DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC)

Non-G Base Tetrads

Tetrads (or quartets) are arrangements of four nucleobases commonly involved in the stability of four-stranded nucleic acids structures. Four-stranded or quadruplex structures have attracted enormous attention in the last few years, being the most extensively studied guanine quadruplex (G-quadruplex). Consequently, the G-tetrad is the most common and well-known tetrad. However, this is not the only possible arrangement of four nucleobases. A number of tetrads formed by the different nucleobases have been observed in experimental structures. In most cases, these tetrads occur in the context of G-quadruplex structures, either inserted between G-quartets, or as capping elements at the sides of the G-quadruplex core. In other cases, however, non-G tetrads are found in more unusual four stranded structures, such as i-motifs, or different types of peculiar fold-back structures. In this report, we review the diversity of these non-canonical tetrads, and the structural context in which they have been found.

A simple reagent-less approach using electrical discharge as a substitution for chelating agent in addressing genomic assay inhibition by divalent cations

Electrical discharge treatment was shown to be a viable substitution for chelating agent in genomic assays. Divalent cation Mg2+ inhibits the performance of DNA hybridization based genomic assays by binding to the DNA and disrupting DNA hybridization. Until now, chelating agents such as ethylenediaminetetraacetic acid (EDTA) was the only option to address the presence of Mg2+ in samples. However, EDTA is a well-known environmental contaminant. In this work, we successfully employed electrical discharge instead of EDTA to render Mg2+ insipid. Its preliminary efficacy was first observed via circular dichroism (CD) and zeta potential analyses. After electrical discharge treatment, the reduction in CD shift at 280 nm was significant for samples with 10-3 and 10-8 M Mg2+. The zeta potential of Mg2+ laden samples were also restored from -4.71 ± 1.38 to -20.59 ± 6.37 mV after electrical discharge treatment. Both CD shift and change in zeta potential suggested that 2 min of electrical discharge treatment could prevent Mg2+ from binding to DNA. The complete efficacy of electrical discharge treatment was demonstrated with the performance recovery (within ∼15% of the control) of a genomic assay variant (NanoGene assay) while analyzing Mg2+ laden samples (10-5-10-3 M). Assuming 10 million samples are analyzed annually, the proposed electrical discharge treatment (∼50 mW per sample) would allow us to trade environmental contamination by ∼50 kg of hazardous EDTA with a single 250 W STC (standard test conditions) solar panel.

Streptomyces IHF uses multiple interfaces to bind DNA

BACKGROUND

Nucleoid associated proteins (NAPs) are essential for chromosome condensation in bacterial cells. Despite being a diverse group, NAPs share two common traits: they are small, oligomeric proteins and their oligomeric state is critical for DNA condensation. Streptomyces coelicolor IHF (sIHF) is an actinobacterial-specific nucleoid-associated protein that despite its name, shares neither sequence nor structural homology with the well-characterized Escherichia coli IHF. Like E. coli IHF, sIHF is needed for efficient nucleoid condensation, morphological development and antibiotic production in S. coelicolor.

METHODS

Using a combination of crystallography, small-angle X-ray scattering, electron microscopy and structure-guided functional assays, we characterized how sIHF binds and remodels DNA.

RESULTS

The structure of sIHF bound to DNA revealed two DNA-binding elements on opposite surfaces of the helix bundle. Using structure-guided functional assays, we identified an additional surface that drives DNA binding in solution. Binding by each element is necessary for both normal development and antibiotic production in vivo, while in vitro, they act collectively to restrain negative supercoils.

CONCLUSIONS

The cleft defined by the N-terminal and the helix bundle of sIHF drives DNA binding, but the two additional surfaces identified on the crystal structure are necessary to stabilize binding, remodel DNA and maintain wild-type levels of antibiotic production. We propose a model describing how the multiple DNA-binding elements enable oligomerization-independent nucleoid condensation.

GENERAL SIGNIFICANCE

This work provides a new dimension to the mechanistic repertoire ascribed to bacterial NAPs and highlights the power of combining structural biology techniques to study sequence unspecific protein-DNA interactions.

Advances in the cellular structural biology of nucleic acids

Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.