PDF电子书：siRNA design （Springer MMB 942 2013）

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! m4 J7 a- k% [! P7 X0 BsiRNA Design  Methods and Protocols" I, e* C$ S, ?5 d( R4 s# u
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Edited by 1 H/ Z7 [2 o: _& ]0 f
Debra J. Taxman% p2 ^4 W* x) `9 v
Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center,0 |6 T: x  J$ A0 r1 K& g1 `
University of North Carolina, Chapel Hill, NC, USA+ o5 r1 H1 o5 H
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ISSN 1064-3745 ISSN 1940-6029 (electronic)
+ \% i, l. @7 U, b; E* BISBN 978-1-62703-118-9 ISBN 978-1-62703-119-6 (eBook)
( n) ~0 S6 ]+ k1 u6 L2 RDOI 10.1007/978-1-62703-119-6, s5 m8 D$ h" N; |9 M+ \3 H
Springer New York Heidelberg Dordrecht London2 ?: M' y/ t& e
Library of Congress Control Number: 20129474065 ?  w7 `9 J5 L; X' v1 A
© Springer Science+Business Media, LLC 2013
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/ u) E  ^2 E( x# Z7 |3 Z2 IDebra J. Taxman (ed.), siRNA Design: Methods and Protocols, Methods in Molecular Biology, vol. 942,
/ j& D  [' W% V0 Z# r5 X' MDOI 10.1007/978-1-62703-119-6_1, © Springer Science+Business Media, LLC 2013! w$ H  b! H& G/ n7 E; y
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Contents4 s, ~. @- ?# P8 y- ]) F4 M" W
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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5 F' x2 m7 R/ R- a/ G2 H5 HContributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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0 t: T% W1 j, B. b6 n. v1 M; w1   What Parameters to Consider and Which Software Tools to Use
  s$ z! _1 @3 V, n; D- Y/ G" Tfor Target Selection and Molecular Design of Small Interfering RNAs . . . . . . .         17 d* f: [' q0 Z% I, Z$ m  S
Olga Matveeva
# m) N; r- f5 G6 j! Z# r2  Methods for Selecting Effective siRNA Target Sequences Using$ ^9 g: f. M, J% x- S/ o; S
a Variety of Statistical and Analytical Techniques . . . . . . . . . . . . . . . . . . . . . . .    6 y  V  Q7 v# s5 m1 L  C
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Shigeru Takasaki# M3 W# Q8 }/ W9 y/ {
3   Designing Functional siRNA with Reduced Off-Target Effects . . . . . . . . . . . .       57, s: `+ [9 ~9 O2 t8 w* W, ?
Yuki Naito and Kumiko Ui-Tei8 c3 q5 ?; I; Q  j* M
4  Design and Screening of siRNAs Against Highly
& c7 ~9 J% p; b* t3 u; n8 M5 ]Structured RNA Targets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .   S) A+ F* X" E+ H
. . .      69
9 W) o4 N  z0 D6 ]+ \. _) ANeda Nasheri, John Paul Pezacki, and Selena M. Sagan2 |+ O: b( k2 H0 J: X
5   Engineering Small Interfering RNAs by Strategic
# _2 m- R/ G! ~Chemical Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 R; r+ L. |2 F
. . .       87; X( J9 I8 x; s9 o0 w5 c" H
Jesper B. Bramsen and Jørgen Kjems0 y9 K% J0 N! K. z! p
6   The Design, Selection, and Evaluation of Highly Specific
, F( `6 q6 E# Y! n: Zand Functional siRNA Incorporating Unlocked Nucleobase Analogs . . . . . . . .   111
1 \* h( Y% I0 e  _Narendra Vaish and Pinky Agarwal
& @; v8 ?3 y/ A- W/ H7   The Design, Preparation, and Evaluation of Asymmetric Small+ `& @0 p3 s" E* }6 D6 W; [
Interfering RNA for Specific Gene Silencing in Mammalian Cells . . . . . . . . . .    1352 N8 N! ?1 `; c0 r( v5 b& n
