User:VolkerMorath

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Extension of the standard compability to RFC10 and RFC25

Team TU_Munich 2012 extended the standard compability to RFC10 and RFC25 by adding the


Editing Part:BBa J04450 (section)


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Adeno-associated Virus


Freiburg10 Ue Capsid coding plasmid.png

Explanation of the Capsid coding plasmid
The Adeno-associated Virus - Capsid coding BioBricks


More...
NameDescriptionAuthorLength
BBa_K404001[AAV2]-Rep-VP123Team Freiburg 20104214
BBa_K404002[AAV2]-Rep-VP123_p5-TATAlessFreiburg Bioware 20104386
BBa_K404003[AAV2]-Rep-VP123(ViralBrick-587KO-empty)_p5-TATAlessFreiburg Bioware 20104386
BBa_K404004[AAV2]-Rep-VP13(ViralBrick-587KO-empty)_p5-TATAlessFreiburg Bioware 20104402
BBa_K404005[AAV2]-Rep-VP23(ViralBrick-587KO-empty)_p5-TATAlessFreiburg Bioware 20104402
BBa_K404006[AAV2]-VP123Freiburg Bioware 20102208
BBa_K404007pCMV_[AAV2]-VP123Freiburg Bioware 20102998
BBa_K404008[AAV2]-VP1Freiburg Bioware 20102202
BBa_K404009pCMV_[AAV2]-VP1Freiburg Bioware 20102910
BBa_K404010[AAV2]-VP2Freiburg Bioware 20101830
BBa_K404011pCMV_[AAV2]-VP2Freiburg Bioware 20102500
BBa_K404012[AAV2]-VP3Freiburg Bioware 20101635
BBa_K404013pCMV_[AAV2]-VP3Freiburg Bioware 20102305
BBa_K404150[AAV2]-VP23 Freiburg Bioware 20101917
BBa_K404151[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20101917
BBa_K404152[AAV2]-VP1up Freiburg Bioware 2010411
BBa_K404153[AAV2]-NLS Freiburg Bioware 201021
BBa_K404154pCMV_Z-EGFR-1907_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20102767
BBa_K404155pCMV_Z-EGFR-1907_Short-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20102785
BBa_K404156pCMV_Z-EGFR-1907_Middle-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20102797
BBa_K404157pCMV_Z-EGFR-1907_Long-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20102809
BBa_K404158pCMV_Z-EGFR-1907_SEG-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20102881
BBa_K404159pCMV_CFP_Middle-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20103337
BBa_K404160pCMV_His-Tag_Middle-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20102641
BBa_K404161pCMV_DARPin-E01_Middle-Linker_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20103082
BBa_K404162pCMV_Z-EGFR-1907_Middle-Linker_[AAV2]-VP23 (ViralBrick-587KO-BAP) Freiburg Bioware 20102857
BBa_K404163pCMV_Z-EGFR-1907_Middle-Linker_[AAV2]-VP23 (ViralBrick-587KO-His-Tag) Freiburg Bioware 20102830
BBa_K404164pCMV_VP1up_NLS_Z-EGFR-1907_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20103211
BBa_K404165pCMV_VP1up_NLS_mVenus_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20103751
