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

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siRNA Design  Methods and Protocols2 g# N6 C8 H/ }6 g! X

3 S8 ^7 q  I7 w! {8 A, AEdited by
2 }% X) f# m. D8 I/ m! B9 ~) Z* MDebra J. Taxman# F2 N" n( O% ~8 J, O
Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center,
3 t3 [7 u8 i6 @, c6 e) m4 sUniversity of North Carolina, Chapel Hill, NC, USA2 q; \  B' [. d
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ISSN 1064-3745 ISSN 1940-6029 (electronic)9 x; t+ v. _8 ?8 M& _( E( L+ m
ISBN 978-1-62703-118-9 ISBN 978-1-62703-119-6 (eBook)6 D. f1 x2 Q$ z3 A
DOI 10.1007/978-1-62703-119-67 Y4 `( ?/ Z* p+ F/ Y) `9 h
Springer New York Heidelberg Dordrecht London! b! l- W1 \4 Z! _2 D+ S
Library of Congress Control Number: 2012947406
9 K6 x4 N4 P2 P6 w  e© Springer Science+Business Media, LLC 2013
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Debra J. Taxman (ed.), siRNA Design: Methods and Protocols, Methods in Molecular Biology, vol. 942,, ?/ m; ~3 r) S1 F1 {" z
DOI 10.1007/978-1-62703-119-6_1, © Springer Science+Business Media, LLC 2013
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2 _  R3 {! R; x$ T. YContents
( m, v. w' ]  LPreface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
" a  I. z3 ~  t2 N. . . . . . . . . . . . . . . .          v
8 {0 C5 c, o' T5 M+ I# nContributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 ^# k$ j' y1 h( H! J! p1 [2 G
. . . . . . . . . . . . . . .       xi. _$ f; [/ ?/ s1 O/ T& j% T, K5 X, R. m
1   What Parameters to Consider and Which Software Tools to Use
+ `- F. e/ f2 Gfor Target Selection and Molecular Design of Small Interfering RNAs . . . . . . .         17 d' G# y+ k- |
Olga Matveeva
# n, P$ L% C* @2  Methods for Selecting Effective siRNA Target Sequences Using" L. X$ `: t7 X: j) P) R
a Variety of Statistical and Analytical Techniques . . . . . . . . . . . . . . . . . . . . . . .    : b( J. U% ?4 \- P1 {( H
17
( Y6 A! g9 J2 i2 l, T' q9 i! pShigeru Takasaki
( k5 V# Q& Y" s- J8 O) \3   Designing Functional siRNA with Reduced Off-Target Effects . . . . . . . . . . . .       571 G$ j8 }. D, c, `) q
Yuki Naito and Kumiko Ui-Tei* O2 I4 f" G; d4 _, K
4  Design and Screening of siRNAs Against Highly
' \( ]7 v: G$ iStructured RNA Targets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
& I9 D5 G3 `6 d7 F: D. . .      69! B" w# S; [& `) m
Neda Nasheri, John Paul Pezacki, and Selena M. Sagan. C  [8 E" {+ L$ \7 I0 u
5   Engineering Small Interfering RNAs by Strategic5 @( i; e* [+ t, w0 Z5 Q
Chemical Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 V& B9 K+ q* Z9 Y  ^6 i* o/ d0 q
. . .       87
) z* M8 T% q5 W2 vJesper B. Bramsen and Jørgen Kjems
; o( N% @) F/ i1 W5 ?6   The Design, Selection, and Evaluation of Highly Specific
( ~# R- g4 u' v! n$ F% rand Functional siRNA Incorporating Unlocked Nucleobase Analogs . . . . . . . .   111
) [, @/ i. ~+ VNarendra Vaish and Pinky Agarwal& m& g& o9 H& @. \
7   The Design, Preparation, and Evaluation of Asymmetric Small
8 [6 w4 M; v" D; j9 d5 YInterfering RNA for Specific Gene Silencing in Mammalian Cells . . . . . . . . . .    135
/ {- F9 u7 _' \7 l$ U- y3 fChanil Chang, Sun Woo Hong, Pooja Dua, Soyoun Kim, and Dong-ki Lee
2 ?0 ^7 `, s0 g, j' B. g3 s8  Design of Nuclease-Resistant Fork-Like Small Interfering, t  I+ C9 k+ v) U6 s8 ]5 r
