( 12) Pa tent Applica tion Publica tion ( 10) Pub. N o. : US 2001/ 0044150 A1 Hohn et a l. ( 43 ) Pub. D a te: N OV. 22, 2001 ( 54) METHOD FOR TRAN SFORMATION OF Rela ted US. Applica tion D a ta AN IMAL CELLS ( 6 3 ) Continua tion of a pplica tion N o. PCT/ EP9 9 / 05256 , ? led on J ul. 22, 19 9 9 . ( 7 6 ) Inv entor s : B a r ba r a Hohn, Ar les heim ( CH) ; Luca ( 3 0) For eig n Applica tion Pr ior ity D a ta Ros s i, N eucha tel ( CH) ; Alicj a Ziem ienowicz, Gda ns k ( PL) ; B is er ka J ul. 24, 19 9 8 ( GB ) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 816 13 83 Relic, Lieg e B E ( ) Publica tion Cla s s i? ca tion Cor r es pondence Addr es s : 51 Int. Cl. 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . C12N 15/ 86 ; C12N 15/ 87 g g y lg g g lg g lg g m m E523 US. Cl. . . . . . . . . . . . . . . . . . . . . . . . . . - 43 5/ 459 . 43 5/ 456 . 43 5/ 46 1 PATEN T AN D TRAD EMARK D EPT ( 57 ) AB STRACT 56 4 MORRIS AVEN UE The pr es ent inv ention r ela tes to a m ethod f or intr oducing SUMMIT, N J 07 9 011027 nucleic a cids into cells f or eg pr oducing tr a ns iently tr a ns f ected or s ta bly tr a ns f or m ed a nim a l cells by us ing a s pe ci? ca lly des ig ned nucleic a cid/ pr otein com plex com pr is ing ( 21) Appl. N o. : 09 / 7 6 8, 412 in oper a ble linka g e to a n ex pr es s ible D N A or to a n olig o nucleotide a Vir D 2 pr otein, pr ef er a bly tog ether W ith a Vir E2 ( 22) Filed: J a n. 24, 2001 pr otein. US 2001/ 0044150 A1 METHOD FOR TRAN SFORMATION OF AN IMAL CELLS FIELD OF THE IN VEN TION [ 0001] The pr es ent inv ention g ener a lly r ela tes to the tr a ns f or m a tion of euka r y otic cells , pa r ticula r ly a nim a l cells , W ith ex og enous nucleic a cids a nd to the g ener a tion of tr a ns g enic or g a nis m s g ener a ted f r om s uch cells . Mor e pa r ticula r , the pr es ent inv ention r ela tes to a m ethod f or intr oducing nucleic a cids into cells f or pr oducing tr a ns iently tr a ns f ected/ tr a ns f or m ed or s ta bly tr a ns f or m ed cells by us ing a s peci? ca lly des ig ned nucleic a cid/ pr otein com plex , a s W ell a s to cells tr a ns f ected or tr a ns f or m ed ther eby . B ACKGROUN D OF THE IN VEN TION [ 0002] Sev er a l m ethods ha v e been dev eloped f or intr o ducing ex og enous D N A m olecules into euka r y otic cells in or der to ta ke a dv a nta g e of the W ides pr ea d bene? ts a r is ing f r om the a pplica tion of r ecom bina nt D N A technolog y to the pr oduction of tr a ns iently tr a ns tected/ tr a ns f or m ed cells a s W ell a s to tr a ns g enic cells a nd or g a nis m s g ener a ted f r om s uch cells . Thes e m ethods include phy s ica l, non- biolog ica l s y s tem s s uch a s electr opor a tion, m icr oinj ection, ca lcium phos pha te or poly ethy lene g ly col ( PEG) m edia ted D N A upta ke or cell f us ion, a nd m icr opr oj ectile bom ba r dm ent, a nd m odi? ed biolog ica l s y s tem s s uch a s Ag r oba cter ium - m edi a ted T- D N A tr a ns f er to pla nt cells ( f or a g ener a l ov er v ieW , s ee cha pter s 2 a nd 3 of Pla nt Genetic Tr a ns f or m a tion a nd Gene Ex pr es s ion, A La bor a tor y Ma nua l , ed. by D r a per , J . et a l. , pub. by B la ckwell Scienti? c Publica tions ( 19 88) ; s ee a ls o Potr y kus , et a l. , D ir ect Gene Tr a ns f er : Sta te of the Ar t a nd Futur e Potentia l , Pla nt Mol. B iol. Rep. 3 : 117 - 128 ( 19 85) ) . [ 0003 ] The m ethods W hich ha v e been dev eloped ha v e a lloW ed the s ta ble tr a ns f or m a tion of a W ide v a r iety of cells a nd or g a nis m s W ith ex og enous D N A. In pa r ticula r , the dev elopm ent of phy s ica l techniq ues s uch a s biolis tics ha s ov er com e a ppa r ent hos t- r a ng e lim ita tions im pos ed by bio log ica l s y s tem s . HoW ev er , a com m on de? ciency of thes e phy s ica l m ethods is tha t they do not pr ov ide a ny m ea ns f or or der ed integ r a tion of the deliv er ed nucleic a cid into the cell g enom e. Cons eq uently thes e m ethods m us t depend upon uncontr olled integ r a tion of the deliv er ed nucleic a cid by poor ly under s tood m echa nis m s , ca us ing ex og enous D N A to be integ r a ted a s m ultiple copies of r a ndom f r a g m ents us u a lly a t a s ing le s ite in the cell g enom e. [ 0004] Im pr ov ing the pr edicta bility of s ta ble tr a ns f or m a tion ev ents a r is ing f r om the phy s ica l intr oduction of ex og enous nucleic a cid into the cell W ould s ig ni? ca ntly im pr ov e the utility a nd ov er a ll ef f iciency of thes e pr oces s es f or pr oducing g enetica lly s ta ble tr a ns f or m ed cells or or g a nis m s ex hibiting s ta ble ex pr es s ion of tr a ns g enes . One a ppr oa ch W hich ha s been ta ken to a ccom plis h this g oa l ha s been to com bine pr oteins W hich pr om ote tr a ns f or m a tion a nd/ or inte g r a tion in biolog ica l s y s tem s W ith non- biolog ica l deliv er y techniq ues . In or der to a chiev e the des ir ed ef f ect, it ha s been cons ider ed neces s a r y to a s s ocia te the pr oteins them s elv es W ith the ex og enous D N A m olecules pr ior to deliv er y to the tr a ns f or m a tion ta r g et cell, thus m im icking a s clos ely a s pos s ible the biolog ica l s y s tem f r om W hich the pr oteins a r e der iv ed ( s ee, eg inter na tiona l a pplica tion no. PCT/ EP9 4/ 0256 6 to Hohn et a l. publis hed Feb. 23 , 19 9 5 a s W O N ov . 22, 2001 9 5/ 0547 1; inter na tiona l a pplica tion no. PCT/ US9 5/ 07 543 to Cona r y , J . et a l. publis hed D ec. 21, 19 9 5 a s W O 9 5/ 3 46 47 ) . [ 0005] The Ag r oba cter ium pla nt tr a ns f or m a tion s y s tem m entioned a bov e is W idely us ed f or the s ta ble tr a ns f or m a tion of hig her pla nts . In this s y s tem g enes to be tr a ns f er r ed a r e ca r r ied by the T- D N A, a W ell- de? ned r eg ion of the Ag r oba cter ium Ti pla s m id. The Ti pla s m id a ls o conta ins a v ir ulence ( v ir ) r eg ion, W hich encodes pr oteins inv olv ed in the tr a ns f or m a tion v ia Ag r oba cter ium of pla nt cells . At lea s t one of thes e pr oteins , Vir D 2 is inv olv ed in ta r g eting to the pla nt nucleus a nd integ r a tion into the pla nt g enom e ( Tinla nd et a l. ( 19 9 2) Pr oc. N a tl. Aca d. Sci. USA 89 : 7 442; Tinla nd et a l. ( 19 9 5) EMB O J . 