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Involvement of single‐nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user‐friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked‐eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild‐type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele‐specific single‐base primer extension and salt‐induced aggregation of DNA‐modified gold nanoparticles (DNA–AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA–AuNPs in gene diagnosis.

Self-assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl2 , spontaneous reduction of the interparticle distance is observed with TEM and cryo-electron microscopy. By contrast, when the terminal-mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA-functionalized nanoparticle assemblies.

A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.

Temperature-responsive diblock copolymers made of poly(N-isopropylacrylamide) (PNIPAAm) generated by reversible addition-fragmentation chain transfer (RAFT) polymerization and a single-stranded DNA (ssDNA) self-assembled into polymer micelles. The micelles consisted of the PNIPAAm core surrounded by the ssDNA corona with a hydrodynamic diameter up to 300 nm in an aqueous medium above the lower critical solution temperature. In a medium of high ionic strength, the formation of the fully matched duplex with the complementary ssDNA on the surface of the polymer micelles induced rapid and spontaneous aggregation. By contrast, the micelles remained dispersed under the identical conditions when single-base-substituted ssDNA was added to form the corresponding terminal-mismatched duplex on the micellar surface. This highly sequence-selective process took place irrespective of the size of the PNIPAAm core.

A technique for tuning interparticle distance in plasmonic gold nanoparticle (AuNP) assemblies has shown great potential for the development of optoelectronic nanodevices. However, it still remains a challenge to reversibly alter the distance in a facile manner. DNA-templated AuNP assemblies are among the mostly investigated plasmonic nanomaterials. In previous work, salt-induced structural shrinkage of DNA-templated AuNP (5 nm in diameter) dimers/trimers is demonstrated only by electron microscopic analyses. In the present study, interparticle distance is modulated in larger AuNP (15 nm or 20 nm in diameter) dimers that exhibit strong surface plasmon resonance (SPR). The reversible SPR shift is achieved by using the temperature-dependent shrinkage/extension of the DNA-templated AuNP dimers. The present proof-of-concept study suggests a potential application of the reversible structural change to optical switching.

Capillary electrophoretic separation of chemically synthesized ssDNA and a single-base-substituted one (normal and mutant ssDNA, respectively) was demonstrated using a PEG-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as an affinity ligand. When the base sequence of PEG-b-ODN was designed to be complementary to part of normal ssDNA including the base-substituted site, the electrophoretic mobility of normal ssDNA significantly decreased whereas that of mutant ssDNA slightly changed. Resolution of the separation strongly depended on the ODN length of the copolymer, the capillary temperature, and the Mg2+ concentration in the running buffer, indicating that the retardation of migration of normal ssDNA was induced by the reversible hybridization with PEG-b-ODN. It was found that the dissociation constant (K(d)) of the duplex between normal ssDNA and the affinity probe ODN should be smaller than 10(-6) M to achieve the good peak separation. In addition, we calculated the mobility of the complex (mu(C)) between normal ssDNA and PEG-b-ODN using a two-state model. The base sequence of affinity probe ODN appropriate to achieve the sufficient resolution will be predicted on the basis of the mu(C) and K(d )values.

Oligopeptides are efficiently hydrolyzed by Ce(IV) to the corresponding amino acids under mild conditions. The pseudo first-order rate constants for the hydrolysis of H-Gly-Phe-OH and H-Gly-Gly-OH at pH 7.0 and 50 degrees C are 3.5 x 10(-1) and 2.8 x 10(-1) h(-1), with [Ce(NH4)2(NO3)6]0=10mM (the half-lives are 2.0 and 2.5 h). The catalytic activity of the Ce(IV) is far greater than those of other lanthanide ions and non-lanthanide ions. No oxidative cleavage was observed under the reaction conditions. Catalytic turnover of the Ce(IV) was also evidenced. The hydrolysis is fast especially when the substrates have no metal-coordinating side chains. Tripeptides and tetrapeptides are hydrolyzed at the similar rates as the dipeptides. In the hydrolysis of tripeptides, the amide linkage near the N-terminus is preferentially hydrolyzed. Neither the N-carbobenzyloxy derivative nor the amide of H-Gly-Phe-OH is hydrolyzed to a measurable extent, showing that both the terminal amino group and the carboxylate are coordinated to the Ce(IV) ion. This complexation is further confirmed by 1H NMR spectroscopy. The Ce(IV) ion is therefore one of the most active catalysts for peptide hydrolysis.

