Difference between revisions of "Phi X 174"
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| − | <p>The <strong>phi X 174</strong> (or <strong>phi X</strong>) bacteriophage was the first organism to have its DNA-based | + | <p><font color="#000000">The <strong>phi X 174</strong> (or <strong>phi X</strong>) bacteriophage was the first organism to have its DNA-based genome sequenced, by Fred Sanger and his team in 1977.<sup class="reference" id="cite_ref-0">[1]</sup> In 1962, Walter Fiers had already demonstrated the physical, covalently closed circularity of phi X 174 DNA.<sup class="reference" id="cite_ref-1">[2]</sup></font></p> |
| − | <p>This phage has a very small amount of DNA. It has 11 genes in 5386 bases (it is single stranded) in a circular topology. Several of them expressing similar function in two groups. The GC-content is 44% and 95% of nucleotides are coding genes.</p> | + | <p><font color="#000000">This phage has a very small amount of DNA. It has 11 genes in 5386 bases (it is single stranded) in a circular topology. Several of them expressing similar function in two groups. The GC-content is 44% and 95% of nucleotides are coding genes.</font></p> |
<p>In 2003 it was reported that the whole genome of phi X 174 had been assembled synthetically from scratch.<sup class="reference" id="cite_ref-2">[3]</sup></p> | <p>In 2003 it was reported that the whole genome of phi X 174 had been assembled synthetically from scratch.<sup class="reference" id="cite_ref-2">[3]</sup></p> | ||
<p> </p> | <p> </p> | ||
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<h2><span class="mw-headline">References</span></h2> | <h2><span class="mw-headline">References</span></h2> | ||
<ol class="references"> | <ol class="references"> | ||
| − | <li id="cite_note-0"><strong>^</strong> Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., "Nucleotide sequence of bacteriophage phi X174 DNA", <em>Nature</em>. 1977 Feb 24;265(5596):687-95 </li> | + | <li id="cite_note-0"><strong>^</strong> Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., "Nucleotide sequence of bacteriophage phi X174 DNA", <em>Nature</em>. <strong>1977</strong> Feb 24;265(5596):687-95 </li> |
| − | <li id="cite_note-1"><strong>^</strong> Fiers, W., and R. L. Sinsheimer, "The structure of the DNA of bacteriophage PhiX 174. III. Ultracentrifuge evidence for a ring structure", <em>J. Mol. Biol.</em> <strong>5:</strong>424-434, 1962 </li> | + | <li id="cite_note-1"><strong>^</strong> Fiers, W., and R. L. Sinsheimer, "The structure of the DNA of bacteriophage PhiX 174. III. Ultracentrifuge evidence for a ring structure", <em>J. Mol. Biol.</em> <strong>5:</strong>424-434, <strong>1962</strong> </li> |
| − | <li id="cite_note-2"><strong>^</strong> <cite style="FONT-STYLE: normal">Smith, Hamilton O.; Clyde A. Hutchison, Cynthia Pfannkoch, J. Craig Venter (2003-12-23). "Generating a synthetic genome by whole genome assembly: {phi}X174 bacteriophage from synthetic oligonucleotides". <em>Proceedings of the National Academy of Sciences</em> <strong>100</strong> (26): 15440-15445. doi:<span class="neverexpand">10.1073/pnas.2237126100</span><span class="reference-accessdate">. Retrieved on 2007-10-08.</span></cite><span class="reference-accessdate"><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Generating+a+synthetic+genome+by+whole+genome+assembly%3A+%7Bphi%7DX174+bacteriophage+from+synthetic+oligonucleotides&rft.jtitle=Proceedings+of+the+National+Academy+of+Sciences&rft.date=2003-12-23&rft.volume=100&rft.issue=26&rft.aulast=Smith&rft.aufirst=Hamilton+O.