14: 3 588- 3 59 5) . W O 9 5/ 0547 1, the contents of W hich is her eW ith incor por a ted by r ef er ence, dis clos es a m ethod f or pr oducing s ta bly tr a ns f or m ed pla nt m a ter ia l, including phenoty pica lly nor m a l looking a nd pr ef er a bly f er tile pla nts , W hich m ethod does not inv olv e Ag r o ba cter ium tr a ns f or m a tion. In pa r ticula r , it dis clos es a s pe ci? ca lly a da pted nucleic a cid/ pr otein com plex com pr is ing a chim er ic r ecom bina nt nucleic a cid, W hich m a y com pr is e, f or ex a m ple, a n ex pr es s ible D N A or a n olig onucleotide oper a bly linked to s uita ble pla nt ex pr es s ion s ig na ls inv olv ing pr om oter a nd ter m ina tion s eq uences a nd cov a lently a s s oci a ted ther eW ith a Vir D 2, a nd, optiona lly , Vir E2 pr otein units . HoW ev er , the tea ching does not m ention potentia l a pplica bility of this tr a ns f or m a tion techniq ue to the ? eld of a nim a l cells . Fur ther m or e, it does not concer n us ing s peci? ca lly des ig ned olig onucleotides a s nucleic a cid com ponent of s a id com plex in a n a ntis ens e- , a ntig ene- or olig oZy m e- a ppr oa ch f or ( tr a ns ient) tr a ns f ection/ tr a ns f or m a tion of euka r y otic cells . [ 0006 ] Since ther e ex is ts a continuous need f or f ur ther techniq ues W hich a r e us ef ul f or the intr oduction of nucleic a cids into a nim a l a nd pla nt cells , e. g . olig onucleotides f or a ntis ens e- or a ntig ene- a ppr oa ches , or f or the per m a nent tr a ns f or m a tion of a nim a l cells , the obj ect of the pr es ent inv ention is ther ef or e to pr ov ide a neW m ethod f or intr o ducing nucleic a cids into euka r y otic cells . SUMMARY OF THE IN VEN TION [ 0007 ] The pr es ent inv ention pr ov ides a n im pr ov ed m ethod f or deliv er ing nucleic a cids a s nucleic a cid/ pr otein com plex to euka r y otic cells , e. g . olig onucleotides or ex og enous D N A f or s ta bly tr a ns f or m ing or tr a ns iently tr a ns f ect ing / tr a ns f or m ing a nim a l, pr ef er a bly m a m m a lia n cells . This im pr ov ed m ethod f or ex a m ple g ener a lly com pr is es pr ov id ing to the cell ta r g eted f or tr a ns f ection/ tr a ns f or m a tion a s peci? ca lly des ig ned nucleic a cid/ pr otein com plex com pr is ing nucleic a cids s uch a s eg ex og enous D N A or olig o nucleotide des ir ed to be intr oduced a nd, if des ir ed, to be integ r a ted in the la ter tr a ns f or m a nt. [ 0008] For ex a m ple, the pr es ent inv ention pa r ticula r ly pr ov ides a n im pr ov ed m ethod f or tr a ns iently tr a ns f ecting / tr a ns f or m ing or f or s ta bly tr a ns f or m ing a nim a l cells W ith ex og enous nucleic a cids s uch a s eg D N A, W hich com bines pos itiv e a ttr ibutes of Ag r oba cter ium tum ef a ciens m edia ted T- D N A tr a ns f er s uch a s hig h- ef ? cient nuclea r ta r g eting a nd integ r a tion, W ith non- biolog ica l deliv er y m ethods . This a s pect of the inv ention e. g . com pr is es pr ov iding a n a nim a l cell W ith the ex og enous D N A f r a g m ent des ir ed to be intr o duced into the nucleus a nd integ r a ted into the a nim a l cell g enom e, bounded by T- D N A bor der s or f unctiona l pa r ts US 2001/ 0044150 A1 ther eof , a long W ith a t lea s t one Ag r oba cter ium - der iv ed pr o tein tha t ta r g ets s a id f r a g m ent to the nucleus a nd pr om otes the integ r a tion of the ex og enous D N A into the hos t cell g enom e. The Ag r oba cter ium - der iv ed pr otein us ed a ccor ding to the inv ention is s elected f r om the g r oup cons is ting of Vir D l, Vir D 2, Vir E2, a nd Vir C. Pr ef er a bly , a com bina tion of Vir D 2 a nd either Vir D l, Vir C, Vir E2, or a s ubcom bina tion ther eof , is us ed. Mos t pr ef er a bly , us e is m a de of the Ag r o ba cter ium - der iv ed pr oteins Vir D 2 a nd Vir E2 in com bina tion, a lthoug h in cer ta in ca s es s ole us e of Vir D 2 m a y be s uf f icient. [ 0009 ] Accor ding to the inv ention, the nucleic a cid/ pr otein com plex com pr is ing the ex og enous nucleic a cid, s uch a s eg a D N A f r a g m ent bounded by T- D N A bor der s eq uences or f unctiona l pa r ts ther eof , m a y be deliv er ed to the a nim a l cell by non- biolog ica l m ea ns s uch a s , but not r es tr icted to, electr opor a tion, m icr oinj ection, induced upta ke, m icr o pr oj ectile bom ba r dm ent, or other m ea ns a s a r e knoW n in the a r t. [ 0010] In a nother a s pect of the inv ention, a nim a l cells or tis s ues s ta bly tr a ns f or m ed W ith a dis cr ete D N A f r a g m ent a r e r eg ener a ted to pr oduce tr a ns g enic a nim a l or g a ns or W hole a nim a ls tha t s ta bly ex pr es s a des ir ed hom olog ous or heter olog ous nucleic a cid a nd, in the la tter ca s e, pa s s it on to pr og eny in W hich s ta ble ex pr es s ion of the tr a ns g ene is inher ited a s a Mendelia n tr a it. [ 0011] Fur ther m or e, the pr es ent inv ention pr ov ides nov el m ea ns f or the in v iv o a nd ex v iv o/ in v itr o tr a ns f or m a tion a nd integ r a tion or tr a ns ient tr a ns f ection/ tr a ns f or m a tion of ex og enous nucleic a cids des ir ed to be ex pr es s ed W ithin a nim a l hos ts or hos t cells , pa r ticula r ly f or the pur pos e of g ene ther a py . [ 0012] In a nother a s pect, the pr es ent inv ention s upplies the pr ocedur es f or intr oducing s m a ll nucleic a cid f r a g m ents into- a nim a l cells - a nd- pla nt m a ter ia l, f or us e in a ntis ens e, a ntig ene, olig oZy m e or m uta g enes is technolog y . D ETAILED D ESCRIPTION OF THE IN VEN TION [ 0013 ] The pr es ent inv ention pr ov ides a n im pr ov ed m ethod f or intr oducing nucleic a cids a s nucleic a cid/ pr otein com plex to euka r y otic cells , e. g . olig onucleotides or ex og enous D N A f or s ta bly tr a ns f or m ing a nim a l cells . N ucleic a cid( s ) a s a com ponent of nucleic a cid/ pr otein com plex a ccor ding to the pr es ent inv ention m a y be a ny ty pe of s ing le or double- s tr a nded nucleic a cid, f or ex a m ple RN A, m odi? ed RN A or D N A, W her ein D N A is the pr ef er r ed f or m . This im pr ov ed m ethod f or ex a m ple g ener a lly com pr is es pr ov id ing to the a nim a l cell ta r g eted f or tr a ns f or m a tion a s peci? ca lly des ig ned nucleic a cid/ pr otein com plex com pr is ing ex og enous nucleic a cid des ir ed to be integ r a ted a nd ex pr es s ed in the la ter tr a ns f or m a nt. In this contex t, the ter m s ex pr es s ed or ex pr es s ible us ed thr oug hout the s peci? ca tion s ha ll m ea n tha t a g iv en nucleic a cid ca n a t lea s t s er v e a s ta r g et f or tr a ns cr iption W ithin the nucleus of a cell to be tr a ns iently or per m a nently tr a ns f ected or tr a ns f or m ed. The ter m T- D N A bor der ( s ) or f unctiona l pa r t( s ) ther eof s ha ll encom pa s s the W hole T- D N A bor der s eq uence( s ) a s W ell a s thos e pa r ts ther eof W hich ha v e f unctiona l cons ens us or clea v a g e s ite or binding dom a in s eq uence( s ) neces s a r y f or a des ir ed pr otein to inter a ct W ith the nucleic a cid a ccor ding to the inv ention. N ov . 