T7.1: Difference between revisions
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#[[T7.1/Reannotation|Reannotation of the T7 Genome]] -- The wild-type T7 genome is a 39,937 base pair linear double-stranded DNA molecule. We annotated the genome by specifying the boundaries of the following functional genetic elements: 57 open reading frames, 57 putative RBSs encoding 60 proteins, and 51 regulatory elements controlling phage gene expression, DNA replication, and genome packaging. A genbank file of the reannotation can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.WT.gb here]. | #[[T7.1/Reannotation|Reannotation of the T7 Genome]] -- The wild-type T7 genome is a 39,937 base pair linear double-stranded DNA molecule. We annotated the genome by specifying the boundaries of the following functional genetic elements: 57 open reading frames, 57 putative RBSs encoding 60 proteins, and 51 regulatory elements controlling phage gene expression, DNA replication, and genome packaging. A genbank file of the reannotation can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.WT.gb here]. | ||
#[[T7.1/Specification|Specification of T7.1 genome]] -- The designed sequence of T7.1 can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.1.gb here]. [[Image:T7-1-sections_alpha-beta.jpg|thumb|T7.1 genome design (sections ''alpha'' and ''beta'').]] | #[[T7.1/Specification|Specification of T7.1 genome]] -- The designed sequence of T7.1 can be found [http://web.mit.edu/endy/www/ncbi/T7.1/T7.1.gb here]. [[Image:T7-1-sections_alpha-beta.jpg|thumb|T7.1 genome design (sections ''alpha'' and ''beta'').]] | ||
#[[T7.1/Construction|Contructing the T7.1 Genome]] | #[[T7.1/Construction|Contructing the T7.1 Genome]] -- We constructed sections ''alpha'' and ''beta''; the as built sequences can be found [[T7.1/Construction#Sequences|here]] | ||
==References== | ==References== |
Revision as of 20:38, 25 August 2005
Project pages on Rebuilding T7 | |
back to Endy Lab |
Background
Wild-type T7 is a superb organism for discovering the primary components of a natural biological system. However, our experience indicates that the original T7 isolate is not best suited for understanding how all the parts of the phage are arganized to encode a functioning whole. We decided to engineer a surrogate genome, which we designated T7.1, that would be easier to study and extend.
Goals
- We wanted to insulate and enable independent manipulation of all identified genetic elements.
- We wanted the T7.1 genome to encode a viable bacteriophage; at the start of this work, we were uncertain how many simultaneous changes the wild-type genome could tolerate.
Method
- Reannotation of the wild-type T7 genome, thus defining the functional genetic elements
- Specification of T7.1 genome design and sequence
- Construct sections individually
- Construct chimeric phages that contain replace a single wild-type section with a rebuit section
- Combine sections of rebuilt phage into a single rebuilt phage
- Characterize chimeric phage
Progress
- Reannotation of the T7 Genome -- The wild-type T7 genome is a 39,937 base pair linear double-stranded DNA molecule. We annotated the genome by specifying the boundaries of the following functional genetic elements: 57 open reading frames, 57 putative RBSs encoding 60 proteins, and 51 regulatory elements controlling phage gene expression, DNA replication, and genome packaging. A genbank file of the reannotation can be found here.
- Specification of T7.1 genome -- The designed sequence of T7.1 can be found here.
- Contructing the T7.1 Genome -- We constructed sections alpha and beta; the as built sequences can be found here