Dotlet Demonstration
From Friday's Lab:
Comparison of nucleotide sequence with introns vs. protein sequence it codes.
in Dotlet:
Using BLAST:
-
Using dotlet load GI 30686594 and GI 19887539 (again omit the labels
from the sequence, but give them a name so you can recognize them :)).
Compare the Arabidopsis proteolipid against itself. Do you see any repetitive units? How many?
Does the choice of scoring matrix make a difference?
[BLOSUM 100] - Compare the Methanopyrus sequence against the one from Arabidopsis.
How many equivalents to the single repeat unit in Arabidopsis do you
find?
- How many repeats do you identify when you compare the Methanopyrus sequence against itself?
In vitro Evolution
In vitro evolution has succeeded to evolving RNA's with novel properties,
e.g. ATP binding. Jack Szostak's lab is working
to evolve RNAs with template directed RNA polymerization capabilities. The principle
selection scheme is depicted in this diagram at Szostak's web page.
In vitro selection became famous with Sol Spiegelman's experiments on the vitro replication of the Phage Qbeta RNA. In this case selection was for the fastest replicating molecules - they become shorter and lost their ability to infect bacteria.
Later inventions are the SELEX procedure to select for RNA with very specific binding properties (see left), and the selection of ribozymes with altered or new properties. In the latter case growth and selection can be either discrete or continuous. See reading materials for further discussion.
How can evolution be improved?
Genetic drift or the co-selection of slightly deleterious mutations lead to the fixation of deleterious mutations. These mutations can be eliminated if recombination occurs between different members of the population. Another advantage of recombination is that positive properties that arose independently in different parts of the molecules can be combined by recombination, molecular breeding, and sexual PCR.
Illustrations for the power of recombination:
Molecular Computation -> See Adleman's Science paper on solving the traveling salesman problem (full text here -- this site on DNA computing with Lego models contains a good summary of this paper, the Lego version is here).How can one evolve proteins in vitro?
- purely combinatorial approaches using sexual PCR, or targeted reshuffling and selection
- utilize puromycin at the end of the mRNA. The protein sticks to the encoding RNA and thus the RNA can be co-purified with the protein (see this article from Szostak's lab.)
LINKS:
Sexual PCR for in vitro evolution of beta-lactam acylasesMaxyGen Homepage
In vitro evolution has succeeded to evolving RNA's with novel properties, e.g. ATP binding. Jack Szostak's lab is working to evolve RNAs with template directed RNA polymerization capabilities. The principle selection scheme is depicted in this diagram from Szostak's web page.