Chanil Chang, Sun Woo Hong, Pooja Dua, Soyoun Kim, and Dong-ki Lee3 Q+ i& m8 N" b, {
8  Design of Nuclease-Resistant Fork-Like Small Interfering
# y1 J. P& l8 f) MRNA (fsiRNA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .   `# `1 S0 b/ \
. . . . .    153
9 Y1 t$ |7 `3 tElena L. Chernolovskaya and Marina A. Zenkova/ E8 q7 S) z/ w  ^& ?% n
9   Designing Dual-Targeting siRNA Duplexes Having Two Active
7 k1 i$ e- ]6 f8 A0 }/ {Strands that Combine siRNA and MicroRNA-Like Targeting . . . . . . . . . . . . .     169
& i# X8 q8 @8 E  D9 }: XPål Sætrom
& {, O$ i# l9 \10  Strategies for Designing and Validating Immunostimulatory siRNAs . . . . . . . .   1799 [5 Z/ o" Q; w4 p- o
Michael P. Gantier
. |1 B% ?% H5 k3 l5 Z11  Designing Efficient and Specific Endoribonuclease-Prepared siRNAs . . . . . . . .    193
' w9 i. D2 e" g' U  EVineeth Surendranath, Mirko Theis, Bianca H. Habermann, and Frank Buchholz' m4 S% j) I1 i: k, N8 x# U* y7 u2 G) B
12  Short Hairpin RNA-Mediated Gene Silencing . . . . . . . . . . . . . . . . . . . . . . . . .   
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+ t) g5 e+ P" ~Luke S. Lambeth and Craig A. Smith9 b; s$ S5 U7 }2 H
Luke S. Lambeth and Craig A. Smith* u. n) u8 O4 H" T9 p. h

1 C9 |" e& U& wx             Contents  e& t$ p5 H9 ]8 h! S
13  Design of Lentivirally Expressed siRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . ' n# Y. _& R- O" }  U2 N, b/ y, m9 T
.    233- u1 |% O4 ~: J1 {$ }
Ying Poi Liu and Ben Berkhout2 F' o/ d6 K2 G: H. _3 s( o
14   Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway& I2 i# D' W0 j8 M% p
to Clinical Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ]& [+ T' B. X8 c# s
. . . . .     259
- O0 a- _5 }+ g* G% YDonald D. Rao, Neil Senzer, Zhaohui Wang, Padmasini Kumar, Chris M. Jay, and John Nemunaitis
  j7 y; u9 O/ j9 s  |: P15  Design and Chemical Modification of Synthetic Short shRNAs* W; B* ^( Z8 E: z
as Potent RNAi Triggers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 V+ o. Y1 m0 i! F$ |; x- J: {6 E
. . .     279/ Q/ @# B3 p, M# E( K
Anne Dallas and Brian H. Johnston
2 b% E5 v7 a, |; {- e16  Production and Application of Long dsRNA in Mammalian Cells . . . . . . . . . .    291
# M$ s- i' O1 k) ~( X) BKaterina Chalupnikova, Jana Nejepinska, and Petr Svoboda2 w7 Q( T5 E6 \4 S4 C6 c
17   Design of RNAi Reagents for Invertebrate Model Organisms
/ A. J4 k- N+ o' ]9 H) Nand Human Disease Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * |% `$ X- N4 g; A
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Thomas Horn and Michael Boutros
; f' U5 N, u( D- D8 }; s18  Construction of shRNA Expression Plasmids for Silkworm Cell- K2 o( ~/ @+ t3 y  q8 D5 O
Lines Using Single-Stranded DNA and Bst DNA Polymerase. . . . . . . . . . . . . .     347, \: N2 I+ ~, M3 y1 o8 F' ^4 y
Hiromitsu Tanaka* G4 U9 T# n7 @- N: ]
19  Designing Effective amiRNA and Multimeric) B* o  j/ H3 V( s2 W
amiRNA Against Plant Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ( `7 S' W, r2 n% ~/ ^* z% E
.    357
0 w. s4 B! n" q) WMuhammad Fahim and Philip J. Larkin( r4 ~6 y4 Y" T, |9 H
20  Downregulation of Plant Genes with miRNA-Induced Gene Silencing . . . . . .   379; e  x5 c" V& `* F; k
Felipe Fenselau de Felippes  }+ H8 u! r  b5 m
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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