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

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siRNA Design  Methods and Protocols3 N/ h% E3 M! N8 v
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Edited by * ]5 e! f0 q/ x3 x- V( k
Debra J. Taxman$ A0 D' B$ K6 i9 J
Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center,
8 q' h; Y* X1 E) {University of North Carolina, Chapel Hill, NC, USA
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. S5 O6 o# N% a& n1 ]ISSN 1064-3745 ISSN 1940-6029 (electronic)1 v# H& t8 ]' Z- `
ISBN 978-1-62703-118-9 ISBN 978-1-62703-119-6 (eBook)
& q- j) \9 S4 y8 B' PDOI 10.1007/978-1-62703-119-6
8 `4 d. N  }6 f! QSpringer New York Heidelberg Dordrecht London
2 l/ U) N+ ^/ j! ~) qLibrary of Congress Control Number: 2012947406
; F- J/ I% ?2 z% D* o© Springer Science+Business Media, LLC 2013! t7 Q7 q" b7 h! h8 Z
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Debra J. Taxman (ed.), siRNA Design: Methods and Protocols, Methods in Molecular Biology, vol. 942,/ \- S9 Z7 C/ X6 `
DOI 10.1007/978-1-62703-119-6_1, © Springer Science+Business Media, LLC 2013! w7 [, s. R9 y) J4 A2 t1 B# g  N

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Contents
8 C/ I6 P. A; M" k" kPreface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7 \- z: ?# R5 @$ q& f/ V3 N, V7 W. . . . . . . . . . . . . . . .          v( r+ K0 u# h! P5 P( c$ [
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . , g6 @$ m$ @$ f/ x2 V2 \: O
. . . . . . . . . . . . . . .       xi5 K2 U# [8 _" A8 v) E
1   What Parameters to Consider and Which Software Tools to Use
" E' O5 d" ~, }" L0 r& Q( ]for Target Selection and Molecular Design of Small Interfering RNAs . . . . . . .         1, ]. _1 W3 \- Z8 `+ j0 o
Olga Matveeva; \- p, h9 k' T& H( z9 Z8 m3 C) ^! f
2  Methods for Selecting Effective siRNA Target Sequences Using6 s7 Q' |: O, J, r: t; b
a Variety of Statistical and Analytical Techniques . . . . . . . . . . . . . . . . . . . . . . .   
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Shigeru Takasaki4 }0 I5 q) w( M4 c9 P2 M4 p
3   Designing Functional siRNA with Reduced Off-Target Effects . . . . . . . . . . . .       57+ i5 r. t; u2 E1 ?( G% s" y: h
Yuki Naito and Kumiko Ui-Tei  I! G- P9 F& i6 g1 b
4  Design and Screening of siRNAs Against Highly" M& |/ \6 v% l' Z  O* e
Structured RNA Targets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
: y) X) C: x! j8 l. . .      69
! {5 I# l  H; E0 ]/ cNeda Nasheri, John Paul Pezacki, and Selena M. Sagan
  T6 f6 d. |" t1 q$ ~0 O5   Engineering Small Interfering RNAs by Strategic7 t" Y) W7 X! A# ?; D- C
Chemical Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Jesper B. Bramsen and Jørgen Kjems
  |  O; I6 P- A! ^7 s3 D; A' `6   The Design, Selection, and Evaluation of Highly Specific
  l" z( ^2 v) J4 N1 |8 _6 K/ Hand Functional siRNA Incorporating Unlocked Nucleobase Analogs . . . . . . . .   1112 K7 `1 w2 P7 H' X7 x
Narendra Vaish and Pinky Agarwal
5 O; l3 O- f0 ~* C7   The Design, Preparation, and Evaluation of Asymmetric Small" F3 _% }" k2 f  L: u
Interfering RNA for Specific Gene Silencing in Mammalian Cells . . . . . . . . . .    135  O9 B( L( I; m& E9 y  j& u
Chanil Chang, Sun Woo Hong, Pooja Dua, Soyoun Kim, and Dong-ki Lee3 H8 j7 T1 I7 _, g" {' {
8  Design of Nuclease-Resistant Fork-Like Small Interfering
& h6 @% X+ _  y  r1 [RNA (fsiRNA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3 O, L. X6 V7 g. B/ w0 Y" s. . . . .    153% a! J$ T3 W5 o* v
Elena L. Chernolovskaya and Marina A. Zenkova$ s: w, c7 F# F0 I
9   Designing Dual-Targeting siRNA Duplexes Having Two Active' @& n$ F) j$ Y, |% x
Strands that Combine siRNA and MicroRNA-Like Targeting . . . . . . . . . . . . .     169# \; Q# j6 o' W* j, R2 r4 m3 r; K) W. F
Pål Sætrom
  f0 a7 x4 }, L+ i10  Strategies for Designing and Validating Immunostimulatory siRNAs . . . . . . . .   179% [$ m1 b2 b4 s& H. m& o
Michael P. Gantier
- R# V" q& p$ @9 Z3 `. z11  Designing Efficient and Specific Endoribonuclease-Prepared siRNAs . . . . . . . .    193
) }- |( k& r" S) o$ TVineeth Surendranath, Mirko Theis, Bianca H. Habermann, and Frank Buchholz
8 s2 [- R6 w1 ~. p12  Short Hairpin RNA-Mediated Gene Silencing . . . . . . . . . . . . . . . . . . . . . . . . .   
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8 v/ Y6 J& p) m" X' RLuke S. Lambeth and Craig A. Smith* t, S" Z) w! B% Q3 m9 q
Luke S. Lambeth and Craig A. Smith' i6 {% i. ]& C3 C

