Laser-Synthesized Germanium Nanoparticles as Biodegradable Material for Near-Infrared Photoacoustic Imaging and Cancer Phototherapy

Biodegradable nanomaterials can significantly improve the safety profile of nanomedicine. Germanium nanoparticles (Ge NPs) with a safe biodegradation pathway are developed as efficient photothermal converters for biomedical applications. Ge NPs synthesized by femtosecond-laser ablation in liquids rapidly dissolve in physiological-like environment through the oxidation mechanism. The biodegradation of Ge nanoparticles is preserved in tumor cells in vitro and in normal tissues in mice with a half-life as short as 3.5 days. Biocompatibility of Ge NPs is confirmed in vivo by hematological, biochemical, and histological analyses. Strong optical absorption of Ge in the near-infrared spectral range enables photothermal treatment of engrafted tumors in vivo, following intravenous injection of Ge NPs. The photothermal therapy results in a 3.9-fold reduction of the EMT6/P adenocarcinoma tumor growth with significant prolongation of the mice survival. Excellent mass-extinction of Ge NPs (7.9 L g-1 cm-1 at 808 nm) enables photoacoustic imaging of bones and tumors, following intravenous and intratumoral administrations of the nanomaterial. As such, strongly absorbing near-infrared-light biodegradable Ge nanomaterial holds promise for advanced theranostics.

Variations in the length of poly-C and poly-T tracts in intron 3 of the human ferrochelatase gene

The third intron of human ferrochelatase (FECH) gene contains according to NCBI, a poly-C (11) and a poly-T (24) tracts which are located approximately 900 bp upstream from the known splice modulating SNP IVS3-48 c/t. Ferrochelatase catalyses the last step in heme biosynthesis and a deficiency of this enzyme results in the hereditary disorder of erythropoietic protopoprhyria (EPP). During the course of mutation analysis in the FECH gene among EPP patients, we observed variations in the length of the poly-C and poly-T tracts. To study these variations, we analyzed a total of 54 individuals of Swiss and Israeli origins. Among them, 37 were control subjects (23 individuals with the genotype t/t and 14 with the genotype c/t), 10 were unrelated EPP patients (genotype c/M) and 7 were unrelated asymptomatic mutation carriers (genotype t/M). The length of poly-C tract varied from 10 to 16, that of poly-T tract from 22 to 24 in the study cohort. Statistic analysis showed that the low-expressed FECH allele (IVS3-48c) is associated with poly-C12, C13 and C15 and poly-T22. In addition, the segregation of poly-C and poly-T tracts was studied in two Israeli EPP families. Instabilities, as seen by both insertion and deletion of one nucleotide between two generations, were observed only in the poly-T tract. The function of the poly-C and poly-T tracts are yet to be explored.

Identification of a recurrent mutation in the protoporphyrinogen oxidase gene in Swiss patients with variegate porphyria: clinical and genetic implications

Variegate porphyria (VP), one of the acute hepatic porphyrias, results from an autosomal dominantly inherited deficiency of protoporphyrinogen oxidase (PPOX), the seventh enzyme in heme biosynthesis. Affected individuals can develop both cutaneous symptoms and potentially life-threatening neurovisceral attacks. Thirty unrelated VP index patients and families are currently known in the Swiss Porphyrin Reference Laboratory in Zürich. In 16 of a total of 24 genetically tested families, we detected a recurrent mutation in the PPOX gene, designated 1082-1083insC, reflecting a prevalence of 67%. Haplotype analysis revealed that 1082-1083insC arose on a common genetic background and, thus, represents a novel founder mutation in the Swiss population. Knowledge on the carrier status within a family does not only allow for adequate genetic counseling but also for prevention of the potentially life-threatening acute porphyric attacks. Hence, future molecular screening in Swiss VP patients might be facilitated by first seeking for mutation 1082-1083insC.

Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions—An NMR Structure and Hydration Study

The introduction of a North-type sugar conformation constrained oxetane T block, 1-(1',3'-O-anhydro-beta-D-psicofuranosyl) thymine, at the T(7) position of the self-complementary Dickerson-Drew dodecamer, d[(5'-C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12)-3')](2), considerably perturbs the conformation of the four central base pairs, reducing the stability of the structure. UV spectroscopy and 1D NMR display a drop in melting temperature of approximately 10 degrees C per modification for the T(7) oxetane modified duplex, where the T(7) block has been introduced in both strands, compared to the native Dickerson-Drew dodecamer. The three dimensional structure has been determined by NMR spectroscopy and has subsequently been compared with the results of 2.4 ns MD simulations of the native and the T(7) oxetane modified duplexes. The modified T(7) residue is found to maintain its constrained sugar- and the related glycosyl torsion conformations in the duplex, resulting in staggered and stretched T(7).A(6) and A(6).T(7) non-linear base pairs. The stacking is less perturbed, but there is an increased roll between the two central residues compared to the native counterpart, which is compensated by tilts of the neighboring base steps. The one dimensional melting profile of base protons of the T(7) and T(8) residues reveals that the introduction of the North-type sugar constrained thymine destabilizes the core of the modified duplex, promoting melting to start simultaneously from the center as well as from the ends. Temperature dependent hydration studies by NMR demonstrate that the central T(7).A(6)/A(6).T(7) base pairs of the T(7) oxetane modified Dickerson-Drew dodecamer have at least one order of magnitude higher water exchange rates (correlated to the opening rate of the base pair) than the corresponding base pairs in the native duplex.

Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern

The structural preorganization of isosequential ssDNA and ssRNA hexamers d/r(GAAAAC)(1) [J. Am. Chem. Soc. 2003, 125, 9948] have been investigated by NMR and molecular dynamics simulations. Analysis of the nuclear Overhauser effect spectrometry (NOESY) footprints in the aqueous solution has shown that there is a substantial population of ordered right-handed helical structure in both hexameric single-stranded DNA and RNA, which are reminiscent of their respective right-handed helical duplex form, despite the fact these single-stranded molecules are devoid of any intermolecular hydrogen bonds. The NMR-constrained molecular dynamics (1.5 ns) derived geometries of the adenine-adenine overlaps at each dinucleotide step of the hexameric ssDNA (1a) and ssRNA (1b) show that the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in 5' to 3' direction in ssDNA (1a) while, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA (1b). This also means that the pi-frame of the 5'-pyrimidine can interact with the relatively positively charged imino and amino protons in the 3' direction in ssRNA and in the 5' direction in ssDNA, thereby stabilizing the twist and slide observed in the stacked oligonucleotides. The differently preferred stacking geometries in ssDNA and ssRNA have direct physicochemical implications for self-assembly and pK(a) modulation by the nearest-neighbor interactions, as well as for the dangling-end stabilization effects and imino-proton reactivity.

Oxetane modified, conformationally constrained, antisense oligodeoxyribonucleotides function efficiently as gene silencing molecules

Incorporation of nucleosides with novel base-constraining oxetane (OXE) modifications [oxetane, 1-(1',3'-O-anhydro-beta-d-psicofuranosyl nucleosides)] into antisense (AS) oligodeoxyribonucleotides (ODNs) should greatly improve the gene silencing efficiency of these molecules. This is because OXE modified bases provide nuclease protection to the natural backbone ODNs, can impart T(m) values similar to those predicted for RNA-RNA hybrids, and not only permit but also accelerate RNase H mediated catalytic activity. We tested this assumption in living cells by directly comparing the ability of OXE and phosphorothioate (PS) ODNs to target c-myb gene expression. The ODNs were targeted to two different sites within the c-myb mRNA. One site was chosen arbitrarily. The other was a 'rational' choice based on predicted hybridization accessibility after physical mapping with self-quenching reporter molecules (SQRM). The Myb mRNA and protein levels were equally diminished by OXE and PS ODNs, but the latter were delivered to cells with approximately six times greater efficiency, suggesting that OXE modified ODNs were more potent on a molar basis. The rationally targeted molecules demonstrated greater silencing efficiency than those directed to an arbitrarily chosen mRNA sequence. We conclude that rationally targeted, OXE modified ODNs, can function efficiently as gene silencing agents, and hypothesize that they will prove useful for therapeutic purposes.