http://www.justachemblog.net/molecule-of-the-week-06/ notes, thoughts, and a little (science) culture while teaching chemistry Fri, 25 Dec 2009 04:19:16 +0000 hourly 1 http://wordpress.org/?v=3.2.1 http://www.justachemblog.net/molecule-of-the-week-06/comment-page-1/#comment-25 pweibel Mon, 29 Sep 2008 04:12:31 +0000 http://www.justachemblog.net/?p=242#comment-25 Very good question. The molecule binds through the minor groove of the DNA, where there is little specificity for interactions. This is because cytosine and thymine present the same hydrogen bonding partners. The 'unique' hydrogen bonding partners are found on the major groove side. Additionally, the molecule really isn't large enough to have a large sequence specificity - which means that if it does preferentially bind to a sequence, it will be short enough that it's most likely repeated around the genome. Very good question. The molecule binds through the minor groove of the DNA, where there is little specificity for interactions. This is because cytosine and thymine present the same hydrogen bonding partners. The ‘unique’ hydrogen bonding partners are found on the major groove side. Additionally, the molecule really isn’t large enough to have a large sequence specificity – which means that if it does preferentially bind to a sequence, it will be short enough that it’s most likely repeated around the genome.

]]> http://www.justachemblog.net/molecule-of-the-week-06/comment-page-1/#comment-24 skassel Mon, 29 Sep 2008 01:29:29 +0000 http://www.justachemblog.net/?p=242#comment-24 I'm referring to specificity of 'binding' to the DNA wrt the base pairs, i.e., is there selectivity to a specific base pair and does the amino acid side chain contribute to the specificity. And does it actually bind or does it intercalate into the DNA strand? I’m referring to specificity of ‘binding’ to the DNA wrt the base pairs, i.e., is there selectivity to a specific base pair and does the amino acid side chain contribute to the specificity. And does it actually bind or does it intercalate into the DNA strand?

]]> http://www.justachemblog.net/molecule-of-the-week-06/comment-page-1/#comment-23 pweibel Mon, 29 Sep 2008 01:10:27 +0000 http://www.justachemblog.net/?p=242#comment-23 I am pretty sure there really is no 'selectivity' in the normal sense for this molecule: you just want something that will bind DNA. I think the selectivity comes from the human control of the irradiation - after that it will (hopefully) deal irreparable damage to all of the DNA in the cell. Is that what you mean? It's kinda like a spray-and-pray tactic combined with super-precise activation. I am pretty sure there really is no ‘selectivity’ in the normal sense for this molecule: you just want something that will bind DNA. I think the selectivity comes from the human control of the irradiation – after that it will (hopefully) deal irreparable damage to all of the DNA in the cell. Is that what you mean? It’s kinda like a spray-and-pray tactic combined with super-precise activation.

]]> http://www.justachemblog.net/molecule-of-the-week-06/comment-page-1/#comment-22 skassel Mon, 29 Sep 2008 01:03:22 +0000 http://www.justachemblog.net/?p=242#comment-22 Pretty cool Paul! My question is of selectivity, or is that where the amino acid side chain comes into play? Pretty cool Paul! My question is of selectivity, or is that where the amino acid side chain comes into play?

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