Improved measurement of absolute mRNA quantity without reverse transcription.

Gene expression studies using microarrays have provided important insights into understanding the mechanisms of transcriptional regulation in a variety of biological and disease phenomena. In a previous study, we developed Photo-DEAN, a universal-microarray-based RNA quantification method that enabled reverse transcription-free multiplex measurement of the absolute amount of RNA. Photo-DEAN promotes high-throughput and bias-less transcriptome analysis without the need for common controls or additional complicated normalization steps.

Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA.

The construction of a protocell from a materials point of view is important in understanding the origin of life. Both self-reproduction of a compartment and self-replication of an informational substance have been studied extensively, but these processes have typically been carried out independently, rather than linked to one another. Here, we demonstrate the amplification of DNA (encapsulated guest) within a self-reproducible cationic giant vesicle (host).

Experiments and simulation models of a basic computation element of an autonomous molecular computing system.

Autonomous DNA computers have been attracting much attention because of their ability to integrate into living cells. Autonomous DNA computers can process information through DNA molecules and their molecular reactions. We have already proposed an idea of an autonomous molecular computer with high computational ability, which is now named Reverse-transcription-and-TRanscription-based Autonomous Computing System (RTRACS).

Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine.

Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer.

Morphological change of a liposome induced by an oligonucleotide tagged with lipophilic unit.

We synthesized a conjugate molecule which consisted of DNA, cholesterol, and poly(ethylene glycol) as a spacer. When DNA duplex containing this simple conjugate was added to a liposome solution, interestingly, a pearling transformation of the liposome was observed. Such a morphological change of the liposome is required in the study of synthesizing an artificial cellular life, because the cell division is one of the essential characteristic of the life system.

DNA polymerization on the inner surface of a giant liposome for synthesizing an artificial cell model.

We have designed a new artificial cell model consisting of a giant liposome, an enzyme, and DNA conjugated with a cholesterol tag by a poly(ethylene glycol) spacer to characterize the model system. The cholesterol tag of the conjugated molecule was anchored to the inner surface of the giant liposome and the single-stranded DNA unit hybridized with a 100-mer template DNA that was added to the water pool inside the liposome. We found that the DNA unit acted as a primer, DNA polymerization proceeded on the inner surface of the liposome.

A new route to 2'-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives.

Oligonucleotides containing 2-thiouridine (s2U) in place of uridine form stable RNA duplexes with complementary RNAs. Particularly, this modified nucleoside has proved to recognize highly selectively adenosine, the genuine partner, without formation of a mismatched base pair with the guanosine counterpart. In this paper, we describe new methods for the synthesis of 2-thiouridine and various 2'-O-alkyl-2-thiouridine derivatives.

Synthesis and properties of 2'-O-alkylated 2-thiouridine derivatives and oligonucleotides containing 2'-O-alkylated 2-thiouridine derivatives.

Oligonucleotides containing 2-thiouridine form stable RNA duplexes with complementary RNAs and show high selectivity in the base pair recognition. Moreover, alkylation of the 2'-hydroxyl group provides new insight into developments of new antisense RNAs capable of formation of more stable duplexes with target RNAs. Oligonucleotides having such properties are desirable as agents for the antisense strategy and SNPs analysis.