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5 TCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACT 3 Upstream element 35 sequence 10 sequence First base transcribed
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Transcription Figure 10.8
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Promoter of the Escherichia coli ribosomal RNA gene, rrnB. Note the 10 and 35 sequences and the upstream element. The rst base transcribed (the transcriptional start site) is noted ( 1), as well as the upstream, downstream, and transcription directions. (Data from W. Ross, et al., 1993. Science 262:1407.)
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III. Molecular Genetics
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10. Gene Expression: Transcription
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Gene Expression: Transcription
BOX 10.1
he overwhelming evidence that molecular events, such as transcription, take place comes from genetic and biochemical analyses and occasionally an electron micrograph of one type or another ( g. 1). Thus, it is refreshing and illuminating to be able to observe some of the processes we know are taking place in real time; that is, to sit at a microscope and actually see these events happen. Such a study on transcription was published in 1991 in Nature by four scientists at Washington University in St. Louis.
Experimental Methods
Observing Transcription in Real Time
Although new methods of microscopy are being developed, normally we cannot see these molecular events taking place; the components are too small. Making them visible in electron microscopes usually re-
quires xation that destroys the ability of the components to actually continue their tasks. The Washington University group overcame this by attaching a gold particle to DNA, thus rendering the motion of that DNA visible under the light microscope ( g. 2). The scientists immobilized the RNA polymerase to a glass coverslip; thus, as transcription took place, the DNA moved and the length of the tether of the gold particle increased. At rst they stopped the process by limiting the concentration of nucleoside triphosphates (NTPs). They
Visualizing transcription. Image of DNA before (a) and after (b) E. coli RNA polymerase (bright oblong object in b) binds to a promoter. Pictures are by scanning force microscopy, a new laser technique that images molecules in water. Image sizes are 300 by 300 nm. Dark brown represents substrate level; the highest point is white at about 10 nm high. Intermediate colors represent intermediate heights. (Courtesy of Martin Guthold and
Carlos Bustamante, Institute of Molecular Biology and HHMI, University of Oregon.)
heat shock. We discuss heat shock proteins and other systems of transcriptional control in chapters 14 and 16. From mutational studies of promoters and the proteins in the RNA polymerase holoenzyme, we now have a picture of a holoenzyme that sets down on a DNA promoter because the sigma factor recognizes the 10 and 35 elements, the proteins recognize the UP element, and the and subunits recognize proteins bound to various other upstream elements, when present ( g. 10.9a). This initiation complex is initially referred to as a closed complex because the DNA has not melted, which is the next step in transcription initiation ( g. 10.9b). After the transcription of 5 10 bases, the sigma factor is released ( g. 10.9c and d ). About seventeen base pairs of DNA are opened, and as transcription proceeds, about twelve bases of RNA
form a DNA-RNA duplex at the point of transcription. Some of this information comes from studies with potassium permanganate (KMnO4), which modi es DNA bases that are single-stranded but not double-stranded. Thus, the lengths of melted DNA can be determined experimentally. Also used is the technique of photocrosslinking, in which two moieties such as DNA and one or two proteins are caused to be permanently crosslinked, verifying their close contact. This is done by attaching a chemical crosslinking element to one of the moieties and then causing crosslinking to occur by shining light, usually ultraviolet, on the mixture. Transcription, like DNA replication, always proceeds in the 5 3 direction. That is, a single base is added de novo and then new RNA nucleotides are added to the 3 -OH free end, as in DNA replication. However, unlike
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