土壌細菌からの直接DNA抽出法 : 異なるDNA抽出法の比較
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(2) 6E, @ @ @ & l t - $ & C ~ @ h T L 3 5 DT, ?a>% %Tb 3 PCR'fis T 3 7'6 L\?z bl, PVPP ( P o l y .. v i n y l p o l y p i r r o l i d o n e ) t Z k 6#%@&?7-> 7z, % L \ 7 PCR ??fTL\, DNA D @ r f r E & ? 7 -xY/LT 8~ @%, L7"zfj$, $gEgg5&*" ,R3s*%?At:S+ %Re. <. fT97co 7 8 a - ; j : ! f / L T t 3 lOObp D%@LfihT 3 f 2 L \a;, 8f;/JJ\%%/j\/L (SPREADEX~EL MINI GEL) T t 3 l b p 3T%%q%T;ti6,. 2. 2.. ssa>fsE!i. f-@-ff27?bB%@ft~i%%. CZ%L\T, L 72". L 7 L \ 6 & 2 , ZHI. 6mfiDSGWfilb l g Dk@&?BB. f-&& 6 O@@DNA &%& DNA #lttj%?& ; 1) k@%$$tZ, @T%% L 7z PVPP (Zoomg/*@ lg) ? ? l l U k 7 $ + V T 4 Y-(Zfili$7z@, 37"CT 1-2 %%74 Y 4 3 - 4 - V s Y 3 - 6 . EL\T 2 0 0 , 1 ~ D 23% sodium dodecyl s u l p h a t e (SDS) ? ? A h , 5O0CT 30 %fikTf&, -80°CTD?@$& g@&?@ 9. BEADS.2)SPB 1 9 y 77- tL 20%SDS, P r o t e i n a s e , $& 0 BEADS3)DNA M ttj 19 y 7 7 bZ 20%SDS,P r o t e i n a s e , Mf&D BEADS, /. 36'@ : k@-!?Y?/b?? (1. Og wet wt) 0 5 { g i% ~ s ~(TE s 7 7 7 - C Z ~ & @ $ e 7 ~ @ )?? L \ ~ E (& 5 3 1 , ~ ~ ~ E D P U U Z I V (LTA EA 777-t~7&7%$@7z@> ??AhE&(5%>@, g l L \ (15000rpm~10 -T*@7Zt$??@q7Fl C S O 4 Y ~ " U / ~ I - / L ~ L \ ~ & E $ @2 ~ ~~ & 9. m. -. I - / ~ ~ , ~ E T D Nb ?A ? f +~6 ,~ / . ; , : *@sf ~ 7 " / ~ (Og 1 .wet. CTRB &. wt) CL ( 1.5M NaC1) , hexadecyltrimethylammonium (UT CTAB k @ < T 6 ) , O . 1 M T r i s HC1 (pH 8 . 0 ) , 0.1M EDTA (pH 8.0) , 0.1M sodium phosphate (pH 8.0) A 9 D DNA # I 8 1 9y 77 -CL A .. fi $$. a%. L\h@&$j$, 7 ' .ST--+! ~ K ? ? A h , 225rpm T & T & 30 ??% Z Y B% ~ SDS 2 L \ h g ? R (65°C) CZ7 2 @?BYC ' -Y 4 Y Y LTglL\ (5000rpmx 10 3 ) L 7 4 + 7 z k B & t r F I B ~ Pa a d v ~ A 2 A h . E A/( a&, * W 7 ? t 3 2 @ ~ r - > - ( r E l C B D 4 Y 7 " ~ / { 1 -. EL, 711-/LMtt:27/L~-/~?kEtZL->T. I L ? ? L ~ ~ L ? ~ E $ @ D N A & Ib/ 2Y$ + 6 ,. DNA ~ t tL ~j Z ,~ 2) V 3 E @ g s i l g z g l L \ ? & t Z L 9 T@#f;/JJ\@f&tg. 2 . 