22, 2001 [ 0014] For ex a m ple, the pr es ent inv ention pa r ticula r ly pr ov ides a n im pr ov ed m ethod f or tr a ns iently tr a ns f ecting / tr a ns f or m ing or f or s ta bly tr a ns f or m ing a nim a l cells W ith ex og enous nucleic a cids s uch a s eg D N A, W hich com bines pos itiv e a ttr ibutes of Ag r oba cter ium tum ef a ciens m edia ted T- D N A tr a ns f er a nd integ r a tion W ith non- biolog ica l deliv er y m ethods . This a s pect of the inv ention com pr is es pr ov iding a n a nim a l cell W ith the ex og enous D N A f r a g m ent des ir ed to be integ r a ted into the a nim a l cell g enom e, bounded by T- D N A bor der s or f unctiona l pa r ts ther eof , a long W ith a t lea s t one Ag r oba cter ium - der iv ed pr otein tha t pr om otes the integ r a tion of the ex og enous D N A into the hos t cell g enom e. The Ag r oba cter ium - der iv ed pr otein us ed a ccor ding to the inv ention pa r ticula r ly includes Vir D l, Vir D 2, Vir E2, a nd Vir C. Pr ef er a bly , a com bina tion of Vir D 2 a nd either Vir D l, Vir C, Vir E2, or a s ubcom bina tion ther eof , is us ed. Mos t pr ef er a bly , us e is m a de of the Ag r oba cter ium - der iv ed pr o teins Vir D 2 a nd Vir E2 in com bina tion. HoW ev er , in cer ta in ca s es s ole us e of Vir D 2 m a y be s uf f icient a nd is a ls o W ithin the s cope of the inv ention. [ 0015] Accor ding to the pr es ent inv ention it ha s s ur pr is ing ly been f ound tha t a nim a l cells der iv ed f r om - v a r ious cell lines a r e s ucceptible f or tr a ns f or m a tion by us ing the D N A/ pr otein com plex a s dis clos ed in W O 9 5/ 0547 1 m entioned a bov e, a nd ca n ef f iciently be tr a ns iently tr a ns f ected by us ing a s im ila r com plex in W hich the nucleic a cid com ponent is in the f or m of a n olig onucleotide ena bling a ntis ens e- , a ntig ene a nd olig oZy m e- a ppr oa ches . Fur ther m or e, it ha s been f ound tha t the Ag r oba cter ium der iv ed v ir ulence pr oteins , Vir D l a nd Vir D 2, inter a ct W hen ex pr es s ed in m a m m a lia n cells . In pa r ticula r , the a bov e m a in obj ect under ly ing the pr es ent inv ention ha s thus been- a chiev ed by us ing the pr oper ties of pr oteins pr oduced by the v ir r eg ion of Ag r oba cter ium s uch a s , f or ex a m ple, Vir D l, Vir D 2 a nd Vir E2, but es pecia lly tha t of the Vir D 2 pr oteins , in non- Ag r oba cter ium tr a ns f or m a tion of a nim a l cells . [ 0016 ] The nucleic a cid/ pr otein com plex a lr ea dy dis clos ed in W O 9 5/ 0547 1 m a y be oba ined by ? r s t pr ov iding a r ecom bina nt nucleic a cid cons tr uct tha t com pr is es in oper a ble linka g e to the elem ents a lr ea dy m entioned a bov e a t lea s t one T- D N A bor der s eq uence or f unctiona l pa r t ther eof a s a s ubs tr a te in the Vir D 2 clea v a g e r ea ction. If the s a id s ubs tr a te inv olv es not the W hole but only pa r t of the T- D N A bor der s eq uence, it is to be ens ur ed tha t the s a id pa r tia l s eq uence s till com pr is es thos e pa r ts of the T- D N A bor der s eq uence tha t encom pa s s the r ecog nition a nd clea v a g e s ite of the Vir D 2 pr otein. [ 0017 ] The chim er ic r ecom bina nt nucleic a cid cons tr uct a s des cr ibed a bov e is pr ef er a bly a s ing le s tr a nded D N A con s tr uct. Als o com pr is ed W ithin the s cope of the inv ention is a double- s ta nded m olecule W ith a s ing le- s tr a nded ov er ha ng W hich is a s ubs tr a te f or Vir D 2, or a chim er ic r ecom bina nt D N A cons tr uct neg a tiv ely s uper coiled ( f or m I) conta ining bor der s eq uences or a t lea s t f unctiona l pa r ts ther eof a s the pr ef er r ed s ubs tr a te f or Vir D 1Vir D 2 ca ta ly Zed clea v a g e. Accor ding to a pr ef er r ed em bodim ent of the inv ention s a id chim er ic r ecom bina nt nucleic a cid/ pr otein com plex f ur ther com pr is es Vir E2 a nd/ or a ny other nucleic a cid binding pr otein, s uch a s r ecA, W hich contr ibutes to ef f icient nuclea r im por t a nd W hich, pr ef er a bly , is a ls o a ble to pr otect the nucleic a cid to be tr a ns f or m ed or tr a ns f ected f r om nuclea s e a tta ck. Pr ef er a bly , the inv ention thus pr ov ides us e of a chim er ic r ecom bina nt nucleic a cid cons tr uct cov a lently US 2001/ 0044150 A1 a s s ocia ted W ith Vir D 2, a nd optiona lly Vir E2, pr oteins f or the tr a ns f or m a tion or tr a ns f ection of a nim a l cells ex v iv o, in v itr o a nd in v iv o. In this contex t it is to be under s tood tha t the pr oteins m entioned her einbef or e a s com ponent of the nucleic a cid/ pr otein com plex a ccor ding to the inv ention s ha ll a ls o m ea n olig opeptides or der iv a tiv es der iv ed ther e f r om or f unctiona l f r a g m ents ther eof r eta ining a t lea s t one f unctiona l cha r a cter is tic neces s a r y to a chiev e the a im s of the pr es ent inv ention. [ 0018] For deta ils concer ning the pr epa r a tion of nucleic a cid/ pr otein com plex es W hich ca n be us ed a ccor ding to the pr es ent inv ention r ef er ence is m a de to the com plete dis clo s ur e of W O 9 5/ 0547 1. HoW ev er , it ha s to be noted tha t the nucleic a cid/ pr otein com plex a ccor ding to the pr es ent inv en tion pr ef er a bly com pr is es both Vir E2 a nd Vir D 2 pr oteins in or der to a chiev e optim um deliv er y a nd/ or tr a ns f or m a tion ef ? ciency , a lthoug h the s ole us e of the Vir D 2 pr otein in the com plex , in pa r ticula r if s a id com plex com pr is es s ing le s tr a nded olig onucleotides , is a ls o W ithin the s cope of the pr es ent inv ention. W ith r es pect to the pr epa r a tion of a com plex in W hich the nucleic a cid com ponent is in the f or m of a n olig onucleotide ena bling a ntis ens e- , a ntig ene- or oli g oZy m e- a ppr oa ches , it is clea r f or a per s on s killed in the a r t hoW to cons tr uct s uch a com plex . [ 0019 ] Upon us ing the D N A/ pr otein com plex a ccor ding to W O 9 5/ 0547 1 f or the tr a ns f or m a tion of a nim a l cells , the tr a ns f or m a tion f r eq uency a nd a ls o the q ua lity of the inte g r a ted D N A ca n be im pr ov ed cons ider a bly . This is es pe cia lly tr ue W ith r eg a r d to s ta ble tr a ns f or m a tion ev ents , W hich occur m or e f r eq uently a s com pa r ed to conv entiona l, non pr otein a s s ocia ted D N A cons tr ucts . [ 0020] The pr es ent inv ention thus com pr is es a m ethod f or intr oducing nucleic a cids into cells , eg f or tr a ns f or m ing or tr a ns iently tr a ns f ecting / tr a ns f or m ing a nim a l cells , com pr is ing [ 0021] ( a ) pr epa r ing a chim er ic r ecom bina nt nucleic a cid cons tr uct tha t com pr is es in oper a ble linka g e to a n ex pr es s ible D N A or to a n olig onucleotide a t lea s t one T- D N A bor der s eq uence or f unctiona l pa r t ther eof , W hich s er v es a s a s ubs tr a te in the Vir D 2 clea v a g e r ea ction, a s de? ned her einbef or e; [ 0022] ( b) clea v ing of the nucleic a cid s ubs tr a te pr e pa r ed a ccor ding to s tep ( a ) by m ea ns of Vir D 2 pr otein, W hich m a y be a ccom pa nied by f ur ther Vir pr oteins s uch a s , f or ex a m ple Vir D 1 a nd/ or Vir E2 a nd/ or a ny other nucleic a cid binding pr otein, W hich is a ble to pr otect s a id nucleic a cid f r om nuclea s e a tta ck; [ 0023 ] ( c) intr oducing the thus clea v ed nucleic a cid com pr is ing a t lea s t the Vir D 2 pr otein cov a lently bound to the 5 end of the clea v a g e s ite into the cells to be tr a ns f or m ed or tr a ns f ected by m ethods knoW n in the a r t. [ 0024] Accor ding to a pr ef er r ed em bodim ent of the a bov e m ethod, clea v ing of the nucleic a cid s ubs tr a te ( b) is ca r r ied out in v itr o. [ 0025] Accor ding to the inv ention the nucleic a cid/ Vir D 2 pr otein com plex is pr ef er a bly a ccom pa nied by f ur ther Vir pr oteins , s uch a s , f or ex a m ple, Vir E2, W hich is knoW n to bind to s s D N A, a nd/ or Vir D 1. Vir E2 ca n be pur i? ed by N ov . 