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Article
Open AccessSequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation
Mitochondrial transcription factor A (TFAM) employs DNA bending to package mitochondrial DNA (mtDNA) into nucleoids and recruit mitochondrial RNA polymerase (POLRMT) at specific promoter sites, light strand pr...
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Article
Open AccessStructures illustrate step-by-step mitochondrial transcription initiation
Transcription initiation is a key regulatory step in gene expression during which RNA polymerase (RNAP) initiates RNA synthesis de novo, and the synthesized RNA at a specific length triggers the transition to ...
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Article
Open AccessThe dynamic landscape of transcription initiation in yeast mitochondria
Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation comple...
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Article
Open AccessHDX-MS reveals dysregulated checkpoints that compromise discrimination against self RNA during RIG-I mediated autoimmunity
Retinoic acid inducible gene-I (RIG-I) ensures immune surveillance of viral RNAs bearing a 5’-triphosphate (5’ppp) moiety. Mutations in RIG-I (C268F and E373A) lead to impaired ATPase activity, thereby driving...
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Article
Open AccessHelicase promotes replication re-initiation from an RNA transcript
To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continu...
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Article
Open AccessDNA loo** mediates nucleosome transfer
Proper cell function requires preservation of the spatial organization of chromatin modifications. Maintenance of this epigenetic landscape necessitates the transfer of parental nucleosomes to newly replicated...
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Article
Open AccessT7 replisome directly overcomes DNA damage
Cells and viruses possess several known ‘restart’ pathways to overcome lesions during DNA replication. However, these ‘bypass’ pathways leave a gap in replicated DNA or require recruitment of accessory protein...
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Chapter
Fluorescent Methods to Study Transcription Initiation and Transition into Elongation
The DNA-dependent RNA polymerases induce specific conformational changes in the promoter DNA during transcription initiation. Fluorescence spectroscopy sensitively monitors these DNA conformational changes in ...
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Chapter
Helicase Unwinding at the Replication Fork
Ring-shaped hexameric helicases play an essential role of double-stranded DNA unwinding during genome replication. The NTPase-powered unwinding activity of the hexameric helicases is required both for replicat...
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Article
Structural basis of RNA recognition and activation by innate immune receptor RIG-I
The binding of helicase to viral RNA and the resulting activation of the retinoic acid inducible gene-I (RIG-I) are central to the innate immune response to viral infection. The structure of the RIG-I helicase...
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Article
ATP-induced helicase slippage reveals highly coordinated subunits
Most helicases — ubiquitous motor proteins that catalyse strand separation of base-paired nucleic acids — use ATP as an energy source. The hexameric helicase of T7 bacteriophage, the gene 4 protein, does not u...
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Article
One motor driving two translocases
In this issue, Wu et al. show that the RecBC helicase, which is involved in repairing double-strand DNA breaks, uses one ATPase motor to drive two translocases along opposite strands of DNA—much as an all-wheel d...
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Protocol
Experimental and Computational Analysis of DNA Unwinding and Polymerization Kinetics
DNA unwinding and polymerization are complex processes involving many intermediate species in the reactions. Our understanding of these processes is limited because the rates of the reactions or the existence ...
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Article
Steps in the right direction
The ring-shaped helicase enzyme Rho moves along RNA using ATP as an energy source. Coordinating ATP hydrolysis with nucleic-acid binding seems to determine the direction and mechanism of helicase movement.
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Article
Coordinating DNA replication by means of priming loop and differential synthesis rate
DNA is replicated by a replisome containing two polymerases that move unidirectionally, sythesizing DNA strands of opposite polarity. DNA synthesis on the leading and lagging strands therefore involves differe...
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Protocol
Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit
Regression analysis is indispensible for quantitative understanding of biological systems and for develo** accurate computational models. By applying regression analysis, one can validate models and quantify...
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Chapter
Viral Helicases
Helicases are motor proteins that use the free energy of NTP hydrolysis to catalyze the unwinding of duplex nucleic acids. Helicases participate in almost all processes involving nucleic acids. Their action is...
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Article
DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase
Helicases are molecular motors that use the energy of nucleoside 5′-triphosphate (NTP) hydrolysis to translocate along a nucleic acid strand and catalyse reactions such as DNA unwinding. The ring-shaped helicase1
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Article
A Brownian motor mechanism of translocation and strand separation by hepatitis C virus helicase
Helicases translocate along their nucleic acid substrates using the energy of ATP hydrolysis and by changing conformations of their nucleic acid–binding sites. Our goal is to characterize the conformational ch...
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Article
DNA is bound within the central hole to one or two of the six subunits of the T7 DNA helicase
Electron microscopic image analysis and protein–DNA crosslinking show that DNA binds asymmetrically to the hexameric bacteriophage T7 gp4b helicase, and binds to only one or two subunits