3 . DNA $653 BIO-SPIN 75 7 A ( 4 IcmX 2.5cm). Be??5 o 3) Bead-beating. (Bio Spec. $kg) ? ? H L \ 7 E %. ,@B2?75 4) CTAB ?A : k t (1. 5M NaC1) 2 1%CTAB ??$ DNA j Httlr19y77-&HL\7 i%?RT1' Y 4 = 4 - V 3 2 2 t T 5 (2 %7~7), 5 9 : k@%$$D5--10{gDSDS'@ j@Tt@Bfj$, P u a $ ~ b A # l t t : 2 4 Y 7 ° a 1 ~ 1 /L?kb%iZ& -> T DNA #ltt)&? L k , UTCrt3 3, 4, 5 c G i ? & t r ~ L \ - i C g $L L \ ~ @ @ i???Z-F0 Bead-Beater &$ : kg-!? Y 7 ' / L (1. Og wet wt) 2 Bead-Beater t Z A h 3ml Sodium Phosphate B u f f e r (SPB) , IXSDS, FIED Beads 2hLIkT@, $&6!'J@ ' B ???T3, glb&? fill$ ( 2 8 0 0 ~x 15 %) q% -f:k$$f&iZ.fib-?'< 0.5M EDAT 2 %a) 1/10 E D BE@% 9 9 A (3M) &?Ah,? k k T 20 %?BYE@? $j$ l o , OOOg T 5 %Ba'JglL\ $ @ a t 2 T ~ @ , @ F E E I E & ? R & Tk $~$ ~ f&2FIB~1' ~ 7 ~ u 1 q 1 lL??Ah?kb%$@, 3=9--1/LT&3D7/L3/I.&?@% L T DNA &I/.;, b 2@7z, % IZ bead-beater ? A T 7'6 6 $j!jEi%+$RJ (S'DS) ~ ~ ~ ~ ~ A ~ D ~ ~ . ; b L % k f T 9 7 c o Z Z T , 947'251<.;,77-&T+L <i&+5, 1 ) s 1~ 9 ~~ 7 7 - c z I%SDS, BED. PVPP %% 2 0. 4g (6$ 0. 5cm) Ah$$@* (dH,O) ?? 0. 5m1, 0.25ml bR% t L A h g l L \ L 7 B < (4100rpm, 5 %), #I% L7z DNA A 7 7 " / L (%?I&) 2 1 0 0 , 1~ A h 4100rpm T 5 %VB@E@ 2 !Elf7 5 , %@fi;,$%b6 2 PCR 2?7L\%rfrG&@Z\"P6 Zk. *<, a,. I R J ~ T B7 ~s t- ~F ~~i a 2m, ~~b ;1a z~a %~? ~ &D&fiXIZ 2 PBh6 1El El D#%@f&C~t3, % @@D~~~fi~$@ 7'6E1fibl,Th6, L< DNA &I/.;, b a&Cr& 5 $;, gi@3-5 u I T ' '3 0. a'-. 2.4.. PCR PD%rfiE. PCR TD?$rfrEC31 6 s. Y $Y-A. rp, % t ~ , $Bb$i v i &$fib%. DNA Dglk@mfi. va. &? B m 2 L T. Nested-PCR T f T 5 ( ~ e n e ~ mPCR p System 2400, P e r k i n Elmer), %?, 27f-519r ( & T i 3 Lane tZ L 6%&E$!?lJ DllR) D 7 ' 7 4 -7-&HL\7 V3 $Bmfi&?@F L7z $3, Zbr 27f-109r 2 357f-519r T Vl, V2 $Bb$i?? B-?' L k ; , PCR %#b3 95"C2 5% 1CYCLE, 95OC1 3, 5g0C40 $9, 72"Cl 3 2 30 CYCLE, 72°C 7 %&? 1CYCLE ~ T Tio Q 27f-519r, 357f-519r D 7 ' 5 1'. -7-$R&&b@TC3&$fB@2&D@rfrEfi~T?%!T 3.27f-109r. Tt3KL\$ZBD~flED@rfrEfi~T?%!T (Lane b.. , 3~6. ~F+ LLjY74 - & H ?-D%R&&h@ L \ ~ D 1991) t3&1C Z % L T ; t i 6 ,.