22, 2001 m ethods knoW n in the a r t s uch a s thos e des cr ibed in Chr is tie et a l [ J B a cter iol 17 0( 6 ) : 26 59 - 26 6 7 ( 19 88) ] . The pur i? ca tion of the Vir D 1 pr otein ca n be a chiev ed a ccor ding to the m ethod dis clos ed in W O 9 5/ 0547 1, W her ea s Vir D 2 ca n be obta ined a s s et f or th in Pa ns eg r a u et a l. [ PN AS 9 0, 1153 8 ( 19 9 3 ) ] . [ 0026 ] As m entioned bef or e, the m a in obj ect of the pr es ent inv ention is the us e of a nucleic a cid/ pr otein com plex com pr is ing oper a bly linked to eg a n ex pr es s ible D N A or to a n olig onucleotide a t lea s t one T- D N Abor der s eq uence or f unctiona l pa r t ther eof , a nd cov a lently a s s ocia ted ther e W ith a Vir D 2 pr otein in a pr oces s f or intr oducing nucleic a cids into a nim a l cells . The nucleic a cid/ Vir D 2 pr otein com plex pr ef er a bly conta ins non- cov a lently a s s ocia ted f ur ther Vir pr oteins s uch a s , f or ex a m ple, Vir D 1 a nd/ or Vir E2, W ith Vir E2 being m os t pr ef er r ed, pa r ticula r ly if us ed in connection W ith s ing le- s tr a nded olig onucleotides . [ 0027 ] The ter m ex og enous D N A or nucleic a cid us ed her ein is m ea nt to include a ny D N A or other nucleic a cid tha t ha s been obta ined by r ecom bina nt nucleic a cid tech nolog y . The ex og enous nucleic a cid to be us ed in the pr oces s a ccor ding to the inv ention f or tr a ns f or m ing or tr a ns f ecting ta r g et cells m a y be either of hom olog ous or heter olog ous or ig in W ith r es pect to the cell ty pe inv olv ed or it m a y be of s y nthetic or ig in or both. The coding nucleic a cid s eq uence ca n be cons tr ucted a ccor ding to conv entiona l m ethods , eg f r om g enom ic D N A, or f r om cD N A. Another pos s ibility is the cons tr uction of a hy br id D N A s eq uence cons is ting of both cD N A a nd g enom ic D N A a nd/ or s y nthetic D N A. The cD N A m a y or ig ina te f r om the s a m e g ene a s the g enom ic D N A, or a lter na tiv ely both the cD N A a nd the g enom ic D N A m a y or ig ina te f r om dif f er ent g enes . In a ny ca s e, hoW ev er , both the g enom ic D N A a nd/ or the cD N A m a y ea ch be pr epa r ed indiv idua lly f r om the s a m e or f r om dif f er ent g enes . [ 0028] The ter m s y nthetic D N A or nucleic a cid includes ( a ) nucleic a cid s eq uences tha t ha v e been pr epa r ed entir ely or a t lea s t pa r tia lly by chem ica l m ea ns a nd ( b) a ntis ens e or s ens e olig onucleotides . For ex a m ple, s y nthetic D N A s eq uences m a y be s uita bly us ed, e. g . , f or m odif y ing na tiv e D N A s eq uences in ter m s of codon us a g e, ex pr es s ion ef ? ciency , etc. [ 0029 ] Another a ppr oa ch a ccor ding to the pr es ent inv en tion is to g ener a te a ntis ens e or a ntig ene RN A or r iboZy m es / olig oZy m es W ithin a g iv en hos t cell by intr oducing into s a id cell a nucleic a cid W ith r ev er s e or ienta tion W hich m a y becom e pa r t of the hos t cells g enom e. In this contex t, intr oducing nucleic a cid f r a g m ents encoding a ntis ens e or a ntig ene olig onucleotides or olig oZy m es cor r es ponding to ev en les s tha n 100 bp of a s peci? c RN A or D N A to be ta r g eted is s uf ? cient f or inhibiting or m odula ting tr a ns la tion. [ 003 0] If the nucleic a cid s eq uence to be tr a ns f er r ed into the r ecipient cell conta ins por tions of m or e tha n one g ene, thes e g enes m a y or ig ina te f r om one a nd the s a m e or g a nis m , f r om s ev er a l or g a nis m s tha t belong to m or e tha n one s tr a in, one v a r iety or one s pecies of the s a m e g enus , or f r om or g a nis m s tha t belong to m or e tha n one g enus of the s a m e or of a nother ta x onom ic unit ( king dom ) . Chim er ic r ecom bina nt nucleic a cid m olecules tha t com pr is e a n ex pr es s ible D N A, but es pecia lly a s tr uctur a l g ene, pr ef er a bly a heter olog ous s tr uctur a l g ene oper a bly linked W ith ex pr es s ion s ig na ls a ctiv e in r ecipient cells , s uch a s enha ncer , pr om oter a nd tr a ns cr iption ter m ina tion s eq uences , a s W ell a s , option US 2001/ 0044150 A1 a lly , W ith f ur ther coding a nd/ or non- coding s eq uences of the 5 a nd/ or 3 r eg ion s uch a s eg s ig na l s eq uence, m a y a ls o be pr ef er a bly us ed W ithin the tr a ns f or m a tion pr oces s a s pa r t of the nucleic a cid/ pr otein com plex us ed a ccor ding to the pr es ent inv ention. It is of ten a dv a nta g eous to incor por a te a lea der s eq uence betW een the pr om oter s eq uence a nd the a dj a cent coding D N A s eq uence, the leng th of the lea der s eq uence being s o s elected tha t the dis ta nce betW een the pr om oter a nd the D N A s eq uence to be ex pr es s ed is the optim um dis ta nce f or ex pr es s ion of the a s s ocia ted s tr uctur a l g ene. [ 003 1] Fur ther m or e, the ex og enous D N A or other nucleic a cid f or m ing pa r t of the nucleic a cid/ pr otein com plex m a y a dditiona lly com pr is e s eq uences encoding one or m or e s electa ble m a r ker s us ef ul in s cr eening f or pos itiv e tr a ns f or m a nts . In g ener a l, thes e m a r ker s a r e pr oteins neces s a r y f or the s ur v iv a l or g r oW th of tr a ns f or m ed hos t cells g r oW n in a s electiv e cultur e m edium . Hos t cells not tr a ns f or m ed W ith the v ector conta ining the s election g ene W ill not s ur v iv e in the cultur e m edium . Ty pica l s election m a r ker s encode pr o teins tha t conf er r es is ta nce to a ntibiotics a nd other - tox ins , e. g . a m picillin, hy g r om y cin, neom y cin, pur om y cin, m eth otr ex a te or tetr a cy cline, com plem ent a ux otr ophic de? cien cies , or s upply cr itica l nutr ients not a v a ila ble f r om com plex m edia . Fur ther ex a m ples of g enes tha t conf er a ntibiotic r es is ta nce include thos e coding f or the ka na m y cin r es is ta nce ( N PT II) g ene der iv ed f r om Tn5 ( B ev a n et a l, N a tur e 3 04: 184- 187 ( 19 83 ) ) , a nd chlor a m phenicol a cety ltr a ns f er a s e. [ 003 2] Suita ble s electa ble m a r ker s f or a nim a l, pa r ticula r ly m a m m a lia n cells a r e thos e tha t ena ble the identi? ca tion of cells com petent to ta ke up the nucleic a cid encoding s a id s electa ble m a r ker , s uch a s dihy dr of ola te r educta s e ( D HFR, m ethotr ex a te r es is ta nce) , thy m idine kina s e, or g enes con f er r ing r es is ta nce to G418 or hy g r om y cin ( s ee eg B lochling er a nd D ig g elm a nn ( 19 84) , Molecula r a nd Cellu la r B iolog y 4: 29 29 - 29 3 1; Rober ts on a nd W ha lley ( 19 88) , N ucl. Acids Res . 