There is considerable interest in developing progressively moving devices on the nanoscale, with the aim of using them as parts of programmable therapeutics, smart materials, and nanofactories. Present here is an entirely light‐induced DNA walker based on orthogonal photocontrol. Implementing two azobenzene derivatives, S‐DM‐Azo and DM‐Azo, enabled precise coordination of strand displacement reactions that powered a biped walker and guided it along a defined track in a non‐autonomous way. This unprecedented type of molecular walker design offers high precision control over the movement in back‐and‐forth directions as desired, and is regulated solely by the sequence of the irradiation wavelengths. This concept may open new avenues for advancing non‐autonomous progressive molecular motors, ultimately facilitating their application at the nanoscale.
Photoregulation is among the most promising tools for development of dynamic DNA nanosystems, due to its high spatiotemporal precision, biocompatibility, and ease of use. So far, azobenzene and its derivatives have shown high potential in photocontrolling DNA duplex hybridization by light-dependent photoisomerization. Despite many recent advances, obtaining sufficiently high photoswitching efficiency under conditions more suitable for work with DNA nanostructures are challenging. Here we introduce a pair of arylazopyrazoles as new photoswitches for efficient and reversible control of DNA hybridization achieved even at room temperature with a low number of required modifications. Their photophysical properties in the native state and in DNA strands result in near-quantitative isomerization rates by irradiation with UV and orange light. To demonstrate the applicability of these photoswitches, we have successfully applied one of them to open and close a DNA hairpin by light at room temperature.
A broad series of homochiral perylene bisimide (PBI) dyes were synthesized that are appended with amino acids and cationic side chains at the imide positions. Self-assembly behavior of these ionic PBIs has been studied in aqueous media by UV/Vis spectroscopy, revealing formation of excitonically coupled H-type aggregates. The interactions of these ionic PBIs with different ds-DNA and ds-RNA have been explored by thermal denaturation, fluorimetric titration and circular dichroism (CD) experiments. These PBIs strongly stabilized ds-DNA/RNA against thermal denaturation as revealed by high melting temperatures of the formed PBI/polynucleotide complexes. Fluorimetric titrations showed that these PBIs bind to ds-DNA/RNA with high binding constants depending on the number of the positive charges in the side chains. Thus, spermine-containing PBIs with six positive charges each showed higher binding constants (logKs =9.2-9.8) than their dioxa analogues (logKs =6.5-7.9) having two positive charges each. Induced circular dichroism (ICD) of PBI assemblies created within DNA/RNA grooves was observed. These ICD profiles are strongly dependent on the steric demand of the chiral substituents of the amino acid units and the secondary structure of the DNA or RNA. The observed ICD effects can be explained by non-covalent binding of excitonically coupled PBI dimer aggregates into the minor groove of DNA and major groove of RNA which is further supported by molecular modeling studies.
First published on the web Xth XXXXXXXXX 200X DOI:Among three novel DBTAA derivatives only DBTAA-propyl-adenine conjugate 1 showed recognition of the consecutive oligo dT sequence by increased affinity and specific induced chirooptical response in comparison to other single stranded RNA and DNA; whereby of particular 10 importance is up until now unique efficient differentiation between dT and rU. At variance, its close analogue DBTAA-hexyl-adenine 2 did not reveal any selectivity among ss-DNA/RNA pointing out to the important role of steric factors (linker length); moreover non-selectivity of the reference compound (3, lacking adenine) stressed the importance of adenine interactions in the 1 selectivity. 15 IntroductionBoth, DNA and RNA exhibit a wide range of structural topologies, among which different single stranded (ss-) sequences are quite numerous. While ss-sequences are ubiquitous part of the RNA folding landscape, there are fewer 20 observations of stable ss-DNA cases, such as hairpins 1 or abasic sites, 2 to name some of them. Since ds-DNA is protected from reaction with a number of chemical and biological nucleases, 3 many studies have been aimed at exploiting the vulnerable ss-DNA. A number of small 25 molecules were synthesized that bind specifically at abasic lesions with an idea to inhibit the DNA repair system and in that way pronounce the action of antitumor drugs. 4 Moreover, recently many research groups have explored the potential of the DNA as a template for arraying multichromophoric 30 systems, among which non-covalent ss-DNA-associated dyes attracted considerable attention. 5 Until now, aryl-nucleobase conjugates efficiently recognized complementary nucleobases by affinity increase, 4 Zn-cyclene derivatives showed highly selective interactions 35 with uracil and thymine caused by specific coordination of Zn with two keto-groups. 6 Very recently, abasic sites and single base bulges in DNA were efficiently recognized by metalloinsertors, 7 or small-ligand-immobilized biosensor was applied for detecting thymine-related single-nucleotide 40 polymorphisms (SNPs). 8 However, longer oligo-dT sequences were not specifically recognised until now, especially in respect to closely related uracil analogues. Within the last decade we showed that small modifications in structure of aryl-nucleobase conjugates can control their selectivity toward 45 various ss-and ds-polynucleotide sequences. 9 On the other hand, for the dibenzotetraaza [14]annulene (DBTAA) derivatives we recently showed that the interactions of side-chains can finely tune selectivity toward various DNA/RNA and consequently control their biological 50 activity. 10a Specific properties of the DBTAA moiety, such as larger aromatic surface than the most of until now used arylmoieties and pronounced out-of-plane flexibility, offered intriguing possibilities in design of novel aryl-nucleobase conjugates. The very last generation of DBTAA derivatives 55 showed high (sub-micromolar) DNA/RNA affinity and selectivity toward dA-d...
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