High concentration of extracellular nucleotides suppresses cell growth via delayed cell cycle progression in cancer and noncancer cell lines.

Tumor necrosis frequently occurs in malignant tumors, showing rapid growth and invasion. This phenomenon is generally regarded as simple ischemic necrosis due to insufficient tumor vessels and blood supply. However, the necrotic tissue contains high amount of nuclear substances, DNA, and nucleoproteins that may affect the surrounding tumor cells by promoting or suppressing the tumor cell growth in vivo. This study focused on the effects of an externally administered water-soluble nuclear crude extract (SNE) containing nuclear protein and oligonucleotides on several human cancer and noncancer cell lines. The results demonstrated that the SNE suppressed cell growth in cancer and noncancer cells in vitro. Through the flow cytometry analysis of the nuclear DNA content, it was observed that the SNE increased and decreased cell proportion in the S and G2/M phases, respectively, thereby suggesting that the cell growth inhibition was due to cell cycle delay, and not due to apoptosis. These studies suggest that the high-concentration of extracellular nucleotides generated as a result of tumor necrosis and/or released from infiltrated neutrophils could suppress the growth of surrounding cancer and intrinsic cells, which provides us some insights into an alternative anticancer strategy for patients with highly malignant necrotic tumor.

Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles.

End-to-end intermolecular interaction between double-stranded DNAs grafted onto individual nanoparticles is regulated by terminal base pairing/unpairing triggered by the photo-isomerization of an azobenzene moiety inserted in the vicinity of the DNA terminal. This is the first example of highly reversible control of blunt-end stacking under both isothermal and isoionic-strength conditions.

Terminal-Specific Interaction between Double-Stranded DNA Layers: Colloidal Dispersion Behavior and Surface Force.

Double-stranded DNA-grafted nanoparticles (dsDNA-NPs) exhibit a unique dispersion behavior under high-salt conditions depending on the pairing status of their outermost base pairs (pairing or unpairing). The dsDNA-NPs having complementary (i.e., pairing) outermost base pairs spontaneously aggregate under high-salt conditions, but not when their outermost base pairs are mismatched (unpairing). In this study, we used colloidal probe atomic force microscopy to examine how the outermost base pairs affect the interaction between the dsDNA-grafted layers (dsDNA layers). To precisely assess the subtle structural differences in the dsDNA layers, we developed a method for the formation of a homogenous dsDNA layer on gold surfaces using hairpin-shaped DNAs. Homogenous dsDNA layers having complementary (G-C) or mismatched (C-C) outermost base pairs were grafted onto the surfaces of colloidal probes and gold substrates. Force-distance curves measured in an aqueous medium under high-salt conditions revealed that the surface forces between the dsDNA layers were bilateral in nature and were governed by the outermost base pairs. Between complementary outermost dsDNA layers, the surface force changed from repulsive to attractive with an increase in the NaCl concentration (10-1000 mM). The attraction observed under high-salt conditions was attributed to the site-specific interaction proceeded only between complementary dsDNA terminals, the so-called blunt-end stacking. In fact, between mismatched outermost dsDNA layers, the repulsive force was mostly dominant within the same NaCl concentration range. Our results clearly revealed that the pairing status of the outermost base pairs has significant implications for the surface forces between dsDNA layers, leading to the unique dispersion behavior of dsDNA-NPs.

Geometric effect on the photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside and pyrimidine base in DNA/RNA heteroduplex.

To clarify the geometric effect of the ultra-fast photocrosslinking reaction of photoreactive oligodeoxyribonucleotide containing 3-cyanovinylcarbazole nucleoside ((CNV)K) on uridine in complementary RNA strands, pseudouridine (Ψ), which is an isomer of uridine with a C5-C1' glycosidic bond, was introduced to the photocrosslink site of (CNV)K in complementary RNA instead of U. The photoreactivity of (CNV)K toward Ψ was two-fold lower than that of U, suggesting that the geometry between the vinyl moiety on (CNV)K and the reactive double bond in the pyrimidine base has a large affect on the photoreactivity of (CNV)K. Contrary to the case of U, the reactivity of the (CNV)K toward Ψ was decreased by the decrease of reaction temperature below the Tm of heteroduplex, suggesting that the flexible structure of the duplex is advantageous for the photocrosslinking reaction with Ψ, whose reactive double bond possesses unfavorable geometry for the photocrosslinking reaction with (CNV)K. These basic findings might contribute to the development of a geometry selective photocrosslinking reaction. This is the first example of a sequence specific photocrosslinking reaction toward Ψ, which is the most abundant posttranscriptionally modified nucleoside.