RNA (fsiRNA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8 p1 M- V; ^  U3 j) ?. . . . .    153
% J7 y. j* E' m: H; v4 s1 U7 x6 GElena L. Chernolovskaya and Marina A. Zenkova
' e, k5 z- W. r/ i, p& g" B9   Designing Dual-Targeting siRNA Duplexes Having Two Active
/ a& T; d" `# yStrands that Combine siRNA and MicroRNA-Like Targeting . . . . . . . . . . . . .     169
' N' Z. J$ S% Y* J  R- j7 L5 TPål Sætrom& c* ]* H& \9 s' |" ^  n/ H$ P- {
10  Strategies for Designing and Validating Immunostimulatory siRNAs . . . . . . . .   179% T( a( u4 s. c2 E) K: _$ g
Michael P. Gantier8 `6 i. H3 T. }* F7 @) J
11  Designing Efficient and Specific Endoribonuclease-Prepared siRNAs . . . . . . . .    193
5 G; T3 J* M  Q7 r4 v# bVineeth Surendranath, Mirko Theis, Bianca H. Habermann, and Frank Buchholz
  O' B+ V4 i2 b; a7 I+ I: N) e12  Short Hairpin RNA-Mediated Gene Silencing . . . . . . . . . . . . . . . . . . . . . . . . .    1 W+ t8 |# U4 G& ?9 g9 \
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Luke S. Lambeth and Craig A. Smith' e; T5 `7 T2 J* j- H# s
Luke S. Lambeth and Craig A. Smith% {8 G( L8 [0 C9 P- F
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x             Contents
: ]4 ~) i& ]/ l( R) C13  Design of Lentivirally Expressed siRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . .
) B' V# X( K$ D5 x% ~9 ~' O7 l.    233
, m- `- [* W3 K, I. SYing Poi Liu and Ben Berkhout
2 w7 J1 U& V/ e/ C14   Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway
4 `" ^8 t( k! b5 ^$ v7 N# ito Clinical Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0 m+ Z0 X* d$ [$ A; A/ e
. . . . .     259
0 t4 u5 J  c" {& D9 k' oDonald D. Rao, Neil Senzer, Zhaohui Wang, Padmasini Kumar, Chris M. Jay, and John Nemunaitis; Q- _. U1 `  Q, z. M. z
15  Design and Chemical Modification of Synthetic Short shRNAs4 X3 W& a+ a2 [1 {0 r6 D1 k5 U
as Potent RNAi Triggers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Anne Dallas and Brian H. Johnston
1 A* h1 a3 w7 G1 x4 L; |+ Y2 ~16  Production and Application of Long dsRNA in Mammalian Cells . . . . . . . . . .    291% ?. _7 S; A& w! L
Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda) O/ g  o% D; q% m  ~
17   Design of RNAi Reagents for Invertebrate Model Organisms
2 e$ R: B+ u6 \) Dand Human Disease Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8 S( B' t6 I" `! R4 x! P1 _! V.    315
! g0 ]  w7 X. i, YThomas Horn and Michael Boutros
7 A: w1 u: V# \4 _9 t18  Construction of shRNA Expression Plasmids for Silkworm Cell0 p, ^$ W! w* \: j2 }
Lines Using Single-Stranded DNA and Bst DNA Polymerase. . . . . . . . . . . . . .     347) W$ h- x& s% S2 l; d
Hiromitsu Tanaka: L6 M' A  Q7 Q; U( l) E4 X- u. E# R' C
19  Designing Effective amiRNA and Multimeric8 G: g2 B5 @( J: c
amiRNA Against Plant Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4 Q* m: j$ X$ N& V& c.    357- _( v- E: d+ q; m; g: A) c: d0 ^
Muhammad Fahim and Philip J. Larkin
% Q1 H: k/ b+ I. P20  Downregulation of Plant Genes with miRNA-Induced Gene Silencing . . . . . .   379! Q. g; s+ Y; P1 A/ q& _2 W; F: \
Felipe Fenselau de Felippes% {* P0 V6 [- g! Z& i
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . : V0 X* V+ Z# X+ @( E  |8 D/ P, u
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