(3) 7°74-7-a> $H&&b* 27f-1091-1 29f2-107CT 29f3-107CT 27f-519r 357f-519r. 2. 5.. ah6 k?BU$h6. % 2& B!l 3rJ 27f : 5'AGAGTTTGATCMTGGCTCAG 109r 1 : 5' ACGYGTTACKCACCCGT 29f 2 : 5' AGAGTTTGATCMTGGCTCAGE 107RcT : 5 ' ACGTGTTACTCACCCGTQ 29 f 3 : 5' AGAGTTTGATCMTGGCTCAGGA 107rCT : 5'ACGTGTTACTCACCCGTCT 27f : 5' AGAGTTTGATCMTGGCTCAG 5 19r : 5' GWATTACCGCGGCKGCTG 357f : 5'CTCCTACGGGAGGCAGCAG 5 19r : 5 'GWATTACCGCGGCKGCTG. *-*-. mx;%al PCR f i ; g b 9 7 ~ g M i a % T , ~ ~ ' U - X Y I L ( 2 %) ( ~ $ L T5 (Mupid, Advance Co., ) DNA a > @ $ g & @ 3 , ~ 7 ~g%@%ti'/~ @, (SPREADEX@ EL MINI GEL) I.ZT%%%@I(Elchrom S c i e n t i f i c Submerged Gel E l e c t r o p h o r e s i s Appratus P/ N2000) ?? LT@E.r"k tr5?t-f6 Z k d4q%T& 6,= %?, -?-4X.-?-3-2 L T M3 -7-3-2 $5L, loading b u f f e r (5x) 1 p 1 CZ PCR &#!I?? 1 1 nnkj.T, s~t7icgw 77-id: 0.75 x TAE, 30 /n\fT 5 . & S E i 2 80V/cm; 17icE@~@r~7 id: 2. *BE%% *Il E *I&$Bi% Y.7-qBf%$BE. &*Illi%*E &*BE@@. i3@@ILf6L\=I2 7266 ( 5 %BaEjfif@9Tg$ZL 7z@~~Yei+B$*6),, 2. 6. @ f5 SYBER Green I n u c l e i c a c i d gel s t a i n (Molecular probes) O E % e % @ & T 10000 %R L T Y I L ~1%rH7t59.3i~7~,. 2. 7.. EZ $@. ~ ~ Y X ~ I L < $ - - Y - AT TO$^%, %%BE 255nm) K Y / ~ e g i %SYBER , Green a>?k%&%jk?? CCD 3 9 7 & f g @ L 7 z F ' Y b~ Y.77(ATTO$*%) iZ k 9 53%L7zo. z 2 129 x I L t z ~ $ $ e A h 6 % ,$YY CTAB %j& f? I f f % h hfc/ C> F'( 193bp). 1. DNA @kb?&l=k Q@l53% ( Z % > , W/n\@%Y)l.. (SPREADEX @E~600). 947h"h. M3 1 L->. :. 2 L->. : CTAB :2 (5g). 3 L-> 4 L->. : @i*53B@Bl$f73fzj&. : fJ%Y>?)l.(Z%). IZPVPP $ A h , SDS T%i;;iLfzj&(5g>. : BEAD-BEATER j& (6g). (1 Og).
(4) 1 t-h@ttj~r~yfix~-w'a T Z ~ g , t ~2 g i;t-gi+ fiiBBT;ti a 7zh, SIBID%~@TI~F$ L~\&ai2 7Tbf2b'Z 2 iz L7z0 % % $ h T 5 7z DNA @ m ? & D p T ,% % ( Z f T q T&Tz%%, PCR iZ k 6@#E-?@i+a>ZT@h7z %?&3-5 iz9b\TT+LL\&Z+%f797zo+&%$& 7z%IlRK k 6 2 %3?&Tf!EHS h 6 +%a>Bfi< g f 2 6 ~ T ZTi2k@%+$a)B&%Ba) Z I g I.r L T k B % f T 3 7 z 0 B I Z iz%%&ZTo. 3. @EBU%% 3. 1. DNA ff8~fS:&DLL$3 BI 1 i Z , %?&5 U9bDk$22fT37z%R%ZTo 7'74 ?--id; 357f-519r %Rb\T@% V2 Ta>$fl B%;k;%Bk, a8 bitrliZ, %?&1 2 2 i2l&a>%?& 2 kdT@$EfixGG < , B@@%DR&fixT$%T ;tia 2 ,@.bh7zo%?&3 i2, f&D%?&TEb h f 2 b>fl'ZE(193bp, 7 VP V J ~ P 9 k,@.bh6) D ,< y p.fiX'ajE3b h , &b\ DNA EJ@+2% Lfz, 2%.. fJj&f? rtg+hhtc/<. CTAB. =/ F' (1 93,194bp). 2. DNA @ ~ ; & kl~%E@/~\?I~DSL\ = (&), S/n\%%YiL(SPREADEX (@ELGOO). M3. :. 94X'7-iJJ. 1 L-=/ : bead-beater. 