&rft.pages=15440-15445&rft_id=info:doi/10.1073%2Fpnas.2237126100&rft_id=http%3A%2F%2Fwww.pnas.org%2Fcgi%2Fcontent%2Fabstract%2F100%2F26%2F15440"><span style="DISPLAY: none"> </span></span></span> </li> | + | <li id="cite_note-2"><strong>^</strong> <cite style="FONT-STYLE: normal">Smith, Hamilton O.; Clyde A. Hutchison, Cynthia Pfannkoch, J. Craig Venter (2003-12-23). "Generating a synthetic genome by whole genome assembly: {phi}X174 bacteriophage from synthetic oligonucleotides". <em>Proceedings of the National Academy of Sciences</em> <strong>100</strong> (26): 15440-15445. doi:<span class="neverexpand">10.1073/pnas.2237126100</span><span class="reference-accessdate">. Retrieved on <strong>2007</strong>-10-08.</span></cite><span class="reference-accessdate"><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Generating+a+synthetic+genome+by+whole+genome+assembly%3A+%7Bphi%7DX174+bacteriophage+from+synthetic+oligonucleotides&rft.jtitle=Proceedings+of+the+National+Academy+of+Sciences&rft.date=2003-12-23&rft.volume=100&rft.issue=26&rft.aulast=Smith&rft.aufirst=Hamilton+O.&rft.pages=15440-15445&rft_id=info:doi/10.1073%2Fpnas.2237126100&rft_id=http%3A%2F%2Fwww.pnas.org%2Fcgi%2Fcontent%2Fabstract%2F100%2F26%2F15440"><span style="DISPLAY: none"> </span></span></span> </li> |
</ol> | </ol> | ||
<p> </p> | <p> </p> | ||
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<li><a class="external text" title="http://www.fermentas.com/techinfo/nucleicacids/mapfx174.htm" rel="nofollow" href="http://www.fermentas.com/techinfo/nucleicacids/mapfx174.htm">Description & Restriction Map: PhiX174 DNA</a> </li> | <li><a class="external text" title="http://www.fermentas.com/techinfo/nucleicacids/mapfx174.htm" rel="nofollow" href="http://www.fermentas.com/techinfo/nucleicacids/mapfx174.htm">Description & Restriction Map: PhiX174 DNA</a> </li> | ||
</ul> | </ul> | ||
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| − | Phi X 174 Genome sequence | ||
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<font face="Courier New"> 1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa<br /> | <font face="Courier New"> 1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa<br /> | ||
61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac<br /> | 61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac<br /> | ||
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5281 tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca<br /> | 5281 tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca<br /> | ||
5341 aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca<br /> | 5341 aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca<br /> | ||
| − | </font | + | </font> |
Latest revision as of 08:35, 25 August 2008
The phi X 174 (or phi X) bacteriophage was the first organism to have its DNA-based genome sequenced, by Fred Sanger and his team in 1977.[1] In 1962, Walter Fiers had already demonstrated the physical, covalently closed circularity of phi X 174 DNA.[2]
This phage has a very small amount of DNA. It has 11 genes in 5386 bases (it is single stranded) in a circular topology. Several of them expressing similar function in two groups. The GC-content is 44% and 95% of nucleotides are coding genes.
In 2003 it was reported that the whole genome of phi X 174 had been assembled synthetically from scratch.[3]
See also
- Bacteriophage MS2
References
- ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., "Nucleotide sequence of bacteriophage phi X174 DNA", Nature. 1977 Feb 24;265(5596):687-95
- ^ Fiers, W., and R. L. Sinsheimer, "The structure of the DNA of bacteriophage PhiX 174. III. Ultracentrifuge evidence for a ring structure", J. Mol. Biol. 5:424-434, 1962
- ^ Smith, Hamilton O.; Clyde A. Hutchison, Cynthia Pfannkoch, J. Craig Venter (2003-12-23). "Generating a synthetic genome by whole genome assembly: {phi}X174 bacteriophage from synthetic oligonucleotides". Proceedings of the National Academy of Sciences 100 (26): 15440-15445. doi:. Retrieved on 2007-10-08.
