G-quadruplex and duplex DNA binding studies of novel Ruthenium(II) complexes containing ascididemin ligands.

In this paper, three new Ruthenium(II) polypyridyl complexes containing ascididemin (ASC) as main ligand have been synthesized and characterized. Their interactions with different G-quadruplex (Htelo, c-myc and c-kit) (Htelo: human telomeric DNA, c-myc: cellular-myelocytomatosis viral oncogene, c-kit: oncogene c-kit promoter sequences) and duplex (ds26) DNA sequences were comparatively studied with the free ligand ASC by a series of spectroscopic techniques including UV-vis (ultraviolet-visible) spectroscopy, FID (fluorescent intercalator displacement) assay, and FRET (fluorescence resonance energy transfer) melting assay. Molecular docking studies were also performed to support the binding mode of the compounds with G-quadruplex DNA. Results indicated that [Ru(bpy)2ASC]·(PF6)2 (1), [Ru(phen)2ASC]·(PF6)2 (2), [Ru(tatp)2ASC]·(PF6)2 (3) (bpy = 2,2'­bipyridine, phen = 1,10­phenanthroline, tatp = 1,4,8,9­tetra­aza­triphenylene) and ASC can effectively bind G-quadruplex and duplex DNA and stabilization ability lies in the order 3 > 2 > 1 > ASC. Complex 3 was determined to be the most promising candidate for further in vitro studies and potential anticancer drug.

Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing.

To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.

Coordination polymer nanoparticles from nucleotide and lanthanide ions as a versatile platform for color-tunable luminescence and integrating Boolean logic operations.

Novel supramolecular coordination polymer nanoparticles (CPNs) were synthesized via the self-assembly of guanosine monophosphate (GMP) and lanthanide ions (Ln3+, including Tb3+, Eu3+ and Ce3+) in aqueous solution. These CPNs (GMP/Tb3+, GMP/Eu3+ and GMP/Ce3+) have an identical coordination environment but exhibit completely different luminescence properties responding to external stimuli such as dipicolinic acid (DPA), ethylene diamine tetraacetic acid (EDTA), pH and metal ions, which has inspired us to tune the emission color of the CPNs and perform multiple logic operations. Firstly, color-tunable luminescence from red to green can be easily achieved by modulating the doping ratio of Tb3+ and Eu3+ into GMP. Notably, trichromatic white light emitting CPNs can be successfully realized by simultaneously doping Tb3+, Eu3+ and Ce3+ into the host or just adjusting the pH of the solution. What's more, by employing GMP/Tb3+ CPNs as a logic operator, we have achieved the implementation of multilayered gate cascades (INH-INH, NOR-OR). When GMP/Eu3+ CPNs served as a logic operator, the logic elements can be integrated as another combinatorial gate (AND-INH). Moreover, by employing the red emission of Eu3+ and blue emission of GMP as the dual-output signal transducer, a set of parallel logic gates was established successfully. These results help elucidate the design rules by which simple logic can be integrated to construct cascaded logic gates and expand the applications of CPNs in light-emitting diode (LED) lamps and biological systems.

A RET-supported logic gate combinatorial library to enable modeling and implementation of intelligent logic functions.

Boolean logic gates integrate multiple digital inputs into a digital output. Among these, logic gates based on nucleic acids have attracted a great deal of attention due to the prospect of controlling living systems in the way we control electronic computers. Herein, by employing Thioflavin T (ThT) as a signal transducer, we integrated multiple components based on RET (a type of proto-oncogene) into a logic gate combinatorial library, including basic logic gates (NOR, INHIBIT, IMPLICATION), a single three-input NOR gate, and combinatorial gates (INHIBIT-OR, NOT-AND-NOR). In this library, gates were connected in series where the output of the previous gate was the input for the next gate. Subsequently, by taking advantage of the library, some intelligent logic functions were realized. Expectedly, a biocomputing keypad-lock security system was designed by sequential logic operations. Moreover, a parity checker which can identify even numbers and odd numbers from natural numbers was established successfully. This work helps elucidate the design rules by which simple logic can be harnessed to produce diverse and complex calculations by rewiring communication between different gates. Together, our system may serve as a promising proof of principle that demonstrates increased computational complexity by linking multiple logic gates together.

Ultrasensitive and universal fluorescent aptasensor for the detection of biomolecules (ATP, adenosine and thrombin) based on DNA/Ag nanoclusters fluorescence light-up system.

We report here an ultrasensitive strategy based on the recognition-induced conformational alteration of aptamer and fluorescence turn-on abilities of guanine-rich (G-rich) DNA sequence in proximity to silver nanoclusters for adenosine triphosphate (ATP), adenosine (A) and thrombin (TB) detection. Herein, we designed two tailored DNA sequences noted as complementary DNA (abbreviated as c-DNA) and signal probe DNA (abbreviated as s-DNA), respectively. c-DNA is designed as a special structure consisting of a sequence complementary to aptamer at the 3'-end and a guanine-rich DNA sequence at the 5'-end; s-DNA contains a cytosine-rich sequence responsible for Ag NCs templated synthesis at the 3'-end and a link sequence (part of aptamer) complementary to partial of the c-DNA at the 5'-end. In the presence of target, the aptamer associated with the target, resulting in the formation of duplex DNA (dsDNA), the DNA-Ag NCs thereafter could close to the guanine-rich sequence, leading to enhanced fluorescence signal readout. The widespread application of the sensing system is achieved success in the detection of three biomolecules. ATP, adenosine and thrombin in the range of 0.5-8.0 µM, 0.5-7.0 µM and 50-900 nM could be linearly detected with the detection limits of 91.6 nM, 103.4 nM and 8.4 nM, respectively. This label-free and turn-on fluorescent sensing system employing the mechanism proposed here turns out to be sensitive, selective, and convenient for the detection of biomolecules without washing and separation steps.