16 : 113 03 - 113 17 ; O B r ia n et a l. ( 19 9 7 ) , Gene 184: 115- 120) . The a nim a l cell tr a ns f or m a nts a r e pla ced under s election pr es s ur e W hich only thos e tr a ns f or m a nts W hich ha v e ta ken up a nd a r e ex pr es s ing the m a r ker a r e uniq uely a da pted to s ur v iv e. In the ca s e of a D HFR or g luta m ine s y ntha s e ( GS) m a r ker , s election pr es s ur e ca n be im pos ed by cultur ing the tr a ns f or m a nts under conditions in W hich the pr es s ur e is pr og r es s iv ely incr ea s ed, ther eby lea d ing to a m pli? ca tion ( a t its chr om os om a l integ r a tion s ite) of both the s election g ene a nd the linked D N A tha t encodes a s tr uctur a l g ene of inter es t des ir ed to be ex pr es s ed in the tr a ns f or m ed cells . Am pli? ca tion is the pr oces s by W hich g enes in g r ea ter dem a nd f or the pr oduction of a pr otein cr itica l f or g r oW th, tog ether W ith clos ely a s s ocia ted g enes W hich m a y encode a des ir ed pr otein, a r e r eiter a ted in ta ndem W ithin the chr om os om es of r ecom bina nt cells . Incr ea s ed q ua ntities of des ir ed pr otein a r e us ua lly s y nthes is ed f r om thus a m pli? ed D N A. For the pur pos e of s cr eening tr a ns ient ex pr es s ion of the des ir ed g ene intr oduced into a s uita ble a nim a l hos t cell a ccor ding to the inv ention the ex og enous D N A m a y a ls o com pr is e s eq uences encoding [ 3 - g a la ctos i da s e, g r een ? uor es cent pr otein ( g f p) , or lucif er a s e. Methods f or the detection of the ex pr es s ion of s a id m a r ker s a r e W ell knoW n in the a r t. Scr eening of a nim a l cells a nd a nim a ls der iv ed f r om s uch cells f or the pr es ence of s peci? c nucleic a cid s eq uences m a y a ls o be per f or m ed by Souther n a na ly s is [ Souther n, J . Mol. B iol. 9 8: 503 ( 19 7 5) ] . D eta ils of this pr ocedur e a r e g iv en in Ma nia tis et a l, Molecula r Cloning : A N ov . 22, 2001 La bor a tor y Ma nua l, Cold Spr ing Ha r bor La bor a tor y , Cold Spr ing Ha r bor , N Y. ( 1 9 89 ) . This s cr eening m a y a ls o be per f or m ed by the us e of Poly m er a s e Cha in Rea ction pr oce dur es ( PCR) . PCR pr ocedur es a r e des cr ibed in deta il in Mullis et a l, Meth. EnZy m ol. 155: 3 3 5- 3 50 ( 19 87 ) a nd Er lich, ( ed. ) , PCR Technolog y , Stockton Pr es s , N eW Yor k ( 19 89 ) . [ 003 3 ] The ex pr es s ion s ig na ls a ctiv e in ta r g et cells us ua lly com pr is e a pr om oter tha t is r ecog nis ed by the hos t or g a nis m a nd is oper a bly linked to the D N A to be ex pr es s ed in the tr a ns f or m a nt. Such a pr om oter m a y be inducible or cons ti tutiv e. The pr om oter s a r e oper a bly linked to s a id D N A by r em ov ing the pr om oter f r om the s our ce D N A by r es tr iction enZy m e dig es tion a nd com bining the is ola ted pr om oter s eq uence W ith the ex pr es s ible D N A s eq uence. B oth the na tiv e pr om oter s eq uence of the s tr uctur a l g ene of inter es t a nd m a ny heter olog ous pr om oter s m a y be us ed to dir ect a m pli? ca tion a nd/ or ex pr es s ion of s a id s tr uctur a l g ene. Suita ble pr om oter s f or a nim a l a nd in pa r ticula r m a m m a lia n hos ts a r e thos e der iv ed f r om the g enom es of v ir us es s uch a s poly om a v ir us , a denov ir us , f oW lpox v ir us , bov ine pa pillom a v ir us , a v ia n s a r com a v ir us , Rous e s a r com a v ir us ( RSV) , cy tom eg a lov ir us ( CMV) , a r etr ov ir us a nd Sim ia n Vir us 40 ( SV40) , f r om heter olog ous m a m m a lia n pr om oter s s uch a s the [ 3 - a ctin pr om oter or a v er y s tr ong pr om oter , eg a r ibos om a l pr otein pr om oter , a nd f r om the pr om oter nor m a lly a s s ocia ted W ith s tr uctur a l g ene s eq uence to be ex pr es s ed, pr ov ided s uch pr om oter s a r e com pa tible W ith the hos t cell s y s tem s . [ 003 4] The tr a ns cr iption of a n ex og enous D N A encoding the des ir ed s tr uctur a l g ene ca n- be incr ea s ed by ins er ting a n enha ncer s eq uence into the D N A a s a com ponent of the nucleic a cid/ pr otein com plex a ccor ding to the inv ention. Enha ncer s a r e r ela tiv ely or ienta tion a nd pos ition indepen dent. Ma ny enha ncer s eq uences a r e knoW n f r om m a m m a lia n g enes ( e. g . ela s ta s e a nd g lobin) . HoW ev er , ty pica lly one W ill em ploy a n enha ncer f r om a euka r y otic cell v ir us . Ex a m ples include the SV40 enha ncer on the la te s ide of the r eplica tion or ig in ( bp 100- 27 0) a nd the CMV ea r ly pr om oter enha ncer . The enha ncer m a y be s pliced into the r ecom bina nt chim er ic s eq uence a t a pos ition 5 or 3 to the coding D N A s eq uence, but is pr ef er a bly loca ted a t a s ite 5 f r om the pr om oter . [ 003 5] Hos t cells to W hich nucleic a cids ca n be deliv er ed by a m ethod a ccor ding to the inv ention include ins ect a nd v er tebr a te cells . In r ecent y ea r s pr opa g a tion of v er tebr a te cells in cultur e ( tis s ue cultur e) ha s becom e a r outine pr oce dur e. Ex a m ples of us ef ul v er tebr a te hos t cell lines a r e epithelia l or ? br obla s tic cell lines s uch a s Chines e ha m s ter ov a r y ( CHO) cells , COS1 cells ( m onkey kidney cells tr a ns f or m ed W ith SV40 T- a ntig en) , CV1 cells ( pa r ent line of the f or m er ) , Ra t1 ( r a t ? br obla s t) cells , N IH 3 T3 cells , HeLa cells , LLC- Pk1 ( pig kidney epithelia l) cells or 29 3 T cells . The hos t cells r ef er r ed to in this dis clos ur e com pr is e cells in in v itr o/ ex v iv o cultur e a s W ell a s cells tha t a r e W ithin a hos t a nim a l. [ 003 6 ] Accor ding to a f ur ther a s pect of the pr es ent inv en tion r ela ting to a ntis ens e- , a ntig ene- or olig oZy m e- a p pr oa ches , the g r oup of hos t cells W hich ca n be ta r g eted a ls o includes pla nt cells or tis s ues , W hich pr ef er a bly ca n be r eg ener a ted to W hole pla nts . [ 003 7 ] Es pecia lly s uita ble f or us e in the pr oces s a ccor ding to the inv ention a r e a ll thos e s tr uctur a l g enes W hich upon US 2001/ 0044150 A1 ex pr es s ion pr oduce pr oteins or poly peptides W hich a r e ben e? cia l f or the tr a ns f or m ed cells , tis s ues or a nim a ls , eg W hich com pens a te ev entua l m uta ta tions , or W hich ha v e pha r m a colog ica l pr oper ties a nd could be us ed a s pha r m a ceutica l a g ents in the tr ea tm ent of dis ea s es . Ex a m ples f or s uch s tr uctur a l g enes include thos e encoding hor m ones , im m unom odula tor s a nd other phy s iolog ica lly a ctiv e s ub s ta nces . [ 003 8] The g