Phase separation of multivalent protein and RNA molecules underlies the biogenesis of biomolecular condensates such as membraneless organelles. In vivo, these condensates encompass hundreds of distinct types of molecules that typically organize into multilayered structures supporting the differential partitioning of molecules into distinct regions with distinct material properties. The interplay between driven (active) versus spontaneous (passive) processes that are required for enabling the formation of condensates with coexisting layers of distinct material properties remains unclear. Here, we deploy systematic experiments and simulations based on coarse-grained models to show that the collective interactions among the simplest, biologically relevant proteins and archetypal RNA molecules are sufficient for driving the spontaneous emergence of multilayered condensates with distinct material properties. These studies yield a set of rules regarding homotypic and heterotypic interactions that are likely to be relevant for understanding the interplay between active and passive processes that control the formation of functional biomolecular condensates.

https://www.pnas.org/content/pnas/116/16/7889.full.pdf

Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties.

A G-quadruplex (G4) is a well-known nucleic acid secondary structure comprising guanine-rich sequences, and has profound implications for various pharmacological and biological events, including cancers. Therefore, ligands interacting with G4s have attracted great attention as potential anticancer therapies or in molecular probe applications. To date, a large variety of DNA/RNA G4 ligands have been developed by a number of laboratories. As protein-targeting drugs face similar situations, G-quadruplex-interacting drugs displayed low selectivity to the targeted G-quadruplex structure. This low selectivity could cause unexpected effects that are usually reasons to halt the drug development process. In this review, we address the recent research on synthetic G4 DNA-interacting ligands that allow targeting of selected G4s as an approach toward the discovery of highly effective anticancer drugs.

/pdf/recent-progress-of-targeted-g-quadruplex-preferred-ligands-1ldw0jj82j.pdf

Recent Progress of Targeted G-Quadruplex-Preferred Ligands Toward Cancer Therapy

Molecular biology provides an inspiring proof-of-principle that chemical systems can store and process information to direct molecular activities such as the fabrication of complex structures from molecular components. To develop information-based chemistry as a technology for programming matter to function in ways not seen in biological systems, it is necessary to understand how molecular interactions can encode and execute algorithms. The self-assembly of relatively simple units into complex products1 is particularly well suited for such investigations. Theory that combines mathematical tiling and statistical-mechanical models of molecular crystallization has shown that algorithmic behaviour can be embedded within molecular self-assembly processes2,3, and this has been experimentally demonstrated using DNA nanotechnology4 with up to 22 tile types5-11. However, many information technologies exhibit a complexity threshold-such as the minimum transistor count needed for a general-purpose computer-beyond which the power of a reprogrammable system increases qualitatively, and it has been unclear whether the biophysics of DNA self-assembly allows that threshold to be exceeded. Here we report the design and experimental validation of a DNA tile set that contains 355 single-stranded tiles and can, through simple tile selection, be reprogrammed to implement a wide variety of 6-bit algorithms. We use this set to construct 21 circuits that execute algorithms including copying, sorting, recognizing palindromes and multiples of 3, random walking, obtaining an unbiased choice from a biased random source, electing a leader, simulating cellular automata, generating deterministic and randomized patterns, and counting to 63, with an overall per-tile error rate of less than 1 in 3,000. These findings suggest that molecular self-assembly could be a reliable algorithmic component within programmable chemical systems. The development of molecular machines that are reprogrammable-at a high level of abstraction and thus without requiring knowledge of the underlying physics-will establish a creative space in which molecular programmers can flourish.

/pdf/diverse-and-robust-molecular-algorithms-using-reprogrammable-4veea1esm5.pdf

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

At the Crossroads of Chemistry, Biology, and Materials: Structural DNA Nanotechnology

This article critically reviews the emerging field of DNA materials science, which is expected to add a new horizon to the conventional materials science landscape. The introduction provides a short overview on recent developments in the non-biological application of DNA and DNA science. We discuss the roles of DNA in photonics and optoelectronics, DNA-assisted preparation of inorganic nanoparticles and aggregates, and electrical and magnetic properties of DNA and their influence on nanoscience and technology. We also explore the potential applications of DNA in the development of innovative memory and communication devices. Self-assembly and new sensing technologies based on DNA are only briefly discussed, partly because of the many excellent published reviews on these subjects.

Materials science of DNA

以纳米材料研究为标志的纳米技术已掀起热潮,并已经深入到诸多学科,生物医学领域也是其中之一.作为生物大分子之一的脱氧核糖核酸(DNA)由于其独特的理化性质,使其在构建超分子方面成为非常有前景的纳米材料之一.本文就其在该领域的国内外研究进展综述如下.

王全立

Papers

DNA nanotechnology