BBa_K404166pCMV_VP1up_NLS_His-Tag_[AAV2]-VP23 (ViralBrick-587KO-Empty) Freiburg Bioware 20103056
BBa_K404167pCMV_VP1up_NLS_mVenus_VP23(ViralBrick-587-KO-BAP)Freiburg Bioware 20103811
BBa_K404168pCMV_VP1up_NLS_mVenus_VP2/3(ViralBrick-587-KO-His)Freiburg Bioware 20103784
BBa_K404204ViralBrick-453-Z34C Freiburg Bioware 2010165
BBa_K404206ViralBrick-587-His-Tag Freiburg Bioware 2010105
BBa_K404210ViralBrick-587KO-Empty Freiburg Bioware 201072
BBa_K404222[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-453-His-Tag) Freiburg Bioware 20104410
BBa_K404223[AAV2]-Rep-VP123_p5-TATAless (ViralBrick-453-RGD) Freiburg Bioware 20104419
BBa_K404224[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-453-Z34C) Freiburg Bioware 20104488
BBa_K404225[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-587-BAP) Freiburg Bioware 20104446
BBa_K404227[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-587-RGD) Freiburg Bioware 20104428
BBa_K404229[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-587KO-BAP) Freiburg Bioware 20104446
BBa_K404232[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-587KO-RGD) Freiburg Bioware 20104428
BBa_K404234[AAV2]-Rep-VP123_P5-TATAless (ViralBrick-587KO-Z34C-Spacer) Freiburg Bioware 20104503
BBa_K404235[AAV2]Rep-VP123_p5TATAless (ViralBrick 453 Z34C-587 HSPG-KO)Freiburg Bioware 20104488
BBa_K404236[AAV2]Rep-VP123_p5TATAless (ViralBrick 453 RGD-587 HSPG-KO)Freiburg Bioware 20104419
BBa_K404241pCMV_[AAV2]VP123 (ViralBrick-453-BAP) Freiburg Bioware 20103049
BBa_K404242pCMV_[AAV2]VP123 (ViralBrick-453-His-Tag)Freiburg Bioware 20103022
BBa_K404243pCMV_[AAV2]VP123 (ViralBrick-453-RGD)Freiburg Bioware 20103031
BBa_K404244pCMV_[AAV2]VP123 (ViralBrick-453-Z34C) Freiburg Bioware 20103100
BBa_K404246pCMV_[AAV2]-VP123ex (ViralBrick-587-BAP)Freiburg Bioware 20103058
BBa_K404247pCMV_[AAV2]-VP123ex (ViralBrick-587-His-Tag)Freiburg Bioware 20103031
BBa_K404248pCMV_[AAV2]-VP123ex (ViralBrick-587-RGD)Freiburg Bioware 20103040
BBa_K404250pCMV_[AAV2]-VP123ex (ViralBrick-587-Beta-lactamase)Freiburg Bioware 20103787
BBa_K404251pCMV_[AAV2]-VP123ex (ViralBrick-587KO-BAP)Freiburg Bioware 20103058
BBa_K404252pCMV_[AAV2]-VP123ex (ViralBrick-587KO-Empty)Freiburg Bioware 20102998
BBa_K404253pCMV_[AAV2]-VP123ex (ViralBrick-587KO-His-Tag)Freiburg Bioware 20103031
BBa_K404254pCMV_[AAV2]-VP123ex (ViralBrick-587KO-RGD)Freiburg Bioware 20103040
BBa_K404255pCMV_[AAV2]-VP123ex (ViralBrick-587KO-Z34C)Freiburg Bioware 20103100
BBa_K404256pCMV_[AAV2]-VP123ex (ViralBrick-587KO-Z34C-Spacer)Freiburg Bioware 20103115
BBa_K404314DARPin-E01 Freiburg Bioware 2010459
Freiburg10 Ue Vector plasmid.png

