and with loops from two to four residues can form basket or crossover type structures in the absence of potassium. The presence of a purine in a loop can block both potassium binding and formation of chair type structures. Modeling of the interactions of cations with these quadruplex structures indicates that the potassium ions required for chair type structures interact with a terminal quartet and residues in the adjacent loop.

Pb EXAFS Studies on DNA Quadruplexes: Identification of Metal Ion Binding Site

“…To investigate this difference further, we carried out EXAFS measurements on an analogue of TBA in which A replaced all T residues in the two -TT-loops. As can be seen in Figure 5, this sequence, TBAA, shows no sign of folding in the presence of KCl, consistent with previous reports that a single A substitution in one of these loops prevents folding in the presence of K + (14). In the presence of Pb 2+ , however, TBAA folds with little difficulty, exhibiting a CD spectrum similar to that of Pb 2+ -TBA, also illustrated in Figure 5.…”

“…This contrasts with the proposed strong binding site for K + in the K + -TBA complex, located between the two -TT-loops and the adjacent quartet, with coordination to five or six of the available carbonyl oxygens from the surrounding thymine and guanine bases (14,15). To investigate this difference further, we carried out EXAFS measurements on an analogue of TBA in which A replaced all T residues in the two -TT-loops.…”

Inhibitors of TLR-9 Act on Multiple Cell Subsets in Mouse and Man In Vitro and Prevent Death In Vivo from Systemic Inflammation

“…The structure and stability of these tetraplex ODNs are influenced by surrounding sequence composition, ODN concentration, and the nature and concentration of monovalent cations, such as sodium and/or potassium, in the ODN diluent (20,21). Evaluation of 2088 and most other G4-containing IRS dissolved in PBS by SEC, a method previously shown to be able to resolve G-tetrad and monomeric G4-containing ODNs (22,23), showed the presence of two distinct peaks (Fig.…”

Mechanism of Action of Novel Antiproliferative Oligonucleotides

“…As described above, DNA replication was assessed by BrdUrd incorporation, and a similar method was used to determine RNA synthesis. This method has been described previously (35,36) and involves detection of incorporated 5-bromouridine (BrU) by indirect immunofluorescent staining with a BrdUrd antibody (which is cross-reactive for BrU). To ensure that the BrU staining represents bona fide RNA synthesis, we carried out a preliminary experiment to assess the effects of treatment with RNase or actinomycin D, an inhibitor of RNA synthesis.…”

“…Immunofluorescent staining of incorporated bromodeoxyuridine (BrdU) or bromouracil were used to assess, respectively, DNA and RNA synthesis. Protein synthesis was determined by incorporation of 35 S-methionine. The results showed that DNA replication (incorporation of BrdU) was undetectable at a timepoint when RNA and protein synthesis were still ongoing.…”