tag:blogger.com,1999:blog-37148773.post5619471378803407633..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: DNA Binding ProteinsLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-37148773.post-48369021830164307042012-09-25T05:30:04.188-04:002012-09-25T05:30:04.188-04:00Why do most of the non-specific DNA-binding protei...Why do most of the non-specific DNA-binding proteins interact with DNA primarily through electrostatic interactions, whereas site-specific DNA-binding proteins interact with DNA primarily through the formation of non-covalent bonds between amino acid side-chains in the protein and bases in the major groove of the DNA?vijay piduguhttps://www.blogger.com/profile/00104026518963411683noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9651702587715684762008-09-16T07:06:00.000-04:002008-09-16T07:06:00.000-04:00...we expect that random spurious transcription sh...<I>...we expect that random spurious transcription should be quite common.</I><BR/><BR/>Hmm - as a layperson, I'm wondering whether the eventual point will be a counter to the "It is transcribed, therefore it must be meaningful and not 'junk'" crowd.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34019274664291904892008-09-16T02:08:00.000-04:002008-09-16T02:08:00.000-04:00This is a great post. Larry, do you have reference...This is a great post. Larry, do you have references for papers that describe the experiments that were done to measure the binding constants? I'd love to read about them.James Thompsonhttps://www.blogger.com/profile/07357445761192070499noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22967747961070244982008-09-15T23:21:00.000-04:002008-09-15T23:21:00.000-04:00anonymous says,Fortunately, the initiation of tran...anonymous says,<BR/><BR/><I>Fortunately, the initiation of transcription is highly regulated by requiring multiple simultaneous binding events by several different proteins, not just one activator molecule, particularly in eukaryotic cells.</I><BR/><BR/>True, but I'm not addressing normal "highly" regulated transcription in tomorrow's posting. <BR/><BR/>Low levels of spurious transcription will occur whenever RNA polymerase binds to DNA and the probability is increased if there's an activator bound nearby. This will happen even when RNAP isn't at a promoter.<BR/><BR/>You seem to think that transcription initiation will only occur when multiple independent binding events occur simultaneously. That's not correct. Some transcription occurs when only one activator is bound and the probability of an initiation event increases when more factors bind.<BR/><BR/>It's a cumulative effect not an all-or-none effect.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18023223743748075452008-09-15T22:21:00.000-04:002008-09-15T22:21:00.000-04:00Fortunately, the initiation of transcription is hi...Fortunately, the initiation of transcription is highly regulated by requiring multiple simultaneous binding events by several different proteins, not just one activator molecule, particularly in eukaryotic cells. The initiation of replication is even more highly regulated, even in relatively genomically non-complex organisms like E. coli. Spurious initiation of DNA replication is generally a major disaster for the cell.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62433209206978904662008-09-15T21:12:00.000-04:002008-09-15T21:12:00.000-04:00Neat! I'm enjoying this...Lee <- Wonders if...Neat! I'm enjoying this...<BR/><BR/>Lee <- Wonders if there will be a test in a week or solee_merrillhttps://www.blogger.com/profile/08757197085138422700noreply@blogger.com