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7,957 Newest Publications in nucleic acids research


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Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast

04-May-2018 | Hewawasam G, Dhatchinamoorthy K, Mattingly M, et al., Nucleic Acids Research, 2018

Nucleic Acids Research, gky169,


Visualizing structure-mediated interactions in supercoiled DNA molecules

19-Apr-2018 | Scott S, Xu Z, Kouzine F, et al., Nucleic Acids Research, 2018

Abstract We directly visualize the topology-mediated interactions between an unwinding site on a supercoiled DNA plasmid and a specific probe molecule designed to bind to this site, as a function of DNA supercoiling and temperature. The visualization relies on containing the DNA molecules within ...


Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity

19-Apr-2018 | Dolot R, Lam C, Sierant M, et al., Nucleic Acids Research, 2018

Abstract Thrombin-binding aptamer (TBA) is a DNA 15-mer of sequence 5′-GGT TGG TGT GGT TGG-3′ that folds into a G-quadruplex structure linked by two T-T loops located on one side and a T-G-T loop on the other. These loops are critical for post-SELEX modification to improve TBA target affinity. ...


Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations

17-Apr-2018 | Sharma A, Jiang C, De S., Nucleic Acids Research, 2018

Abstract Although the catalog of cancer-associated mutations in protein-coding regions is nearly complete for all major cancer types, an assessment of regulatory changes in cancer genomes and their clinical significance remain largely preliminary. Adopting bottom-up approach, we quantify the ...


The nonstop decay and the RNA silencing systems operate cooperatively in plants

17-Apr-2018 | Szádeczky-Kardoss I, Csorba T, Auber A, et al., Nucleic Acids Research, 2018

Abstract Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the ...


Multiple RPAs make WRN syndrome protein a superhelicase

14-Apr-2018 | Lee M, Shin S, Uhm H, et al., Nucleic Acids Research, 2018

Abstract RPA is known to stimulate the helicase activity of Werner syndrome protein (WRN), but the exact stimulation mechanism is not understood. We use single-molecule FRET and magnetic tweezers to investigate the helicase activity of WRN and its stimulation by RPA. We show that WRN alone is a ...


Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus

12-Apr-2018 | Miyazono K, Ishino S, Makita N, et al., Nucleic Acids Research, 2018

Abstract Because base deaminations, which are promoted by high temperature, ionizing radiation, aerobic respiration and nitrosative stress, produce mutations during replication, deaminated bases must be repaired quickly to maintain genome integrity. Recently, we identified a novel lesion-specific ...


Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif

10-Apr-2018 | Kawalek A, Bartosik A, Glabski K, et al., Nucleic Acids Research, 2018

Abstract ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in the separation of ori domains by binding to parS palindromes, mainly localized close to oriC. In Pseudomonas aeruginosa neither ParB deficiency nor modification of all 10 parSs is ...


RNA-splicing factor SART3 regulates translesion DNA synthesis

24-Mar-2018 | Huang M, Zhou B, Gong J, et al., Nucleic Acids Research, 2018

Abstract Translesion DNA synthesis (TLS) is one mode of DNA damage tolerance that uses specialized DNA polymerases to replicate damaged DNA. DNA polymerase η (Polη) is well known to facilitate TLS across ultraviolet (UV) irradiation and mutations in POLH are implicated in skin carcinogenesis. ...


Protein-mediated loops in supercoiled DNA create large topological domains

10-Mar-2018 | Yan Y, Ding Y, Leng F, et al., Nucleic Acids Research, 2018

Abstract Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria ...


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