Explanation of the Vector Plasmid
The Adeno-associated Virus - Vector plasmid BioBricks


More...
NameDescriptionAuthorLength
BBa_K404100[AAV2]-left-ITRFreiburg Bioware 2010147
BBa_K404101[AAV2]-right-ITR Freiburg Bioware 2010138
BBa_K404108hGH terminatorFreiburg Bioware 2010481
BBa_K404114[AAV2]-left-ITR_pCMV Freiburg Bioware 2010809
BBa_K404115[AAV2]-left-ITR_phTERT Freiburg Bioware 2010612
BBa_K404116hGH_[AAV2]-right-ITR Freiburg Bioware 2010632
BBa_K404117[AAV2]-left-ITR_pCMV_betaglobin Freiburg Bioware 20101310
BBa_K404118[AAV2]-left-ITR_phTERT_betaglobin Freiburg Bioware 20101113
BBa_K404119[AAV2]-left-ITR_pCMV_betaglobin_mVenus_hGH_[AAV2]-right-ITR Freiburg Bioware 20102687
BBa_K404120[AAV2]-left-ITR_pCMV_betaglobin_CFP_hGH_[AAV2]-right-ITR Freiburg Bioware 20102687
BBa_K404121[AAV2]-left-ITR_pCMV_betaglobin_mCherry_hGH_[AAV2]-right-ITR Freiburg Bioware 20102826
BBa_K404122[AAV2]-left-ITR_pCMV_betaglobin_mGMK_TK30_hGH_[AAV2]-right-ITR Freiburg Bioware 20103659
BBa_K404123[AAV2]-left-ITR_phTERT_betaglobin_mVenus_hGH_[AAV2]-right-ITR Freiburg Bioware 20102490
BBa_K404124[AAV2]-left-ITR_phTERT_betaglobin_mGMK_TK30_hGH_[AAV2]-right-ITR Freiburg Bioware 20103462
BBa_K404125[AAV2]-left-ITR_phTERT_betaglobin_CD_hGH_[AAV2]-right-ITR Freiburg Bioware 20103057
BBa_K404126[AAV2]-left-ITR_pCMV_betaglobin_CD_hGH_[AAV2]-right-ITR Freiburg Bioware 20103254
BBa_K404127[AAV2]-left-ITR_pCMV_betaglobin_mVenus_[AAV2]-right-ITR Freiburg Bioware 20102200
BBa_K404128[AAV2]-left-ITR_pCMV_mVenus_hGH_[AAV2]-right-ITR Freiburg Bioware 20102190
BBa_K404129[AAV2]-left-ITR_phTERT_betaglobin_mCherry_hGH_[AAV2]-right-ITR Freiburg Bioware 20102629

The Adeno-associated Virus - Other system parts


More...
NameDescriptionAuthorLength
BBa_K404090[AAV2]-Rep40ex Freiburg Bioware 2010940
BBa_K404092[AAV2]-Rep68ex Freiburg Bioware 20101612
BBa_K404094[AAV2]-AAPex Freiburg Bioware 2010616
BBa_K404103p5 promoterFreiburg Bioware 2010166
BBa_K404104p5-TATAless promoterFreiburg Bioware 2010164
BBa_K404105p40 promoterFreiburg Bioware 2010182
BBa_K404107Beta-Globin-IntronFreiburg Bioware 2010495
BBa_K404201ViralBrick-453-BAP Freiburg Bioware 2010114
BBa_K404202ViralBrick-453-His-Tag Freiburg Bioware 201087
BBa_K404203ViralBrick-453-RGD Freiburg Bioware 201096
BBa_K404205ViralBrick-587-BAP Freiburg Bioware 2010132
BBa_K404207ViralBrick-587-RGD Freiburg Bioware 2010114
BBa_K404208ViralBrick-587-Beta Lactamase (BLA) Freiburg Bioware 2010174
BBa_K404209ViralBrick-587KO-BAPFreiburg Bioware 2010132
BBa_K404211ViralBrick-587KO-His-Tag Freiburg Bioware 2010105
BBa_K404212ViralBrick-587KO-RGD Freiburg Bioware 2010114
BBa_K404213ViralBrick-587KO-Z34C Freiburg Bioware 2010174
BBa_K404214ViralBrick-587KO-Z34C-SpacerFreiburg Bioware 2010189
BBa_K404302Z-EGFR-1907 Freiburg Bioware 2010174
BBa_K404303Z-EGFR-1907_Short-Linker Freiburg Bioware 2010192
BBa_K404304Z-EGFR-1907_Middle-Linker Freiburg Bioware 2010204
BBa_K404305Z-EGFR-1907_Long-Linker Freiburg Bioware 2010216
BBa_K404306Z-EGFR-1907_SEG-Linker Freiburg Bioware 2010288

Virus Construction Kit

Freiburg10 Virus Construction Kit logo.png
info AT biobricks DOT org



Viral Vectors are modified viruses that are used in molecular biology to transfer genetic material into desired cells. The adventage of viral vectors is that the different viral mechanismns can be employed to transduce the target cell in an specific and efficient manner. This process is called transduction when eucaryotic cells are the target of the gene transfer.

