Use of alternative alkali chlorides in RT and PCR of polynucleotides containing G quadruplex structures

Stable G-Quadruplex Structures of Oncogene Promoters Induce Potassium-Dependent Stops of Thermostable DNA Polymerase

Amplification of GC-rich regions of genomic DNA is hindered either by high stability of DNA double helix or as a result of alternative structure formation by a guanine-rich DNA strand. Such potential G-quadruplex (G4) sequences are fairly common in promoters of the human genome. The efficiency of PCR amplification of promoter sequences for several human oncogenes (MYC, NRAS, TERT, KRAS, KIT) was studied. We demonstrate that the efficiency of DNA polymerase is reduced in the presence of potassium ions. The primer-extension technique localized DNA polymerase stops at the 3'-ends of potential quadruplex sequences. The structural and thermodynamic properties of short G-rich oligonucleotides corresponding to the stops of DNA polymerase were analyzed. These oligonucleotides formed stable parallel G4 in the presence of potassium ions. Correlation between the stability of G4 structure and efficiency of DNA polymerase stops was revealed. The results provide a method for detecting new G4 structures in extended genomic sequences and also clarify the mechanism of inhibition of DNA polymerase in G-rich regions of DNA.

The Effects of Saline Stress on the Growth of Two Shrub Species in the Qaidam Basin of Northwestern China

Soil salinization is a serious issue in the Qaidam Basin and significantly limits economic development. To explore the salt tolerance of two shrubs in this area, we determined several parameters, including the Soil and Plant Analyzer Development (SPAD), net photosynthetic rate (Pn), transpiration rate (Tr), intercellular carbon dioxide (Ci, μmol mol−1), stomatal conductance (Gs, umol m−2s−1), and water use efficiency (WUE) under different salt concentrations (0, 100, 200, 300, and 400 mmol·L−1). In addition, the shrubs of Elaeagnus angustifolia and Lycium barbarum of salt tolerance were evaluated. The photosynthetic parameters of E. angustifolia were more sensitive to salinity than those of L. barbarum, and SPAD, Pn, Tr, and WUE of E. angustifolia decreased significantly with increasing salt concentrations (P < 0.05), while in L. barbarum, SPAD, Pn, and Tr decreased significantly with increasing salt concentrations (P < 0.05), but the WUE of L. barbarum showed no significantly variation under the salt concentration gradient. The results of correlation matrix of photosynthetic index also indicated that the minimum salt tolerance of E. angustifolia and L. barbarum were 108.4 and 246.3 mmol·L−1, respectively. Our results provide a scientific basis for the selection of salt-tolerant plant species in of northwest China.

Sequence Requirements of Intrinsically Fluorescent G-Quadruplexes

G-Quadruplexes are four-stranded nucleic acid structures typically stabilized by GGGG tetrads. These structures are intrinsically fluorescent, which expands the known scope of nucleic acid function and raises the possibility that they could eventually be used as signaling components in label-free sensors constructed from DNA or RNA. In this study, we systematically investigated the effects of mutations in tetrads, loops, and overhanging nucleotides on the fluorescence intensity and maximum emission wavelength of >500 sequence variants of a reference DNA G-quadruplex. Some of these mutations modestly increased the fluorescence intensity of this G-quadruplex, while others shifted its maximum emission wavelength. Mutations that increased the fluorescence intensity were distinct from those that increased the maximum emission wavelength, suggesting a trade-off between these two biochemical properties. The fluorescence intensity and maximum emission wavelength were also correlated with multimeric state: the most fluorescent G-quadruplexes were monomers, while those with the highest maximum emission wavelengths typically formed dimeric structures. Oligonucleotides containing multiple G-quadruplexes were in some cases more fluorescent than those containing a single G-quadruplex, although this depended on the length and sequence of the spacer linking the G-quadruplexes. These experiments provide new insights into the properties of fluorescent G-quadruplexes and should aid in the development of improved label-free nucleic acid sensors.

A topological transition from bimolecular quadruplex to G-triplex/tri-G-quadruplex exhibited by truncated double repeats of human telomere

Human telomeric G-rich sequences can fold back into various conformations depending upon the salt (Na⁺ or K⁺) at physiological pH. On the basis of results obtained by native PAGE electrophoresis, circular dichroism, and UV-melting experiments, we report here that truncated sequences of human telomere (d-GGGTTAGGG; GM9, d-AGGGTTAGGG; GM10, d-TAGGGTTAGGG; GM11) adopt a varied range of quadruplex conformations as a function of the cation present. By correlating CD and gel electrophoresis experiments; it was concluded that the GM9 oligonucleotide can self-associate to form a tetramer quadruplex (antiparallel; AP) in Na⁺ solution and a mixture of G-triplex (AP) or tri-G-quadruplex (parallel; P) along with a tetramer G-quadruplex structure (AP) in K⁺. The GM10 oligonucleotide formed a bimolecular G-quadruplex in both Na⁺ and K⁺ solutions, while GM11 associated to form a bimolecular G-quadruplex (AP) structure in Na⁺ solution and a mixture of bimolecular G-quadruplex (AP) and bimolecular G-quadruplex (P) along with parallel G-triplex or antiparallel tri-G-quadruplex in K⁺. All the UV-melting profiles, thermal difference spectra, and CD melting curves suggested the formation of a variety of G-quadruplex conformations by the DNA sequences studied in Na⁺ and K⁺ ions. Hypothetical models for different conformations adopted by these DNA molecules have also been proposed, which may further enhance our knowledge about the divergent topologies of guanine quadruplexes.