enes tha t pa r ticula r ly com e into cons ider a tion W ithin the s cope of this inv ention ther ef or e include, but a r e not lim ited to, f or ex a m ple, m a m m a l- s peci? c g enes , s uch a s the ins ulin g ene, the s om a tos ta tin g ene, the inter leukin g enes , the t- PA g ene, etc. , or g enes of m icr obia l or ig in, s uch a s the N PT II g ene, etc. a nd s y nthetic g enes , s uch a s the ins ulin g ene, etc. [ 003 9 ] Apa r t f r om na tur a lly occur r ing s tr uctur a l g enes tha t code f or a us ef ul a nd des ir a ble pr oper ty or a pha r m a colog ica l a g ent, W ithin the s cope of this inv ention it is a ls o pos s ible to us e g enes tha t ha v e been m odi? ed pr ev ious ly in a s peci? c m a nner us ing chem ica l or g enetic eng ineer ing m ethods . [ 0040] Fur ther m or e, the br oa d concept of the pr es ent inv ention a ls o includes g enes tha t a r e pr oduced entir ely or pa r tia lly by chem ica l s y nthes is . Genes or D N A s eq uences tha t m a y be us ed W ithin the s cope of the pr es ent inv ention a r e ther ef or e both hom olog ous a nd heter olog ous g ene( s ) or D N A a nd a ls o s y nthetic g ene( s ) or D N A a ccor ding to the de? nition g iv en W ithin the s cope of the pr es ent inv ention. The ins ulin g ene m a y be m entioned a t this point a s a n ex a m ple of a s y nthetic g ene. [ 0041] Alter na tiv ely , olig onucleotides ca n be us ed cor r e s ponding in s eq uence to a cellula r s eq uence to be ta r g eted, either in the s a m e ( a ntig ene) coding dir ection, a s s uch or ca r r y ing a m uta tion, or in the a ntis ens e coding dir ection. [ 0042] Pos s ible m ethods f or the dir ect tr a ns f er of the nucleic a cid/ pr otein com plex a ccor ding to the inv ention into a cell com pr is e, f or ex a m ple, the tr ea tm ent of cells us ing pr ocedur es tha t m odif y the pla s m a m em br a ne, f or ex a m ple, poly ethy lene g ly col tr ea tm ent, lipos om e- ba s ed technolo g ies , hea t s hock tr ea tm ent or electr opor a tion, or a com bi na tion of thos e pr ocedur es ( s ee eg Chu et a l. ( 19 87 ) , N ucl. Acids Res . 15: 13 11- 13 26 ; Hodg s on a nd Sola im a n ( 19 9 6 ) , N a tur e B iotech. 14: 3 3 9 - 3 42; Shillito et a l. ( 19 85) , B io Technolog y 3 : 109 9 - 1103 ) . [ 0043 ] In the electr opor a tion techniq ue, cells tog ether W ith the nucleic a cid/ pr otein com plex us ed a ccor ding to the inv ention a r e s ubj ected to electr ica l puls es of hig h ? eld s tr eng th. This r es ults in a r ev er s ible incr ea s e in the per m e a bility of biom em br a nes a nd thus a lloW s the ins er tion of the nucleic a cid/ pr otein com plex a ccor ding to the inv ention. Electr opor a ted cells r eneW their cell m em br a ne, div ide a nd f or m a g g r eg a tes or m onola y er s of tr a ns f or m ed cells . Selec tion of the tr a ns f or m ed cells ca n ta ke pla ce W ith the a id of the a bov e- des cr ibed phenoty pic m a r ker s . [ 0044] A f ur ther m ethod f or the dir ect intr oduction of the nucleic a cid/ pr otein com plex us ed a ccor ding to the inv en tion into cells , W hich is ba s ed on pur ely chem ica l pr ocedur es a nd W hich ena bles the tr a ns f or m a tion to be ca r r ied out v er y ef ? ciently a nd r a pidly , is des cr ibed in J or da n et a l. ( 19 9 6 ) , N ucl. Acids Res . 24: 59 6 - 6 01) . N ov . 22, 2001 [ 0045] Als o s uita ble f or the tr a ns f or m a tion of eg a nim a l cells is dir ect g ene tr a ns f er us ing co- tr a ns f or m a tion [ Schocher RJ et a l, B io/ Technolog y , 4: 109 3 - 109 6 ( 19 86 ) ] . Co- tr a ns f or m a tion is a m ethod tha t is ba s ed on the s im ul ta neous ta king up a nd integ r a tion of v a r ious D N A m olecules ( non- s electa ble a nd s electa ble g enes ) into the r ecipient s g enom e a nd tha t ther ef or e a lloW s the detection of cells tha t ha v e been tr a ns f or m ed W ith non- s electa ble g enes . [ 0046 ] Fur ther m ea ns f or ins er ting the nucleic a cid/ pr otein com plex us ed a ccor ding to the inv ention dir ectly into a cell com pr is e us ing pur ely phy s ica l pr ocedur es , f or ex a m ple by m icr oinj ection us ing ? nely dr a W n m icr opipettes [ N euha us et a l ( 19 87 ) ] or by bom ba r ding the cells W ith m icr opr oj ectiles tha t a r e coa ted W ith the tr a ns f or m ing or tr a ns iently tr a ns f ecting nucleic a cid [ Micr opr oj ectile B om ba r dm ent ; W a ng Y- C et a l, Pla nt Mol. B iol. 11: 43 3 - 43 9 ( 19 88) ] or a r e a cceler a ted thr oug h a nucleic a cid conta ining s olution in the dir ection of the cells to be tr a ns f or m ed by a pr es s ur e im pa ct ther eby being ? nely a tom iZed into a f og W ith the s olution a s a r es ult of the pr es s ur e im pa ct [ EP- A- 43 4, 6 16 ] . Micr o pr oj ectile bom ba r dm ent ha s been a dv a nced a s a n ef f ectiv e tr a ns f or m a tion techniq ue f or eg a nim a l cells . [ 0047 ] The lis t of pos s ible tr a ns f or m a tion a nd tr a ns f ection m ethods g iv en a bov e by W a y of ex a m ple is not cla im ed to be com plete a nd is not intended to lim it the s ubj ect of the inv ention in a ny W a y . [ 0048] The pr es ent inv ention a ls o concer ns the pr epa r a tion of tr a ns g enic a nim a l cells , including oocy tes , s per m a tocy tes a nd Zy g otes etc. , tr a ns g enic or g a ns a nd tr a ns g enic a nim a ls , a s W ell a s the cells a nd a nim a ls obta ined by us e of a m ethod a ccor ding to the inv ention. [ 0049 ] A tr a ns g enic a nim a l W hich ca n be pr oduced a ccor ding to the inv ention pr ef er a bly is a m a m m a l, W ith pig s , r odents a nd r um ina nts being m os t pr ef er r ed. Addition a lly , the pr es ent inv ention ca n be us ed f or s om a tic g ene ther a py in hum a ns , W hich us e is a ls o pa r t of the inv ention. [ 0050] The m ethod a ccor ding to the inv ention ca n be a dv a nta g eous ly us ed to incr ea s e The tr a ns f or m a tion ef ? ciency of non- Ag r oba cter ium m edia ted tr a ns f or m a tion pr o ces s es , in tha t, f or ex a m ple, les s tr a ns f or m ing D N A is needed a s com pa r ed to the conv entiona l techniq ues . In a ddition the q ua lity of the integ r a ted D N A ca n be im pr ov ed by the pr ecis ion of the integ r a tion pr oces s , a nd pos s ible r ea r r a ng em ents W hich a r e likely to ha ppen to na ked D N A ca n be a v oided. [ 0051] The m ethod a ccor ding to the inv ention thus pr o v ides v a lua ble m ea ns f or the tr ea tm ent of v a r ious dis or der s s ucceptible to g ene ther a py a nd ena bles the pr oduction of tr a ns g enic a nim a ls , W her e the ef f iciency of integ r a tion of na ked D N A is a lim iting f a ctor . Fur ther m or e, the m ethod is us ef ul in the tr ea tm ent of ca ncer cells , a s a neW non- v ir a l s y s tem W ithout LTR a nd pos s ible ha Za r ds connected W ith them . A s pecia l f ea tur e of the com plex es us ed a ccor ding to the inv ention is their D N As e r es is ta nce a nd their a bility to a ls o ta r g et non div iding cells , due to their nuclea r ta r g eting potentia l. [ 0052] The inv ention is f ur ther des cr ibed, f or the pur pos es of illus tr a tion only , in the f olloW ing ex a m ples . US 2001/ 0044150 A1 EXAMPLES Ex a m ple 1 Cons tr uction of Pla s m ids f or Monitor ing the Intr a cellula r Loca lis a tion of Vir D 2 Pr otein [ 0053 ] The N ter m ina l g f p f us ion v ector p[ 3 a ct- N GFP, conta ining the [ 3 - a ctin pr om oter a nd SV40 ter m ina tor is us ed ( Ludin et a l. ( 19 9 6 ) Gene 17 3 : 107 - 111) . v ir D 2 is cloned a s entir e g ene, or a s a m uta nt g ene conta ining only the N - ter m ina l ( Ros s i et a l. ( 19 9 3 ) Mol. Gen Genet. 