External links
Phi X 174 Genome sequence
1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa
61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac
121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt
181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag
241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt
301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc tgagtccgat
361 gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa tccgtacgtt
421 tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg gatttaaccg
481 aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac cgctctcgtg
541 ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga taccctcgct
601 ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat cccgtcaaca
661 ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt attaatggcg
721 tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta cgcgcaggaa
781 acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt gcggaaggag
841 tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc cgcagccgtt
901 gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg gtcaacaatt
961 ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata ttcaaactgg
1021 cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc agattggtcg
1081 tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga tggacgccgt
1141 tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta ctgtagacat
1201 ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta agttcatgaa
1261 ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata ttgaccatgc
1321 cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt tgtttcaggg
1381 ttatttgaat atctataaca actattttaa agcgccgtgg atgcctgacc gtaccgaggc
1441 taaccctaat gagcttaatc aagatgatgc tcgttatggt ttccgttgct gccatctcaa
1501 aaacatttgg actgctccgc ttcctcctga gactgagctt tctcgccaaa tgacgacttc
1561 taccacatct attgacatta tgggtctgca agctgcttat gctaatttgc atactgacca
1621 agaacgtgat tacttcatgc agcgttacca tgatgttatt tcttcatttg gaggtaaaac
1681 ctcttatgac gctgacaacc gtcctttact tgtcatgcgc tctaatctct gggcatctgg
1741 ctatgatgtt gatggaactg accaaacgtc gttaggccag ttttctggtc gtgttcaaca
1801 gacctataaa cattctgtgc cgcgtttctt tgttcctgag catggcacta tgtttactct
1861 tgcgcttgtt cgttttccgc ctactgcgac taaagagatt cagtacctta acgctaaagg
1921 tgctttgact tataccgata ttgctggcga ccctgttttg tatggcaact tgccgccgcg
1981 tgaaatttct atgaaggatg ttttccgttc tggtgattcg tctaagaagt ttaagattgc
2041 tgagggtcag tggtatcgtt atgcgccttc gtatgtttct cctgcttatc accttcttga
2101 aggcttccca ttcattcagg aaccgccttc tggtgatttg caagaacgcg tacttattcg
2161 ccaccatgat tatgaccagt gtttccagtc cgttcagttg ttgcagtgga atagtcaggt
2221 taaatttaat gtgaccgttt atcgcaatct gccgaccact cgcgattcaa tcatgacttc
2281 gtgataaaag attgagtgtg aggttataac gccgaagcgg taaaaatttt aatttttgcc
2341 gctgaggggt tgaccaagcg aagcgcggta ggttttctgc ttaggagttt aatcatgttt
2401 cagactttta tttctcgcca taattcaaac tttttttctg ataagctggt tctcacttct
2461 gttactccag cttcttcggc acctgtttta cagacaccta aagctacatc gtcaacgtta
2521 tattttgata gtttgacggt taatgctggt aatggtggtt ttcttcattg cattcagatg
2581 gatacatctg tcaacgccgc taatcaggtt gtttctgttg gtgctgatat tgcttttgat
2641 gccgacccta aattttttgc ctgtttggtt cgctttgagt cttcttcggt tccgactacc