Key properties of a viral vector

  • Safety: Viral vectors are often engineered on the basis of an human infectious virus. To reduce the risks for people that handle the virus and patient of an viral vector base therapy the genetic material of the viurs is manipulated in a way to knock-out the ability of the viral vector to reproduce. To reach this requirement the genes coding for the production of the viral capsid are often provided in trans to ensure that the viral vector does not contain the information for
  • Low toxicity: For any use the effect the viral vector has on the transduced cells is important to consider. The cytopathic effect describes the effect of the physiology and morphology the infection with a viral particle has. For the use in vivo the immune response that is triggered by the viral vector has to be considered.
  • Stability: Some viruses evolved a genome organisation that makes it possible to rearrage its genome easily. This feature has been used in the evolution to outflank the immune system of host organisms successfully but is absolute not desired in gene transfer with viral vectors and has to be reduced therefor.
  • Cell type specificity: Many viruses evolved in a way that they are able to transduce many different cell types giving them a wide host cell range. For experimental and therapeutical applications a more narrow cell specificity can be desired. There viral vector systems should provide the possibility to modify the viral tropism in order to target specific cell types.
  • Identification: ????




Main applications of viral vectors:


Double stranded DNA Viruses

The Adenovirus

Adenovirus
200px
Group: ds DNA Virus
Family: Adenoviridae
Genus: Mastadenovirus
Host range Human, mammals
Capacity: 35000bp














The Simian virus 40

The SV40 is a non-enveloped polyomavirus virus, containing a double stranded DNA genome of 5.2 kb. In comparism to other gene transfer vectors the genome of the virus is circular. Thus it lacks the terminal repeat regions characterizing many other viral vectors with linear genomes. The icosahedral capsid of the virus is formed by three virus-encoded proteins (VP1, VP2, and VP3), transcribed by the SV40 late promoters (LP). On the opposite strand the early (EP) promoters are located, driving the expression of the large T antigen (Tag) and a small t antigen (tag). Near a unique BglI site, there are the regulatory sequences, the origin of replication, and packaging signals. According to that the early and late polyadenylation signals are close to each other as well.

SV40 derived vectors have repeatedly proven to be effective, for example in gene delivery to the liver or hematopoietic progenitor cells. The vectors can be stable produced at a very high titer, lacking in immunogenicity and providing high levels of transgene expression in both resting and dividing cells. The principle limitation is the size of insert (≤5 kb) which can be packaged by SV40-derived vectors.

[]
200px
Group: ds DNA Virus
Family: Polyomaviridae
Genus: Polyomavirus
Host range Human, monkeys
Capacity: 5200bp














Single stranded DNA Viruses

The Adeno-associated Virus

Adeno-associated Virus
200px
Group: ss DNA Virus
Family: Parvoviridae
Genus: Dependovirus
Host range Human, vertebrates
Capacity: 4700bp

In the iGEM competition 2010 the Team Freiburg bioware constructed a Virus Construction Kit that makes the Adeno-associated virus (AAV2) available for all users of the parts registry. The Adeno-associated virus is a well studied vector for eukaryotic gene transfer.












Double stranded RNA Viruses

Single stranded RNA (+) Viruses

Single stranded RNA (-) Viruses

Double stranded RNA retro-transcribing Viruses

Single stranded RNA retro-transcribing Viruses

The Lentivirus

Lentivirus
200px
Group: ds DNA Virus
Family: Retroviridae
Genus: Lentivirus
Host range Vertebrate
Capacity: 9750bp














References: 1)http://expasy.org/viralzone/