2 L-> 3 L-> 4 L-9. j&. : b e a d - b e a t e r ( ~ ~ A # h $ ! / S ' ~ - / ~ - 2, 0 % S D S , : bead-beater(~PB/S'71-, :. t-39;& '5. 20%SDS,. y ~ --i?, f. BEADS). ?~f-%',B E A D S ). ~->:cTAB;&. 7'7 4 7-b2 357f-519r &Hb\@b'/i V2 TD$$B %;ki&B7"r0 %{L bead-beating %?&Tid;fC$&iZ k 6 % % % % (Cullen b , 1998) %&q7zi$, g fd: 9 REi%t&j$J (SDS) a>B2@% (Proteinase K) A 9 D / x ~ 7 7 - - 2 H L \ 7 ~ % 3 ? ,1, 2 , 3 1/-7 Ti2853 0 ?S~F$!%fil~ Tz0 Z;lzC2 Cullen %k-&L7"ro 5 1/-Ya3 CTAB ?&C24V - 7 0 b 39?&,1 , 2 , 3 V--j.D Bead-Beating ?&T C"a#bhf2b\lxY F (193, 194bp, 7 1/P 71x3 P - k 1 E . b h 6 ) fixJLbh7z0 z z T, + % ~ fY ~ ~ J L ~ D ~ L \ ~ L ~ L ~ % S f Y 7 ° / l / a > & f i ~ $ f 2 b \t23, b h 6 DNA *;ki DR3iS'filfJ 9 @ b 6 f 22D?Ehitr4;ti60 f,$qT* @Sf ~ 7 ~ 1 ~ g ~ & # f , & ~ % & 6 Z2 & 2 :1 ~ L+ ~ 3 iZ%Tk 5 br, bead-beater :lf, CTAB ?& fz, i;f: l g , 3g 2 b 3 9?&TChO.l g , l g 2 H b \ 7 k. @ L7z0 LA1 L, S f ~ 7 ~ ~ L D & T i " a 3 $ -2 i1<9 C3iZ 2 X/ y @ b b f2is13fzO fz?? L , *%Sf ~ 9 ' ll/gfi:&b\k+f2b\!l*k kd, 4+b$L9lx2 p.(2 3$ < f2 37z0 Q 4 i-h 16s Y $ Y --A DNA a>@fCfJjb$I (V 1) % E i ~ 9 '4 7~ ~ ~ B ~ ~ &?z%3?T%;;5, ~ b \ k % H & & b - @27f-109rl i2 ( e $ $ B ) , 29f2-107CT ($I&$flE), 29f3-107CT (?7AP&k$flE) T 6 6 0 %@$i?&%i~42%l3@, $I&$$E,Y-7AEt&$FllBi2%f26$$B%fi@% \ LTk S ~ ~ , O%@$i?iki~k667A/%1.&$fl@2 Y~AP$$ t&$i3@iZ$fT6l<YFDl<P-Yi&iZ2 X/ym c ~ h - 7L ~A ~~L0 , ~ 3 ~%~ ; t i 6 3 % f l E i ~ V - 7 2 k 4 5 k CTAB ?&iZf&D%?&Ti2R h h fJb\{cEDlx7 F (114bp) fixBb h , ft?ID%?& 1 9 I ~ % $ $ ' $ D D N A B ~ YT~2~7~z@ k l <R . b h 9 ,.
(5) Sfii6 k i S - c f > ?)Lf. 3. 4. M3 1 L-> 3 L->. :. 5 L-> 7 L->. :. $3 DNA. IZ 6$&5k%/n\6DZZ. (SPREADEX @EL600). V4Z.7-33 2 L-> : BEAD-BEATER l g 4 L-=/ : BEAD-BEATER 3g. : BEAD-BEATER l g. : BEAD-BEATER+PVPP l g. l-39;2. l-39% 0.1g. 6 L->. :. : CATBjS l g. 8 L->. : C A T B j S 3g. 1g. 3'7 4 ? - D @ & ~ ; ~ - ~ ~ I Z & Q( a~) ,ESPREADEX D ' ~ @EL300 ' ~ ~ ~ L. 1 L->. : 27f -109rl. 2 L->. : 29f2-107rl. CT CT. 3 L->. : 29f3-107rl. 7 L->. : 27f -109rl. 8 L-9. : 29f2-107rl C T. 9 L->. : 29f3-109rl. I. 4 L-> BEAD-BEATER ;%. : 27f -109rl 5 L-=/ : 29f2-107r C T 6 L-> : 29f3-107r C T. CT. rhcaz%a>mw -e-g~~f-~ 7 ~ 9 7 CTAB E T-ta+$t~&L\~@ 2 DNA a > B l l ~ d 4 q % T h 6 ~ 2 i24&a>fi?&. ( a ) , &/n\%i%Yi'lL. 2 b k 4 7 ? B E E 4 F ??B?R. ( 6 5 0 ~ )TE6B7779 TL\EIt 2 tz .L6 2 , ~ \ b 6,3 2 iC%-?%a> DNA @186?~7, '%i%?El$E,DNA dr/y. b a g , D N A d r / . ; r ba>E&Zk&7z0. t ~.