# Z5 @* d- ^9 Gx             Contents
/ G1 j2 n: t; U13  Design of Lentivirally Expressed siRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 y& f% D2 c+ R; X8 m' a
.    2339 S& q' [; }1 K: O2 Y7 E: s
Ying Poi Liu and Ben Berkhout
! S; ~- ]; M9 f' V$ Z14   Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway; L1 z+ _$ u; \: H5 B
to Clinical Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . % Y2 I  ~0 u+ k* S9 P! c, C
. . . . .     259
+ h+ t. o3 y  c$ g' c; ODonald D. Rao, Neil Senzer, Zhaohui Wang, Padmasini Kumar, Chris M. Jay, and John Nemunaitis
& H) q3 @! X& ?; Y4 l! N15  Design and Chemical Modification of Synthetic Short shRNAs
# ?* R! z5 v3 Q* I7 H# U: `6 ?as Potent RNAi Triggers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Anne Dallas and Brian H. Johnston; m$ m! c* q" G' o. Y; }) k+ k
16  Production and Application of Long dsRNA in Mammalian Cells . . . . . . . . . .    291
3 y% S! Y: a& k2 UKaterina Chalupnikova, Jana Nejepinska, and Petr Svoboda$ S# W5 `+ r% q4 X( @( k2 V
17   Design of RNAi Reagents for Invertebrate Model Organisms6 G- e& m2 k) A% w. j' i
and Human Disease Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
! Z6 l& d9 F& ?3 }+ i.    315
# @- e% g  \  v7 v1 w' G/ YThomas Horn and Michael Boutros
$ I/ W  [6 O* ^; e; B/ t8 k18  Construction of shRNA Expression Plasmids for Silkworm Cell" K/ ^& G: C5 ?/ g
Lines Using Single-Stranded DNA and Bst DNA Polymerase. . . . . . . . . . . . . .     347+ O# F9 S  K% k
Hiromitsu Tanaka0 h$ M+ Y2 {+ v. H' Q. b; b
19  Designing Effective amiRNA and Multimeric
# p* J+ v2 S4 o- Z9 h  L0 YamiRNA Against Plant Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
) S0 C1 ?) j1 `, W' f+ [1 c2 H1 \# l) P.    357
8 V2 v4 k1 m4 u& {) Z  ^1 l2 FMuhammad Fahim and Philip J. Larkin$ L7 A  T- i: Y' l" Q4 T
20  Downregulation of Plant Genes with miRNA-Induced Gene Silencing . . . . . .   379
; [/ O# n2 k  V* ^( K1 U# oFelipe Fenselau de Felippes' e, K! n" z+ N# o: K; `; Q
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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