Dynamic alternative DNA structures in biology and disease

Wang, Guliang; Vásquez, Karen M.

doi:10.1038/s41576-022-00539-9

Cited by 91 publications

(54 citation statements)

References 331 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2e), 77.04% and 84.63% have no GATC sites, respectively. Among the 22.96% and 15.37% of reads with at least one GATC sites, the majority (17.33% and 11.99% respectively) of GATC sites are located within genomic regions with simple sequence repeats (see Methods) that tend to form secondary structure, making it less accessible to DpnII digestion 54, 55 . This characterization illustrates that mEnrich-seq not only enriches bacterial taxa of interest, but also carries some by-product reads that are either due to methylation at (partially) overlapping motif sites in background taxa, or depleted restriction motifs in a subset of gDNA molecules.…”

Section: Resultsmentioning

confidence: 99%

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Cao

Kong

Fan

et al. 2022

Preprint

View full text Add to dashboard Cite

Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that can sequence specific bacterial taxa of interest (pathogens, beneficial microbes, or low-abundance taxa), but not the vast background of other taxa in a microbiome sample. To address this need, we developed mEnrich-seq, a method that can enrich taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self vs. non-self genome differentiation provided by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes (REs), individually or in combination, to deplete host DNA and most background microbial DNA while enriching bacterial taxa of interest. This core idea is integrated with library preparation procedures in a way that only non-digested DNA libraries are sequenced. We performed in-depth evaluations of mEnrich-seq and demonstrated its use in several applications to enrich (up to 117-fold) genomic DNA of pathogenic or beneficial bacteria from human urine and fecal samples, including several species that are hard to culture or of low abundance. We also assessed the broad applicability of mEnrich-seq and found that 3130 (68.03%) of the 4601 strains with mapped methylomes to date can be targeted by at least one commercially available RE, representing 54.78% of the species examined in this analysis. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest directly from the microbiome.

show abstract

Section: Resultsmentioning

confidence: 99%

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Cao

Kong

Fan

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Indeed, G4s can boast of being at the very heart of special attention for two decades now. However, accumulating evidence now shows that other higher-order nucleic acid structures deserve to be granted such a special treatment: this includes i-motifs, R-loops, triplex-DNA, and DNA junctions, for which ligands and protocols have been yet to be devised, but not in a finely orchestrated manner (as G4s were), which has somewhat dampened the advance of these investigations. Let us wager that the coming years will deliver fascinating advances in these areas, which will undoubtedly find multiple applications in the field of genetics and genetic diseases.…”

Section: Discussionmentioning

confidence: 99%

Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology

Monchaud

2023

Acc. Chem. Res.

View full text Add to dashboard Cite

Metrics & MoreArticle Recommendations CONSPECTUS: Biomimetics is defined as a "practice of making technological design that copies natural processes", with the idea that "nature has already solved the challenges we are trying to solve" (Cambridge Dictionary). The challenge we decided to address several years ago was the selective targeting of G quadruplexes (G4s) by small molecules (G4 ligands). Why? Because G4s, which are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences, are suspected to play key biological roles in human cells and diseases. Selective G4 ligands can thus be used as small-molecule modulators to gain a deep understanding of cell circuitry where G4s are involved, thus complying with the very definition of chemical biology (Stuart Schreiber) applied here to G4 biology. How? Following a biomimetic approach that hinges on the observation that G4s are stable secondary structures owing to the ability of Gs to self-associate to form G quartets, and then of G quartets to self-stack to form the columnar core of G4s. Therefore, using a synthetic G quartet as a G4 ligand represents a unique example of biomimetic recognition of G4s.We formulated this hypothesis more than a decade ago, stepping on years of research on Gs, G4s, and G4 ligands. Our approach led to the design, synthesis, and use of a broad family of synthetic G quartets, also referred to as TASQs for template-assembled synthetic G quartets (John Sherman). This quest led us across various chemical lands (organic and supramolecular chemistry, chemical biology, and genetics), along a route on which every new generation of TASQ was a milestone in the growing portfolio of ever smarter molecular tools to decipher G4 biology. As discussed in this Account, we detail how and why we successively develop the very first prototypes of (i) biomimetic ligands, which interact with G4s according to a bioinspired, like−likes−like interaction between two G quartets, one from the ligand, the other from the G4; (ii) smart ligands, which adopt their active conformation only in the presence of their G4 targets; (iii) twice-as-smart ligands, which act as both smart ligands and smart fluorescent probes, whose fluorescence is triggered (turned on) upon interaction with their G4 targets; and (iv) multivalent ligands, which display additional functionalities enabling the detection, isolation, and identification of G4s both in vitro and in vivo. This quest led us to gather a panel of 14 molecular tools which were used to investigate the biology of G4s at a cellular level, from basic optical imaging to multiomics studies.

show abstract

“…[7,8] Additionally, triple-helical DNA, which is formed when purines pair simultaneously from both their WC and HS interfaces, is overrepresented in regulatory regions of chromosomes and has been implicated in various key biological processes. [9,10] Apart from its linear arrangement of nucleobases, genetic DNA thus exhibits a set of unique non-canonical conformations and shapes. These conformational variations in the DNA structure, extending beyond the typical double helix, have significant implications in the origins and progression of various diseases, as well as in the overarching process of biological evolution.…”

Section: Introductionmentioning

confidence: 99%

Folding Double‐Stranded DNA into Designed Shapes with Triplex‐Forming Oligonucleotides

Samanta

Mandrup

et al. 2023

Advanced Materials

View full text Add to dashboard Cite

The compaction and organization of genomic DNA is a central mechanism in eukaryotic cells, but engineered architectural control over double‐stranded DNA (dsDNA) is notably challenging. Here, long dsDNA templates are folded into designed shapes via triplex‐mediated self‐assembly. Triplex‐forming oligonucleotides (TFOs) bind purines in dsDNA via normal or reverse Hoogsteen interactions. In the triplex origami methodology, these non‐canonical interactions are programmed to compact dsDNA (linear or plasmid) into well‐defined objects, which demonstrate a variety of structural features: hollow and raster‐filled, single‐ and multi‐layered, with custom curvatures and geometries, and featuring lattice‐free, square‐, or honeycomb‐pleated internal arrangements. Surprisingly, the length of integrated and free‐standing dsDNA loops can be modulated with near‐perfect efficiency; from hundreds down to only six bp (2 nm). The inherent rigidity of dsDNA promotes structural robustness and non‐periodic structures of almost 25.000 nt are therefore formed with fewer unique starting materials, compared to other DNA‐based self‐assembly methods. Densely triplexed structures also resist degradation by DNase I. Triplex‐mediated dsDNA folding is methodologically straightforward and orthogonal to Watson‐Crick‐based methods. Moreover, it enables unprecedented spatial control over dsDNA templates.

show abstract

Dynamic alternative DNA structures in biology and disease

Cited by 91 publications

References 331 publications

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology

Folding Double‐Stranded DNA into Designed Shapes with Triplex‐Forming Oligonucleotides

Contact Info

Product

Resources

About