23 9 : 3 45- 3 53 ) , or C ter m ina l N LS, or m uta nt g ene in W hich both nuclea r loca lis a tion ( N LS) s eq uences a r e deleted. For detection of the pr otein by a nti- Vir D 2 a ntibodies , v ir D 2 is cloned in m a m m a lia n ex pr es s ion v ector pcD N A3 ( Inv itr og en) . Ex a m ple 2 Cons tr uction of Pla s m id f or Monitor ing the Intr a cellula r Loca lis a tion of Vir D 1 Pr otein [ 0054] Vir D 1 g ene is a m pli? ed by PCR us ing pVCK225 ( V. C. Kna uf a nd E. W . N es ter , Pla s m id 8, 45- 54 ( 19 82) ) a s a tem pla te. The hea m a g g lutinin ( HA) epitope ta g g ed con s tr uct pHA- D 1 is pr epa r ed by lig a ting a n HA epitope encoding olig onucleotide to the 5 end of the v ir D 1 PCR pr oduct, in- f r a m e W ith the initia tor m ethionin codon, in the m a m m a lia n ex pr es s ion v ector pcD N A3 ( Inv itr og en) . Ex a m ple 3 Monitor ing Intr a cellula r Loca liza tion of Vir D 2 Pr otein in Ma m m a lia n Cells [ 0055] W hen ov er ex pr es s ed in m a m m a lia n cells ( HeLa , 29 3 ) , Vir D 2 pr otein s hoW s ex clus iv ely nuclea r loca lis a tion, W hich is m onitor ed either by GFP- Vir D 2 f us ion, or by im m unor ea ction of v ir D 2 tr a ns f ected cells W ith a nti- Vir D 2 a ntibodies . The pr es ence of a ny of tW o loca lis a tion s ig na ls , on the N - a nd C- ter m inus of the Vir D 2, is s uf ? cient f or ef ? cient nuclea r loca lis a tion, W hile deletion of both N LS s eq uences r ender s the pr otein cy topla s m ic. Ov er ex pr es s ion of Vir D 2 pr otein in m a m m a lia n cells does not ha v e a v is ible neg a tiv e ef f ect on their g r oW th a nd div is ion. Ex a m ple 4 Monitor ing Intr a cellula r Loca lis a tion of Vir D 1 Pr otein in Ma m m a lia n Cells [ 0056 ] W hen ov er ex pr es s ed in m a m m a lia n cells ( HeLa , 29 3 ) , Vir D 1 pr otein s hoW s ex clus iv ely cy topla s m ic loca li s a tion W hich is m onitor ed by im m unor ea ction of pHA- D 1 tr a ns f ected cells W ith a n a nti- HA epitope 12CA5 m ono clona l a ntibody ( B oehr ing er ) . Ov er ex pr es s ion of Vir D 1 pr o tein in m a m m a lia n cells does not ha v e a v is ible neg a tiv e ef f ect on their g r oW th a nd div is ion. Ex a m ple 5 Pr oduction of M13 s s D N A f or Ana ly s is of N uclea r Ta r g eting by Gene Ex pr es s ion [ 0057 ] Fir s t, the g f p cy cle3 g ene is cloned f r om potGFP cy cle3 v ector ( Cr a m er i et a l. ( 19 9 6 ) N a tur e B iotechnolog y 14: 3 15- 3 19 ) into the Sm a l s ite of pB lues cr ipt SKII a s Stul f r a g m ent. Stul ends a r e blunted W ith T4 D N A poly m er a s e. Then, g f pcy cle3 g ene is cloned a s N otl/ Ps tl f r a g m ent in the cor es ponding s ites of M13 v ector conta ining the r ig ht bor der N ov . 22, 2001 s eq uence, na m ed Y3 ( M13 RB MCS) . Pha g e inf ection is done in E. coli N M522. B a cter ia a r e g r oW n f or 5h a t 3 7 C. a nd s s D N A is ola ted f r om the s uper na ta nt by Q ia g en pla s m id pur i? ca tion kit. Ex a m ple 6 Pr oduction of the Com plex es Us ed in D ir ect As s a y f or Pr otein Im por t a nd Micr oinj ection [ 0058] D N A is ? uor es cently la beled by intr oducing r hoda m ine dUTP into the PCR r ea ction pr oduct. The pr im er s us ed f or the PCR both conta in the r ig ht bor der ( RB ) s eq uence a t ea ch ex tr em ity of D N A, in oppos ite or ienta tion. The PCR pr oduct is then hea t dena tur ed a nd the r es ulting s s D N A of 1 kb leng th r ea cted W ith Vir D 2 pr otein f or 1 h a t 3 7 C. The r ea ction is s topped on ice a nd a nd incuba ted on ice W ith Vir E2 pr otein, f or a nother 3 0 . Ex a m ple 7 Micr oinj ection of the T- D N A Com plex es into Ma m m a lia n Cells [ 0059 ] T- D N A com plex es , pr oduced in the s a m e W a y a s ex pla ined a bov e, a r e m icr oinj ected into the cy topla s m of m a m m a lia n cells ( HeLa ) a nd nuclea r ta r g eting is m onitor ed. Since loW a m ounts of s s D N A a r e us ed in this a s s a y , intens ity of the s ig na l ha s to be incr ea s ed by a nti- r hoda m ine a ntibod ies . N uclea r ta r g eting is a ls o being m onitor ed by us ing a n a ctiv e g ene pr es ent on s s D N A. The g r een- ? uor es cent pr o tein g ene ( g f p) is cloned in a M13 v ector conta ining the r ig ht bor der s eq uence. ( Function of the g f p is tes ted by m icr oin j ection of both ds , a nd s s D N A into the nucleus of HeLa cells . ) Pha g e s s D N A is pr oces s ed W ith Vir D 2, a nd Vir E2 is a dded. Com plex es a r e m icr oinj ected in the cy topla s m of HeLa cells a nd ex pr es s ion of GFP is m onitor ed a f ter 12- 24h. Ex a m ple 8 Sta ble Integ r a tion of T- D N A D er iv ed f r om the Ar ti? cia l Com plex es [ 006 0] For tes ting the a bility of a r ti? cia l com plex es to integ r a te T- D N A in the m a m m a lia n g enom e, a hy g r om y cin r epor ter g ene is cloned in a n M13 v ector conta ining the r ig ht bor der s eq uence. Alter na tiv ely , D N A is pr oduced by PCR, in W hich ea ch of the pr im er s conta in the r ig ht bor der s eq uence. s s D N A is com plex ed W ith Vir D 2 a nd Vir E2 pr oteins , a nd inj ected in the cy topla s m of HeLa cells . Af ter s election r es is ta nt clones a r e picked a nd their D N A a na ly s ed f or the pa tter n of integ r a tion. Ex a m ple 9 N uclea r Ta r g eting of the T- D N A Com plex es [ 006 1] Ar ti? cia l com plex es , cons is ting of Vir D 2 pr otein cov a lently a tta ched to the s ing le s tr a nded D N A, a nd Vir E2 pr otein, a r e tes ted in dir ect a s s a y of pr otein im por t into HeLa nuclei. s s D N A is r hoda m ine la belled by PCR a nd dig itonin per m ea bilis ed HeLa nuclei a r e us ed a s a ta r g et ( Ada m et a l. ( 19 9 0) J our na l of Cell B iolog y 111: 807 - 816 ) . Indeed, the T- D N A com plex is ef ? ciently ta r g eted to the HeLa nuclei. Ef ? cient ta r g eting is dependent on the f unction of nuclea r loca lis a tion s ig na l of Vir D 2. Ex a m ple 10 Ana ly s is of Vir D 2- Vir D 2 a nd Vir D 1 - Vir D 2 Inter a ctions in Ma m m a lia n Cells [ 006 2] Pr otein- pr otein inter a ctions a r e v er i? ed in m a m m a lia n s y s tem by s tudies of s ubcellula r loca lis a tion of US 2001/ 0044150 A1 Vir D 1, Vir D 2 a nd