Biology subjects

Minev, D.

Publications and source records attributed to Minev, D..

3 recordsLinked to original sources

bioRxiv2022

Multi-micron crisscross structures from combinatorially assembled DNA-origami slats

Living systems achieve robust self-assembly across length scales. Meanwhile, nanofabrication strategies such as DNA origami have enabled robust self-assembly of submicron-scale shapes.However, erroneous and missing linkages restrict the number of unique origami that can be practically combined into a single supershape. We introduce crisscross polymerization of DNA-origami slats for strictly seed-dependent growth of custom multi-micron shapes with user-defined nanoscale surface patterning. Using a library of ~2000 strands that can be combinatorially assembled to yield any of ~1e48 distinct DNA origami slats, we realize five-gigadalton structures composed of >1000 uniquely addressable slats, and periodic structures incorporating >10,000 slats. Thus crisscross growth provides a generalizable route for prototyping and scalable production of devices integrating thousands of unique components that each are sophisticated and molecularly precise. One-sentence summaryCrisscross polymerization of DNA-origami slats can yield micron-scale structures with uniquely addressable nanoscale features.

synthetic biology↗

bioRxiv2019

Robust nucleation control via crisscross polymerization of DNA slats

Natural biomolecular assemblies such as actin filaments or microtubules polymerize in a nucleation-limited fashion1,2. The barrier to nucleation arises in part from chelate cooperativity, where stable capture of incoming monomers requires straddling multiple subunits on a filament end3. For programmable self-assembly from building blocks such as synthetic DNA4-23, it is likewise desirable to be able to suppress spontaneous nucleation24-31. However, existing approaches that exploit just a low level of cooperativity can limit spontaneous nucleation only for slow growth, near-equilibrium conditions32. Here we introduce ultracooperative assembly of ribbons densely woven from single-stranded DNA slats. An inbound "crisscross" slat snakes over and under six or more previously captured slats on a growing ribbon end, forming weak but specific half-duplex interactions with each. We demonstrate growth of crisscross ribbons with distinct widths and twists to lengths representing many thousands of slat additions. Strictly seed-initiated extension is attainable over a broad range of temperatures, divalent-cation concentrations, and free-slat concentrations, without unseeded ribbons arising even after a hundred hours to the limit of agarose-gel detection. We envision that crisscross assembly will be broadly enabling for all-or-nothing formation of microstructures with nanoscale features, algorithmic self-assembly, and signal amplification in diagnostic applications requiring extreme sensitivity.

synthetic biology↗

bioRxiv2019

Rapid and scalable in vitro production of single-stranded DNA

We present a rapid, scalable, user-friendly method for in vitro production of high-purity single-stranded DNA (ssDNA) ranging from 89-3315 nucleotides in length. PCR with a forward primer bearing a methanol-responsive polymer generates a tagged amplicon that enables selective precipitation of the modified strand under denaturing conditions. We demonstrate that the recovered ssDNA can be used for CRISPR/Cas9 homology-directed repair in human cells, DNA-origami folding, and fluorescent in situ hybridization.

molecular biology↗