Lanthanide ion-induced hydrolyses of methyl esters, ethyl esters, and amides of α-amino acids were systematically studied. In the hydrolysis of the alkyl esters, all the lanthanide ions are effective and the catalytic activities decrease in the order Ce(III), Nd(III) > Sm(III) > Eu(III) > Gd(III), Ce(IV) > Pr(III) > Dy(III), Tb(III), Er(III), Ho(III), Tm(III) > La(III), Lu(III), Yb(III). For the hydrolysis of the amides, however, the Ce(IV) ion is overwhelmingly more active than other lanthanide(III) and non-lanthanide ions. The results are interpreted in terms of the difference in the rate-limiting step for these two reactions. © 1998 John Wiley & Sons, Ltd.

The Front Cover picture shows a colorimetric single‐nucleotide polymorphism (SNP) genotyping method using spontaneous aggregation of DNA‐modified gold nanoparticles (DNA–AuNPs). Simple and rapid SNP genotyping of the human cytochrome P450 2C19 monooxygenase gene is reported. Allele‐specific single‐base primer extension using a fragment of the gene isolated from human hair roots, followed by salt‐induced aggregation of DNA–AuNPs, results in a rapid color change from red to blue or no color change, thereby allowing SNP discrimination by the naked eye. More information can be found in the Communication by T. Takarada and co‐workers on page 508 in Issue 6, 2016 (DOI: 10.1002/open.201600110).

A drop in melting point of 21.5°C is induced by the UV-photolytic trans→cis isomerization of the duplex formed between an oligonucleotide bearing two D-threoninol-tethered azobenzene moieties in the side chain and its complementary counterpart. On irradiation with visible light, the dissociated single-stranded oligonucleotides regenerate the duplex.

Highly sensitive and selective DNA detection has attracted extensive attention for its importance in clinical gene diagnosis. Recently, we developed a simple method for visually detecting single nucleotide mutation by using spontaneous aggregation of DNA-linked colloidal nanoparticles, which was prepared through the phase transition of the amphiphilic copolymer consisting of DNA as the hydrophilic part and thermo-responsive poly (N-isopropylacrylamide) as the hydrophobic part. Adding the complementary DNA into the nanoparticles dispersion, the nanoparticles aggregated rapidly by a non-crosslinking mechanism, based on the salting-out techniques. The aggregation of DNA-linked colloidal nanoparticles was induced by the duplex formation on their surfaces. The instabilization of the nanoparticles would be derived from the decrease of both electrostatic repulsion and entropic effect of the DNA strand tethered to the surfaces of nanoparticles. In contrast, the nanoparticles kept dispersing in the presence of the point-mutated DNA under the identical conditions. Moreover, we improved this method for detecting single nucleotide mutation of sample DNA longer than the DNA attached to the surfaces of the nanoparticles.

We have developed an affinity capillary electrophoresis for gene mutation assay. We show a method for separating a mixture of oligodeoxynucleotides having single-base difference using oligodeoxynucleotide-polyacrylamide conjugate. Because the conjugate behaved similarly to nonionic polyacrylamide in terms of migration rate, it can be used as a pseudoimmobilized affinity ligand in a polyacrylamide-coated capillary. Oligodeoxynucleotide having an oncogene sequence and a version with one base substituted were completely separated by this method. The magnesium-ion concentration was found to be a key factor in achieving efficient separation of oligodeoxynucleotides with the same chain length.