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Research paper : Development of novel chemical reagents for reliable genetic analyses (Y. Komatsu et al.)−5−Synthesiology - English edition Vol.4 No.1 (2011) rising in the new field. We feel it is important to continue R&D to seek new advantages to develop the technologies in the niche field, instead of simply ending with the licensing of the product.4.2 Labeling reagentIn the development of the first-generation amino linker, we found that the amino group close to the aromatic residue reacts efficiently with the target molecules. To extend this principle to other issues, we planned the development of a reagent that labels nucleic acids isolated samples. Since the amino-linker is a reagent related to probe modification, we aimed to construct the complementary relationship by developing a superior labeling reagent.To efficiently label DNA or RNA recovered from living samples, the binding efficiency of the reagents with nucleic acids is one of the important factors. While enzymes are useful for labeling of nucleic acids[6], the efficiency frequently depends on the target sequences. We thought that a labeling reagent could be a universally useful tool just like the amino linker, because it reacts with the “aldehyde groups” generated naturally or artificially in both DNA and RNA. Since there were already several marketed reagents labeling aldehydes, the developed product must have higher performance than the existing products. To obtain high reactivity to nucleic acid, we synthesized a reagent with linked aromatic group in proximity to the aminooxy group, which is known to react with the aldehyde group, using the know-how we obtained in developing the amino linker (the aromatic residue improves affinity to the nucleic acid) (Fig. 6). Since the incorporation of the hydrophobic group made the reagent poorly insoluble, we synthesized another compound which had a guanidino group of a positive charge. We expected the reagent molecule would not only increase the affinity to the negatively charged nucleic acid but also become water soluble. As a result of the reaction, the new labeling reagent with both the aromatic and the guanidino groups showed much higher reactivity to the aldehyde group in nucleic acid as compared with the commercially available reagent, and could sensitively detect aldehyde groups produced in the genomic DNA[7]. The reactivity can decrease the amounts of genes required for the analysis, and achieve highly sensitive gene detection. In addition, the synergetic effect of the aromatic and guanidino groups provided important findings for the creation of other functional molecules binding with nucleic acids. The patent was filed in 2007 for this product, and papers were presented at the academic societies in 2009. As a result, we received requests for samples from several research institutes, and its activity is under evaluation at this moment. We hope to have this labeling reagent used widely in society in the future.5 DiscussionSince the “progress of the research” and “patents” were major points in our R&D, we shall discuss them in detail.5.1 Progress of the researchThe research was started in the latter half of 2003, and the reagent went on worldwide sale by 2007. There were several factors for this realization. As described above, the realization of a chemical reagent used in biological analyses must not only cover wide-ranging research fields from organic chemistry to biosciences, but solve several issues including stability and cost. To achieve valuable effects within the limited budget and human resources, we thought that a development of some universal technology was necessary. Therefore, we selected the research of the amino-linker that was used “commonly” in several analyses. While this was a Fig. 5 Outline of the property of ssH-linkerThe deprotection speed of the hydrophobic protecting group and reaction to the amino group increased.Fig. 6 Schematic diagram of the reaction with labeling reagentThe + and – indicate the positively charged guanidino group and the negatively charged phosphodiester group, respectively. The AP site is a structure of damaged DNA lacking the nucleobase, and possesses the aldehyde group.High bonding efficiencyNH2HNHNDeprotection is easy and rapid purification is possibleBonding moleculeHydrophobic protecting groupDNA terminalssH-linkerH3COSNHHNONHOOOHNNHHNOOH2NOHNNH2n+- - - - BiotinHydrophilic interaction regionHydrophobic interaction regionNH2ONucleobaseAP siteDNA double strandn=0.1

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