Reorganization of Self-Assembled DNA-Based Polymers Using Orthogonally Addressable Building Blocks

Taking advantage of the addressability and programmability of DNA/DNA non-covalent interactions we report here the rational design of orthogonal DNA-based addressable tiles that self-assemble into polymer-like structures that can be reconfigured and reorganized by external inputs. The different tiles share the same 5-nucleotide sticky ends responsible for self-assembly but are rationally designed to contain a specific regulator-binding domain that can be orthogonally targeted by different DNA regulator strands (activators and inhibitors). We show that by sequentially adding specific activators and inhibitors it is possible to re-organize in a dynamic and reversible way the formed polymer-like structures to display well-defined distributions: homopolymers made of a single tile, random polymers in which different tiles are distributed randomly and block structures in which the tiles are organized in segments.

Reorganization of Self-Assembled DNA-Based Polymers Using Orthogonally Addressable Building Blocks

Taking advantage of the addressability and programmability of DNA/DNA non-covalent interactions we report here the rational design of orthogonal DNA-based addressable tiles that self-assemble into polymer-like structures that can be reconfigured and reorganized by external inputs. The different tiles share the same 5-nucleotide sticky ends responsible for self-assembly but are rationally designed to contain a specific regulator-binding domain that can be orthogonally targeted by different DNA regulator strands (activators and inhibitors). We show that by sequentially adding specific activators and inhibitors it is possible to re-organize in a dynamic and reversible way the formed polymer-like structures to display well-defined distributions: homopolymers made of a single tile, random polymers in which different tiles are distributed randomly and block structures in which the tiles are organized in segments.

DNA bioelectric field: a futuristic bioelectric marker of cancer, aging and death – A working hypothesis

Telomeres are associated with the ends of DNA double strands. The lengths of the telomeres are controlled by the telomerase enzyme. The shortening of the telomeres is known to relate to aging. In cancers, telomere lengths are abnormally short. Telomeres could act as buffers shielding the part of DNA coding for the proteins. For cancer cells, germ cells and stem cells the length of the telomeres is not varying. There is an analogy with microtubules, which are highly dynamical and carry a longitudinal electric field, whose strength correlates with the microtubule length. Could sticky ends generate a longitudinal field along DNA double strand with strength determined by the lengths of the sticky ends? In the standard picture the flux of the longitudinal electric field would be proportional to the difference of the negative charges associated with the sticky ends. In TGD framework, DNA strands are accompanied by the dark analog of DNA with codons realized as 3-proton units at magnetic flux tubes parallel to DNA strands and neutralizing the negative charge of ordinary DNA except at the sticky ends. This allows considering the possibility that opposite sticky ends carry opposite charges generating a longitudinal electric field along the magnetic flux tube associated with the system. DNA/Telomere bioelectric field could serve as a novel bioelectric marker to be used for prognostic and diagnostic purposes in researches of cancer, aging, surgery grafts and rejuvenation. We propsed that DNA bioelectric field can be used as a futuristic bioelectric marker of cancer, aging and death.

Determinants of cyclization–decyclization kinetics of short DNA with sticky ends

Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.

Supramolecular assembly of DNA-constructed vesicles

The self-assembly of DNA hybrids with tetraphenylethylene sticky ends into vesicular architectures is demonstrated.

Determinants of cyclization-decyclization kinetics of short DNA with sticky ends

Cyclization of DNA with sticky ends is commonly used to construct DNA minicircles and to measure DNA bendability. The cyclization probability of short DNA (<150 bp) has a strong length dependence, but how it depends on the rotational positioning of the sticky ends around the helical axis is less clear. To shed light upon the determinants of the cyclization probability of short DNA, we measured cyclization and decyclization rates of ~100-bp DNA with sticky ends over two helical periods using single-molecule Fluorescence Resonance Energy Transfer (FRET). The cyclization rate increases monotonically with length, indicating no excess twisting, while the decyclization rate oscillates with length, higher at half-integer helical turns and lower at integer helical turns. The oscillation profile is kinetically and thermodynamically consistent with a three-state cyclization model in which sticky-ended short DNA first bends into a torsionally-relaxed teardrop, and subsequently transitions to a more stable loop upon terminal base stacking. We also show that the looping probability density (the J factor) extracted from this study is in good agreement with the worm-like chain model near 100 bp. For shorter DNA, we discuss various experimental factors that prevent an accurate measurement of the J factor.

DNA Origami as a Tool to Design Asymmetric Gold Nanostructures

DNA origami technology provides a versatile approach for the chemical assembly of gold nanostructures. In this study the bottom-up approach of self-assembly using DNA in the origami process has been successfully applied to arrange five AuNPs asymmetrically. The DNA origami templates were modified to have binding sites that were extended with sticky ends to facilitate the attachment of the AuNPs. With the help of thiol chemistry, the AuNPs which were covered with DNA complementary to the sticky ends introduced on the DNA origami surfaces, we were able to attach the nanoparticles to the designed sites. It was realized that there were slight differences in the designed distances and the determined ones which were accounted for potentially by the deposition of the structures on the grids for imaging. The structures were characterized with gel electrophoresis and TEM. This asymmetric arrangement has the potential of exhibiting plasmonic behavior and circular dichroism when light is incident on the structure.