(6) BEAD-BEATER $2. DNA ~ ~ k l ~ r n 7 ?@%iE@ (83rn7) D N A d V y ba>& D N A d V y ba>&. 2. bgP?&. 3 8 3r~7F. 1. 40°C (5 /n\). 0 @LX%&. CTAB ?&. %Xi.(5 3). 65°C (2 8%r~7). 0. 0. ?8&. $865. 3) DNA @ j g C C PVPP h &ML\kA 7 A @ j ~ f i x g F $ 3 . 2 . PVPP $HL\Ta) DNA %9$ T h 9 Tco k?!(O&%?&ThbLkl L7'r DNA i3S 2 kZ%LTzd; 5 trjE&T;ti 9. &&a>@t~@&$X/TL\6?z& #&fixiZ\ZT;ti6,, L \ < ~ f i h ~ % ? & & % L ? z % & R ,3IR*rn Clegg. C.D., K.Ritz and B.S. Griffiths 1997. PVPP kr dc 6 A 7~ # % g f i ' R $ $;'ro ~2 h t~.~ i C - h , Direct extraction of microbial community DNA z ~ > % ? ~ ~ z T L \ TL E< FS d T E Cullen b [ Z from humified upland soils, Letters in d; 5 2 PVPP A 7A%@&--ElfT->TzfS,Sephadex Applied Microbiology ,25 : 30-33. G-75 C L % ~ L T Z A ~ A @ ~1!E&f & Tj Z 2TfCullen.D. W. and P. R. Hirsch 1998. Simple and 3 T h 6 2 L \ 5 z 2 Tffi', %E%L?c%R, -El Rapid Method for Direct Extraction of a> PVPP 27 7A%%? i3i2 2 X/ Pa>h$$E@ 2 ,Fib Microbial DNA from Soil for PCR, Soil d?J5?8&iS;%&T3 Tzfix PCR Ta>@$gfilRkfJ?iSh Biol. Biochem. , 30 : 983-993. 9TzTz&, + & a > @ E @ @ E D % % f i ~ ~ 7 6~2h Jizhong.Z., Mary. A. B. and James M. Tiedje 1996. ,E,bd?JTzo5 Tz, Sephadex G-75 I.L*@ Lk7S 7. <. A%%%&L\%%fil436hf2iSb~?z?z&, PCR a> @@%SLf2fJ'b, i$%%&f6 PVPP ? J y A % % & 3 Eli31 b 5 El779 to. DNA Recovery from Soils of Diverse Composition, Appl. Environ. Mocrobiol. , 316-322. Lane. D. J. 1991. Nucleic Acid Techniques in Bacterial Systematics, 115-175. 4. % ;fi e Woose. C.R. 1987. Microbiol. Rev, 51 : 221-271. 1) ENA hbLkl%?&a>5 %, %iZ$$%+%2 I%@ $T ?%lf~fJT 6f i b 9 Tz BEAD-BEATER &, b 3 9 ?&, M+$+?fi, IhT%S, RL4%k ( b 3 9 El @@I , 1998. ;iPrB%zT, % M q 10-66599. CTAB ?&@hk@L?c%R, I&a>%?&TiC-hE b h f2Lj DNA I < Y F ( 7 k3'5'1x3' 9 - 2 , F , b h S El@?, ~J\%AP, iF@G$Z,+$fiEfT 1999, 3% 66 EE@ZIL%& p. 91. a ) f i : q + b i m j w . DNA BQ+T~~CTAB ?% fix%.% &Ah->Tzo DNA #ILkl@~~~@~n'l%TiC-h q 6 W 1995. S%&%&fjfj% 18 3,1-6 7 b1 @/37T%7T6, b 3 9?&fi:!$fZhTL\Tzo %Z&4k, 2) $@%a> El & T h 6 * k @ % ! & @ 3 6 & 8 jR%- %, EE%$&,ST?@& 1992. % # ~ ~ ~ # ! ?. 2 T%i&%~a>&&+%&k@T6@R. +@Z%?&, k@%!+@R%2#G, ??$Biz. Cr&w-ct~&Ba>-tf~7"1~Bbr-f&~~fJ?L\ z 163-164. 2 ilx*i319 Tzo.
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