its der iv a tiv e deleted in both N LSs in HeLa a nd HEK29 3 cells us ing GFP- Vir D 2 f us ion f or loca li s a tion of Vir D 2 a nd HA epitope f or loca lis a tion of Vir D 1. Vir D 2 pr otein loca lis es ex clus iv ely in the nuclei W hen ex pr es s ed in m a m m a lia n cells . D eletion of both N LS s eq uences r ender s the pr otein cy topla s m ic. HoW ev er , this double m uta nt is tr a ns loca ted to the nucleus in the pr es ence of W ild ty pe Vir D 2 pr otein, indica ting Vir D 2- Vir D 2 inter a ction in m a m m a lia n cells . Als o the Vir D 1 pr otein, by its elf loca lis ing in the cy topla s m , m ov es to the nucleus W hen co- ex pr es s ed W ith the W ild ty pe Vir D 2 pr otein, indica ting Vir D 1- Vir D 2 inter a ction in m a m m a lia n cells . Ex a m ple 11 Pur i? ca tion of the Vir D 2 Pr otein [ 006 3 ] A s eq uence ta g encoding s ix his tidine r es idues is a dded to the C- ter m ina l of the Vir D 2 pr otein. The r ecom bina nt pr otein is ex pr es s ed in E. coli B L21 a nd pur i? ed by his tidine- nickel a f ? nity chr om a tog r a phy f olloW ed by g el ? ltr a tion a nd hepa r in a f ? nity chr om a tog r a phy a ccor ding to s ta nda r d m ethods knoW n in the a r t. Ex a m ple 12 Pr oduction of Sing le Str a nded Vir D 2 Pr oces s ing Subs tr a tes Conta ining the Hy g r om y cin Res is ta nce Gene [ 006 4] Fir s t, the hy g r om y cin r es is ta nce g ene conta ining the D r a l/ Fs pl r es tr iction f r a g m ent of pTK- Hy g ( Clonetech) is cloned into the Hincl s ite of the Y3 v ector ( de? ned in ex a m ple 5) . The r ecom bina nt pla s m id is tr a ns f or m ed into E. c0li N M522 a nd s s pha g e D N A is is ola ted. Olig onucle otides com plem enta r y to the EcoRV a nd Ka s i s ites in the pha g e D N A a r e us ed to m edia te the clea v a g e of the s s D N A by EcoRV a nd Ka s I r es tr iction nuclea s es . The obta ined EcoRV/ Ka s i s s D N A f r a g m ent conta ins the hy g r om y cin r es is ta nce g ene pos itioned doW ns tr ea m of the r ig ht bor der s eq uence. Ex a m ple 13 Tr a ns f ecion of Ar ti? cia l T- D N A Com plex es into HeLa Cells [ 006 5] The s s D N A EcoRV/ Ka s I f r a g m ent is r ea cted W ith either Vir E2 or Vir D 2 pr oteins a lone or is ? r s t r ea cted W ith v ir D 2 f olloW ed by r ea ction W ith v ir E2. The r es ulting pr o tein: s s D N A com plex es a s W ell a s unr ea cted s s D N A a r e tr a ns f ected into HeLa cells us ing Eug ene- 6 tr a ns f ection r ea g ent ( B oehr ing er - Ma nnheim ) . Hy g r om y cin r es is ta nt clones a r e s elected in tW o independent ex per im ents . The num ber of hy g r om y cin r es is ta nt clones obta ined is s ig ni? ca ntly hig her f or cells tr a ns f ected W ith s s D N A+Vir D 2 a nd s s D N A+Vir D 2+Vir E2 com plex es ( ta ble 1) s ug g es ting tha t the pr oteins f a cilita te s ta ble integ r a tion of the hy g r om y cin r es is ta nce g ene by either pr otecting the s s D N A f r om deg r a da tion by hos t cells nuclea s es a nd/ or by f a cilita ting the nuclea r im por t of the com plex . Tr a ns g ene copy num ber a nd tr a ns g ene integ r ity is a na ly Zed f or s ev er a l lines f r om ex per i m ent 1. Pr elim ina r y da ta indica te tha t the hy g r om y cin g ene integ r a tes a t s ing le dis tinct loci in a ll line a na ly Zed s o f a r . Pr elim ina r y r es ults a ls o indica te tha t both Vir E2 a nd Vir D 2 N ov . 22, 2001 pr oteins pr otect the s s D N A pr ior to its integ r a tion into the g enom e. As ex pected the pr otectiv e a ction of Vir E2 s eem s to r es ult f r om the pr otein coa ting the entir e leng th of the s s D N A, W her ea s the cov a lent a tta chm ent of the Vir D 2 pr otein to the 5 end of the T- D N A s peci? ca lly pr otects the 5 end. TAB LE 1 N um ber of hy g r om y cin r es is ta nt clones obta ined in tr a ns f ection ex per im ents Tr a ns f ected D N A Res is ta nt clones Res is ta nt clones ( com plex ) Ex per im ent 1 Ex per im ent 2 s s D N A 6 11 s s D N A + Vir EZ 6 29 s s D N A + Vir D Z 7 3 4 s s D N A + Vir D Z + Vir EZ 12 44 1. A m ethod f or intr oducing nucleic a cids into cells , com pr is ing : ( a ) pr epa r ing a chim er ic r ecom bina nt nucleic a cid con s tr uct tha t com pr is es in oper a ble linka g e to a n ex pr es s ible D N A or to a n olig onucleotide a t lea s t one T- D N A bor der s eq uence or f unctiona l pa r t ther eof , W hich s er v es a s a s ubs tr a te in the Vir D 2 clea v a g e r ea ction, a s de? ned her einbef or e; ( b) clea v ing of the nucleic a cid s ubs tr a te pr epa r ed a ccor d ing to s tep ( a ) by m ea ns of Vir D 2 pr otein, W hich m a y be a ccom pa nied by f ur ther Vir pr oteins s uch a s , f or ex a m ple Vir D 1 a nd/ or Vir E2 a nd/ or a ny other nucleic a cid binding pr otein, W hich is a ble to pr otect s a id nucleic a cid f r om nuclea s e a tta ck; ( c) intr oducing the thus clea v ed nucleic a cid com pr is ing a t lea s t the Vir D 2 pr otein cov a lently bound to the 5 end of the clea v a g e s ite into the cells to be tr a ns f or m ed by m ethods knoW n in the a r t. 2. A m ethod a ccor ding to cla im 1, W her ein the tr a ns f or m a tion or tr a ns f ection is a chiev ed by a m ethod s elected f r om the g r oup cons is ting of m icr oinj ection, electr opor a tion of cells , dir ect g ene tr a ns f er a nd ba llis tic pa r ticle a cceler a tion. 3 . Us e of a s ubs ta ntia lly pur e nucleic a cid/ pr otein com plex com pr is ing a chim er ic r ecom bina nt nucleic a cid con s tr uct cov a lently a s s ocia ted W ith a Vir D 2 pr otein obta ina ble by the m ethod a ccor ding to cla im 1 f or the tr a ns f or m a tion or tr a ns f ection of a nim a l cells . 4. Us e a ccor ding to cla im 3 , W her ein the chim er ic nucleic a cid cons tr uct com pr is es a n ex pr es s ible D N A s eq uence under the contr ol of a nim a l or v ir a l ex pr es s ion s ig na ls . 5. Us e a ccor ding to cla im 4, W her ein the s a id ex pr es s ible D N A s eq uence encodes f or a s tr uctur a l g ene. 6 . Us e a ccor ding to cla im 4, W her ein the s a id a nim a l ex pr es s ion s ig na ls a r e pr om oter a nd ter m ina tion s eq uences f unctiona l in a nim a l cells . 7 . Us e a ccor ding to cla im 3 , W her ein the chim er ic nucleic a cid cons tr uct includes a n olig onucleotide, f or a ntis ens e- , a ntig ene- or olig oZy m e- a ppr oa ches . * * * * *
Ward A. Thompson v. City of Lawrence, Kansas Ron Olin, Chief of Police Jerry Wells, District Attorney Frank Diehl, David Davis, Kevin Harmon, Mike Hall, Ray Urbanek, Jim Miller, Bob Williams, Craig Shanks, John Lewis, Jack Cross, Catherine Kelley, Dan Ward, James Haller, Dave Hubbell and Matilda Woody, Frances S. Wisdom v. City of Lawrence, Kansas Ron Olin, Chief of Police David Davis, Mike Hall, Jim Miller, Bob Williams, Craig Shanks, John L. Lewis, Jack Cross, Kevin Harmon, Catherine Kelley, Dan Ward and James Haller, Jr., 58 F.3d 1511, 10th Cir. (1995)