2701 ctcccgactg cctatgatgt ttatcctttg aatggtcgcc atgatggtgg ttattatacc
2761 gtcaaggact gtgtgactat tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt
2821 ggtttcatgg tttggtctaa ctttaccgct actaaatgcc gcggattggt ttcgctgaat
2881 caggttatta aagagattat ttgtctccag ccacttaagt gaggtgattt atgtttggtg
2941 ctattgctgg cggtattgct tctgctcttg ctggtggcgc catgtctaaa ttgtttggag
3001 gcggtcaaaa agccgcctcc ggtggcattc aaggtgatgt gcttgctacc gataacaata
3061 ctgtaggcat gggtgatgct ggtattaaat ctgccattca aggctctaat gttcctaacc
3121 ctgatgaggc cgcccctagt tttgtttctg gtgctatggc taaagctggt aaaggacttc
3181 ttgaaggtac gttgcaggct ggcacttctg ccgtttctga taagttgctt gatttggttg
3241 gacttggtgg caagtctgcc gctgataaag gaaaggatac tcgtgattat cttgctgctg
3301 catttcctga gcttaatgct tgggagcgtg ctggtgctga tgcttcctct gctggtatgg
3361 ttgacgccgg atttgagaat caaaaagagc ttactaaaat gcaactggac aatcagaaag
3421 agattgccga gatgcaaaat gagactcaaa aagagattgc tggcattcag tcggcgactt
3481 cacgccagaa tacgaaagac caggtatatg cacaaaatga gatgcttgct tatcaacaga
3541 aggagtctac tgctcgcgtt gcgtctatta tggaaaacac caatctttcc aagcaacagc
3601 aggtttccga gattatgcgc caaatgctta ctcaagctca aacggctggt cagtatttta
3661 ccaatgacca aatcaaagaa atgactcgca aggttagtgc tgaggttgac ttagttcatc
3721 agcaaacgca gaatcagcgg tatggctctt ctcatattgg cgctactgca aaggatattt
3781 ctaatgtcgt cactgatgct gcttctggtg tggttgatat ttttcatggt attgataaag
3841 ctgttgccga tacttggaac aatttctgga aagacggtaa agctgatggt attggctcta
3901 atttgtctag gaaataaccg tcaggattga caccctccca attgtatgtt ttcatgcctc
3961 caaatcttgg aggctttttt atggttcgtt cttattaccc ttctgaatgt cacgctgatt
4021 attttgactt tgagcgtatc gaggctctta aacctgctat tgaggcttgt ggcatttcta
4081 ctctttctca atccccaatg cttggcttcc ataagcagat ggataaccgc atcaagctct
4141 tggaagagat tctgtctttt cgtatgcagg gcgttgagtt cgataatggt gatatgtatg
4201 ttgacggcca taaggctgct tctgacgttc gtgatgagtt tgtatctgtt actgagaagt
4261 taatggatga attggcacaa tgctacaatg tgctccccca acttgatatt aataacacta
4321 tagaccaccg ccccgaaggg gacgaaaaat ggtttttaga gaacgagaag acggttacgc
4381 agttttgccg caagctggct gctgaacgcc ctcttaagga tattcgcgat gagtataatt
4441 accccaaaaa gaaaggtatt aaggatgagt gttcaagatt gctggaggcc tccactatga
4501 aatcgcgtag aggctttgct attcagcgtt tgatgaatgc aatgcgacag gctcatgctg
4561 atggttggtt tatcgttttt gacactctca cgttggctga cgaccgatta gaggcgtttt
4621 atgataatcc caatgctttg cgtgactatt ttcgtgatat tggtcgtatg gttcttgctg
4681 ccgagggtcg caaggctaat gattcacacg ccgactgcta tcagtatttt tgtgtgcctg
4741 agtatggtac agctaatggc cgtcttcatt tccatgcggt gcactttatg cggacacttc
4801 ctacaggtag cgttgaccct aattttggtc gtcgggtacg caatcgccgc cagttaaata
4861 gcttgcaaaa tacgtggcct tatggttaca gtatgcccat cgcagttcgc tacacgcagg
4921 acgctttttc acgttctggt tggttgtggc ctgttgatgc taaaggtgag ccgcttaaag
4981 ctaccagtta tatggctgtt ggtttctatg tggctaaata cgttaacaaa aagtcagata
5041 tggaccttgc tgctaaaggt ctaggagcta aagaatggaa caactcacta aaaaccaagc
5101 tgtcgctact tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa
5161 tgctcacaat gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg
5221 acgcgacgcc gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc
5281 tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca
5341 aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca
