Solution structure of 2',5' d(G4C4). Relevance to topological restrictions and nature's choice of phosphodiester links

Global challenges in microplastics: From fundamental understanding to advanced degradations toward sustainable strategies

Currently, the global production and usage of plastics have increased rapidly with the expansion of synthetic polymers. Since plastics' degradation processes are prolonged and thus microplastics (MPs) potentially persist for very long periods in the environment. To date, there is a need for knowledge on the relevance of different potential entry pathways and the number of MPs entering the environment via different routes. Despite the vast quantity of studies that have been undertaken, many unanswered issues remain about the environmental impacts of MPs. The real impacts on a population subjected to many MPs of different structure, dimensions, and shapes over a lifetime are still hard to elucidate. Significantly, MPs can accumulate toxic substances, such as persistent organic pollutants, on their material surface. Hence, it represents a potential concentrated source of environmental pollution or acts as a vector of toxic pollutants in the food chain's interconnection with some severe health implications. Herein, we mainly discussed the global challenges in MPs, including the current production and use status of plastics and their impact on the environment. Additionally, finding the degradation of tiny fragment plastics (MPs level) is essential to remove plastics altogether. Some of the approaches to methods, including biodegradation, physical degradation, physicochemical degradation, have been successfully reviewed. More importantly, the sustainable concepts of using microorganisms and photocatalysis for MPs' degradation have been successfully proposed and demonstrated.

Review on plastic wastes in marine environment - Biodegradation and biotechnological solutions

The marine plastic pollution has drastic effect on marine species. The importance in environmental issues increases the demand to develop a significant technology which does not burden the marine environment or marine life forms. To mitigate the foreseen problems of micro and nanoplastic contamination, different biotechnological solutions has to be considered. Microbial communities exposed to plastic contaminated sites can adapt and form dense biofilms on the plastic surface and produce active catalytic enzymes. These enzymes can be able to degrade the synthetic polymers. In view of their high catalytic activity, microbial enzymes can be applicable for the degradation of synthetic polymers. This review highlights the toxicity of micro and nanoplastics on marine organisms, biodegradation of plastics and futuristic research needs to solve the issues of plastic pollution in marine environment.

Structural insights into RNA duplexes with multiple 2΄-5΄-linkages

2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2΄-5΄-linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050-3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2΄-5΄-linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2΄-5΄-linkages in the same duplex. Our results show that the local structural perturbations caused by 2΄-5΄ linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2΄-5΄-linkages comparing to the native 3΄-5΄-linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2΄-5΄-linkages.

Unimolecular antiparallel G-quadruplex folding topology of 2′–5′-isoTBA sequences remains unaltered by loop composition

Unlike 3′–5′-linked TBA, the 2′–5′-linked isoTBA formed only unimolecular antiparallel G-quadruplexes independent of loop length.

Structural insights into the effects of 2'-5' linkages on the RNA duplex

The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2'-5' linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.

Functional isoDNA aptamers: modified thrombin binding aptamers with a 2'-5'-linked sugar-phosphate backbone (isoTBA)

The regioisomeric 3'-deoxy-2'-5'-linked thrombin binding DNA aptamers (isoTBAs) were chemically synthesized and their ability to form unimolecular anti-parallel G-quadruplexes in the presence of K(+) ions was evaluated. These modified sequences retain the function of the native thrombin binding aptamer (TBA), exhibit better stability against exonuclease and are capable of slowing down the process of blood clotting.

Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2'-5' linked oligonucleotides

2'-endo locked or frozen (S-type)/3'-endo locked or frozen (N-type) nucleoside analogues were synthesized. Conformational analysis based on (3)J(HH) and NOE measurements is presented which is further confirmed by X-ray crystal structural studies. 2'-5'isoDNA oligonucleotides (ON) were synthesized using these modified nucleoside analogues and UV-T(m) studies of the resultant 2'-5'isoDNA : RNA duplexes reflect the site- and sequence-dependent effects and confirm that the S-type sugar conformations were preferred over the N-type sugar geometry in such duplexes.

Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective

"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.

Solution structure and thermodynamics of 2',5' RNA intercalation

As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.