An autobiographic conversation with Roger D Kornberg on his work on transcription regulation

Kornberg, Roger D.

doi:10.1038/sj.cdd.4402250

Cited by 4 publications

(3 citation statements)

References 22 publications

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“…An octameric complexo fh istone proteins binds and wraps~150 bp of duplex DNAi n an NCP structure,w hich then is further assembled into higher-order structures in the nucleus. [98,99] Since al arge portion of the eukaryotic genome is bound in these structures,w hich curvest he helix gently around the histone core,i ti sr elevant to ask whether CT can occur through histone-bound DNAt oa ffect genome-wide reactions. Using the DNA-intercalating [Rh(phi) 2 (bpy)] 3 + photooxidant tethered to DNAi nt he presenceand absence of histones,w eo bserved long-range oxidative damage to 5'guanine bases in 5'-GG-3' doubletsa nd 5'-GGG-3' triplets.…”

Section: Dna Charge Transport In Biology:i Nitial Observationsmentioning

confidence: 99%

Redox Signaling through DNA

O’Brien

Silva

Barton

2016

Israel Journal of Chemistry

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Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.

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Section: Dna Charge Transport In Biology:i Nitial Observationsmentioning

confidence: 99%

Redox Signaling through DNA

O’Brien

Silva

Barton

2016

Israel Journal of Chemistry

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“…7 However, besides the time/labor involvement and the production of large amounts of toxic organic wastes, most of the present chromatin extraction methods cannot preserve the native chromatin structure. [8][9][10][11][12] The formaldehyde xation process results in the cross-linking of proteins and these and other components contribute to impurities in the extraction, ascertained by mass spectrometry. 13,14 Further, in the conventional methods, chromatin is sheared into shorter fragments via either nuclease digestion or sonication to separate them from cell debris via centrifugation; 15,16 the heavy and large chromatin bers containing higher-order structures are precipitated and discarded with the cell debris.…”

Section: Introductionmentioning

confidence: 99%

A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin

Zhou

Irudayaraj

2015

Analyst

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Native chromatin contains valuable genetic, epigenetic and structural information. Though DNA and nucleosome structures are well defined, less is known about the higher-order chromatin structure. Traditional chromatin extraction methods involve fixation, fragmentation and centrifugation, which might distort the higher-order structural information of native chromatin. We present a simple approach to isolate native chromatin from cultured mammalian cells using salicylic acid coated magnetic nanoparticles (SAMNPs). Chromatin is magnetically separated from cell lysates without any filtration or high-speed centrifugation. The purified chromatin is suitable for the examination of histone modifications and other chromatin associated proteins as confirmed by western blotting analysis. The structure of chromatin was determined by confocal fluorescence microscopy, transmission electron microscopy (TEM) and atomic force microscopy (AFM). High-resolution AFM and TEM images clearly show a classical bead-on-a-string structure. The higher-order chromatin structure is also determined via electron microscopy. Our method provides a simple, inexpensive and an environmentally friendly means to extract native chromatin not possible before, suitable for both biochemical and structural analysis.

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“…The importance of ncRNAs was recognized by the award of the Nobel prize in 2006, and CDD had the honour of hosting the corresponding Nobel lectures. [4][5][6][7][8] In this issue, we focus more specifically on the role of miRs in differentiation and in cell death.…”

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confidence: 99%