Difference between revisions of "Part:BBa K4347006"
 
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<partinfo>BBa_K4347006 short</partinfo>
 
<partinfo>BBa_K4347006 short</partinfo>
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Sac7e is a DNA binding protien from the “7 kDa DNA-binding” family which is composed of chromatin proteins from the Sulfolobales archaeal order. Sac7e was isolated from thermoacidophilic archaeon <em> Sulfolobus acidocaldarius </em> and is structurally homologous to DNA binding protien Sso7d isolated from thermophilic archaeon <em> Sulfolobus solfataricus </em>[[Part:BBa_K4347006#References|<sup>[1]</sup>]].
 
Sac7e is a DNA binding protien from the “7 kDa DNA-binding” family which is composed of chromatin proteins from the Sulfolobales archaeal order. Sac7e was isolated from thermoacidophilic archaeon <em> Sulfolobus acidocaldarius </em> and is structurally homologous to DNA binding protien Sso7d isolated from thermophilic archaeon <em> Sulfolobus solfataricus </em>[[Part:BBa_K4347006#References|<sup>[1]</sup>]].
  
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Structural homologue Sso7d from 2021 Fudan team: https://parts.igem.org/Part:BBa_K3790002
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Structural homologue Sso7d from 2021 Fudan team: https://parts.igem.org/Part:BBa_K3790002.
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===Usage and Biology===
 
===Usage and Biology===
  
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DBA binding protiens from the 7 kDa DNA-binding family are highly thermostable and resistant to extreame pH conditions. These protiens have high affinity for double stranded DNA, thus their biological role is to bind genomic DNA in order to prevent its melting at the high growth temperatures of thermophilic archaea[[Part:BBa_K4347006#References|<sup>[1]</sup>]].
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[[File:BBa K4347006 sac7e.PNG|300px|right|thumb|DNA binding protien "Sac7e" modelled in Pymol.]]
  
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Previous work shows that fusing Sso7d (Sac7e homologue) to Taq polymerase (Bst polymerase homologue) improves processivity and improves PCR amplification[[Part:BBa_K4347006#References|<sup>[2]</sup>]]. We hope to use more thermally stable homologues to create a new fusion protien that will improve processivity in LAMP amplification.  
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DNA binding protiens from the 7 kDa DNA-binding family are highly thermostable and resistant to extreame pH conditions. These protiens have high affinity for double stranded DNA, thus their biological role is to bind genomic DNA in order to prevent its melting at the high growth temperatures of thermophilic archaea[[Part:BBa_K4347006#References|<sup>[1]</sup>]]. These protiens fold as an SH3-like domain capped by a C-terminal α-helix[[Part:BBa_K4347006#References|<sup>[2]</sup>]] and they sharply kink the double DNA helix upon binding into the minor groove[[Part:BBa_K4347006#References|<sup>[3]</sup>]].  
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These proteins are hyper-thermostable and resistant to pH extremes. Sac7e is thermally stable to 85.5°C.  
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Previous work shows that fusing Sso7d (Sac7e homologue) to Taq polymerase (Bst polymerase homologue) improves processivity and improves PCR amplification[[Part:BBa_K4347006#References|<sup>[4]</sup>]]. We hope to use the more thermostable homologues to create a new fusion protien that will improve processivity in LAMP amplification.  
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Sac7e is thermally stable to 85.5°C and compared to other similar proteins, Sac7e showed the highest affinity for dsDNA (KD = 11 μM), with binding sites ~ 6-8 bases per protein[[Part:BBa_K4347006#References|<sup>[1]</sup>]].
  
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Compared to other similar proteins, Sac7e showed the highest affinity for dsDNA (KD = 11 μM), with binding sites ~ 6-8 bases per protein.
 
  
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[[File:BBa K4347006 sac7e.PNG|300px|center|thumb|DNA binding protien "Sac7e" modelled in Pymol.]]
 
  
 
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===References===
 
===References===
 
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<br>
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1. https://www.nature.com/articles/srep37274
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1. Kalichuk, V., Béhar, G., Renodon-Cornière, A., Danovski, G., Obal, G., Barbet, J., Mouratou, B., &amp; Pecorari, F. (2016). The archaeal “7 KDA DNA-binding” proteins: Extended characterization of an old gifted family. Scientific Reports, 6(1). https://doi.org/10.1038/srep37274  
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2. Edmondson, S. P., Qiu, L., &amp; Shriver, J. W. (1995). Solution structure of the DNA-binding protein sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry, 34(41), 13289–13304. https://doi.org/10.1021/bi00041a004
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3. Robinson, H., Gao, Y.-G., McCrary, B. S., Edmondson, S. P., Shriver, J. W., &amp; Wang, A. H.-J. (1998). The hyperthermophile chromosomal protein sac7d sharply kinks DNA. Nature, 392(6672), 202–205. https://doi.org/10.1038/32455
  
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2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC373405/
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4. Wang, Y. (2004). A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Research, 32(3), 1197–1207. https://doi.org/10.1093/nar/gkh271

Latest revision as of 20:36, 18 July 2022

Sac7e

Sac7e is a DNA binding protien from the “7 kDa DNA-binding” family which is composed of chromatin proteins from the Sulfolobales archaeal order. Sac7e was isolated from thermoacidophilic archaeon Sulfolobus acidocaldarius and is structurally homologous to DNA binding protien Sso7d isolated from thermophilic archaeon Sulfolobus solfataricus [1].

Structural homologue Sso7d from 2021 Fudan team: https://parts.igem.org/Part:BBa_K3790002.

Usage and Biology

DNA binding protien "Sac7e" modelled in Pymol.

DNA binding protiens from the 7 kDa DNA-binding family are highly thermostable and resistant to extreame pH conditions. These protiens have high affinity for double stranded DNA, thus their biological role is to bind genomic DNA in order to prevent its melting at the high growth temperatures of thermophilic archaea[1]. These protiens fold as an SH3-like domain capped by a C-terminal α-helix[2] and they sharply kink the double DNA helix upon binding into the minor groove[3].

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Previous work shows that fusing Sso7d (Sac7e homologue) to Taq polymerase (Bst polymerase homologue) improves processivity and improves PCR amplification[4]. We hope to use the more thermostable homologues to create a new fusion protien that will improve processivity in LAMP amplification.

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Sac7e is thermally stable to 85.5°C and compared to other similar proteins, Sac7e showed the highest affinity for dsDNA (KD = 11 μM), with binding sites ~ 6-8 bases per protein[1].



Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 5
    Illegal XhoI site found at 209
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


References


1. Kalichuk, V., Béhar, G., Renodon-Cornière, A., Danovski, G., Obal, G., Barbet, J., Mouratou, B., & Pecorari, F. (2016). The archaeal “7 KDA DNA-binding” proteins: Extended characterization of an old gifted family. Scientific Reports, 6(1). https://doi.org/10.1038/srep37274

2. Edmondson, S. P., Qiu, L., & Shriver, J. W. (1995). Solution structure of the DNA-binding protein sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry, 34(41), 13289–13304. https://doi.org/10.1021/bi00041a004

3. Robinson, H., Gao, Y.-G., McCrary, B. S., Edmondson, S. P., Shriver, J. W., & Wang, A. H.-J. (1998). The hyperthermophile chromosomal protein sac7d sharply kinks DNA. Nature, 392(6672), 202–205. https://doi.org/10.1038/32455

4. Wang, Y. (2004). A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Research, 32(3), 1197–1207. https://doi.org/10.1093/nar/gkh271