In an effort to resolve this discrepancy, we tried modifying the theory. We investigated how the distribution of the angles between adjacent base pairs of the double helix affects the cyclization efficiency. We found that only the incorporation of sharp kinks in the angle distribution provides the desired increase of the cyclization efficiency. We did not find a model, however, that fits all cyclization data for DNA fragments of different lengths. Therefore, we carefully reinvestigated the cyclization of 100-bp DNA fragments experimentally and found their cyclization efficiency to be in remarkable agreement with the traditional model of DNA bending. We also found an explanation for the discrepancy between our results and those of Cloutier and Widom.DNA bending ͉ DNA cyclization ͉ DNA flexibility ͉ DNA kinks T he flexibility of the DNA double helix is extremely important for its functioning and has been studied for nearly 50 years (reviewed in ref. 1). It is now generally accepted that the major mechanisms of DNA bending are the small fluctuations between the planes of adjacent base pairs (2). Correspondingly, DNA conformational properties are well described by the worm-like chain (WLC) model (3). Calculations based on this model accurately reproduce experimental data on hydrodynamic properties of DNA molecules (4-6), equilibrium distributions of topological states (7-12), and light and neutron scattering data on supercoiled DNA (13-16). One of the most impressive tests of the WLC model was the single-molecule measurement of DNA extension under the action of a force applied to the ends of the double helix (17). Initially, Bustamante and coworkers (17) tried to fit the experimental results by applying the theory for a freely jointed chain, the only theory being considered at that time, but found a large discrepancy between theoretical and experimental results for large extensions of the molecule. It was soon understood that the WLC model gives a different result in the case of large extensions. The force-extension dependence for the WLC was found to be in excellent agreement with the experimental data (18,19).Theoretical analysis and computations based on the WLC also accurately predict the cyclization efficiency of small DNA fragments, 200-350 bp in length (20-24). For even shorter fragments, this model predicts a very low efficiency of cyclization, and until recently, quantitative measurements of this efficiency had not been attempted. Therefore, it was a complete surprise when Cloutier and Widom (hereafter referred as CW) reported that DNA fragments of Ϸ100 bp in length are cyclized several orders of magnitude more efficiently than the current theory predicts (25). It is known, on the other hand, that microscopically different models of polymer chains can give similar or even identical results for many properties. So, even excellent agreement between a model prediction and a set of experimental data does not necessary mean that the model provides an adequate microscopic description of polymer flexibility. The d...

Viral infections continue to represent major challenges to public health, and an enhanced mechanistic understanding of the processes that contribute to viral life cycles is necessary for the development of new therapeutic strategies . Viperin, a member of the radical S-adenosyl-L-methionine (SAM) superfamily of enzymes, is an interferon-inducible protein implicated in the inhibition of replication of a broad range of RNA and DNA viruses, including dengue virus, West Nile virus, hepatitis C virus, influenza A virus, rabies virus and HIV. Viperin has been suggested to elicit these broad antiviral activities through interactions with a large number of functionally unrelated host and viral proteins. Here we demonstrate that viperin catalyses the conversion of cytidine triphosphate (CTP) to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP), a previously undescribed biologically relevant molecule, via a SAM-dependent radical mechanism. We show that mammalian cells expressing viperin and macrophages stimulated with IFNα produce substantial quantities of ddhCTP. We also establish that ddhCTP acts as a chain terminator for the RNA-dependent RNA polymerases from multiple members of the Flavivirus genus, and show that ddhCTP directly inhibits replication of Zika virus in vivo. These findings suggest a partially unifying mechanism for the broad antiviral effects of viperin that is based on the intrinsic enzymatic properties of the protein and involves the generation of a naturally occurring replication-chain terminator encoded by mammalian genomes.

Charge-reversal functional gold nanoparticles first prepared by layer-by-layer technique were employed to deliver small interfering RNA (siRNA) and plasmid DNA into cancer cells. Polyacrylamide gel electrophoresis measurements of siRNA confirmed the occurrence of the charge-reversal property of functional gold nanoparticles. The expression efficiency of enhanced green fluorescent protein (EGFP) was improved by adjuvant transfection with charge-reversal functional gold nanoparticles, which also had much lower toxicity to cell proliferation. Lamin A/ C, an important nuclear envelope protein, was effectively silenced by lamin A/C-siRNA delivered by charge-reversal functional gold nanoparticles, whose knockdown efficiency was better than that of commercial Lipofectamine 2000. Confocal laser scanning microscopic images indicated that there was more cy5-siRNA distributed throughout the cytoplasm for cyanine 5-siRNA/ polyethyleneimine/cis-aconitic anhydride-functionalized poly(allylamine)/polyethyleneimine/11-mercaptoundecanoic acid-gold nanoparticle (cy5-siRNA/PEI/PAH-Cit/PEI/MUA-AuNP) complexes. These results demonstrate the feasibility of using charge-reversal functional gold nanoparticles as a means of improving the nucleic acid delivery efficiency.Keywords gold nanoparticles; charge-reversal polyelectrolyte; drug delivery; layer-by-layer assembly; siRNA delivery Over the past decade, due to good biocompatibility, easy synthesis, monodispersity, and ready functionalization, gold nanoparticles have emerged as an attractive candidate for delivery of various payloads into cells, such as small drug molecules or large biomolecules, 1-5 such as DNA and siRNA. [6][7][8][9][10][11][12][13] The intracellular release could be triggered by glutathione (GSH), 3 pH, or external (e.g., light) stimuli. 1,4,[14][15][16][17] siRNA has emerged recently as a promising method for biological research and holds great potential for treatment of human * Address correspondence to liangxj@nanoctr.cn. ⊥ These authors contributed equally to this work. Supporting Information Available:Preparation process of charge-reversal polyelectrolyte-coated gold nanoparticles using layer-bylayer technique; TEM images of colloidal AuNPs after the coating steps; fluorescence microscope image of 293T cells transfected with DNA/PEI/PAH-Cit/PEI/MUA-AuNP complexes; and cell viability of HeLa cells treated with PEI/PAH-Cit/PEI/MUA-AuNPs and nucleic acid complexes by MTT assay. This material is available free of charge via the Internet at http://pubs.acs.org. [18][19][20] Nucleic acid was mostly loaded by gold nanoparticles through thiol linkages or electrostatic interaction with cationic gold nanoparticles. [6][7][8][9][10][11][12][13]21,22 Elbakry et al. first developed the PEI/siRNA/PEI-AuNP system to deliver siRNA into cells and knockdown the expression of target gene based on the self-assembly layer-by-layer technology. 11 PEI, which has strong escape capacity from the endosome due to its so-called "proton sponge" effect and is usually a gold standa...

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