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

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siRNA Design  Methods and Protocols
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+ p& ^( s5 J) P+ EEdited by $ y9 r/ N) ?9 m/ c
Debra J. Taxman) C: V) V$ u$ q6 V5 v% q
Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center,2 s7 l  b0 e9 S
University of North Carolina, Chapel Hill, NC, USA
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. R8 b5 w1 g. F+ n! u+ t: QISSN 1064-3745 ISSN 1940-6029 (electronic)' I& }8 l4 z4 y
ISBN 978-1-62703-118-9 ISBN 978-1-62703-119-6 (eBook); [. ~& j8 D, D/ _0 q! W
DOI 10.1007/978-1-62703-119-6
' {, K& ^/ j! `, b4 z- d3 s: V# v) iSpringer New York Heidelberg Dordrecht London' Y% v$ h8 f( Y; U6 ]8 ]# v
Library of Congress Control Number: 20129474065 Y" b- ]$ T1 w7 z( a
© 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,
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Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1 u) g4 ^3 w6 gContributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1   What Parameters to Consider and Which Software Tools to Use
& Y6 {. E6 o: \$ H; c  y! X, Afor Target Selection and Molecular Design of Small Interfering RNAs . . . . . . .         1
  R0 x" B$ p2 ROlga Matveeva: H8 F/ @# ?5 a/ F) y/ }
2  Methods for Selecting Effective siRNA Target Sequences Using
. y' x: r' a4 j! u, u& b8 da Variety of Statistical and Analytical Techniques . . . . . . . . . . . . . . . . . . . . . . .   
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Shigeru Takasaki) W' C6 B/ b" x8 D) A* l
3   Designing Functional siRNA with Reduced Off-Target Effects . . . . . . . . . . . .       57
7 s9 v9 y6 y/ _( P8 rYuki Naito and Kumiko Ui-Tei) i& S) L+ a) ^3 J
4  Design and Screening of siRNAs Against Highly, e0 N# t: V' ?0 s1 Y5 R1 ^
Structured RNA Targets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0 d" P: U; @3 X
. . .      69
, C7 U4 c7 x6 U4 {Neda Nasheri, John Paul Pezacki, and Selena M. Sagan
" |" h; Q$ i* k( T" x" C5   Engineering Small Interfering RNAs by Strategic
: i5 _5 M. @0 m! t! zChemical Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . # K! }+ \1 t: D  c# L* X4 t
. . .       87
' Y' u' \# }9 ?; u3 t9 S! D; ~( a" @, i) b9 GJesper B. Bramsen and Jørgen Kjems3 j2 c* x; x- j$ M9 x
6   The Design, Selection, and Evaluation of Highly Specific; B- ^: o  ^( j
and Functional siRNA Incorporating Unlocked Nucleobase Analogs . . . . . . . .   111* e: _* H# h) I4 J& {
Narendra Vaish and Pinky Agarwal
, C0 l# G4 n& k( f' _. O, L5 v7   The Design, Preparation, and Evaluation of Asymmetric Small& y; m& \( l+ `. V2 J
Interfering RNA for Specific Gene Silencing in Mammalian Cells . . . . . . . . . .    135( B: w' ~/ w+ l3 w0 X
Chanil Chang, Sun Woo Hong, Pooja Dua, Soyoun Kim, and Dong-ki Lee
* b( J# [" z* X' z. ^8  Design of Nuclease-Resistant Fork-Like Small Interfering6 w. j5 H! F: t! j
RNA (fsiRNA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4 w3 ]) d1 [2 Y. . . . .    153
% I9 x$ s6 @) ^! [8 x* w5 p. eElena L. Chernolovskaya and Marina A. Zenkova2 d! T& D0 ?, c: h/ [
9   Designing Dual-Targeting siRNA Duplexes Having Two Active7 d+ H5 j3 O1 k7 i3 L# n' m
Strands that Combine siRNA and MicroRNA-Like Targeting . . . . . . . . . . . . .     1695 T' z; E  k0 c0 L, {8 S
Pål Sætrom
; s2 {( C  B! j) ], ~, ~10  Strategies for Designing and Validating Immunostimulatory siRNAs . . . . . . . .   179/ a2 C" _: V( @- d$ u: n
Michael P. Gantier9 j1 b' P2 T9 w. ]5 u
11  Designing Efficient and Specific Endoribonuclease-Prepared siRNAs . . . . . . . .    193% U& v. ~/ o) A! l+ a5 \' }
Vineeth Surendranath, Mirko Theis, Bianca H. Habermann, and Frank Buchholz
% s# F) _$ d+ I  C) e12  Short Hairpin RNA-Mediated Gene Silencing . . . . . . . . . . . . . . . . . . . . . . . . .   
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! v# j8 c& Y/ R& d5 S0 ALuke S. Lambeth and Craig A. Smith+ v$ L6 N( ]+ K8 F7 V  X
Luke S. Lambeth and Craig A. Smith4 U' N; T% H; r+ O
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x             Contents
6 A0 D  O# V7 z0 M3 {/ b9 _13  Design of Lentivirally Expressed siRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 e9 J9 V" [! d
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Ying Poi Liu and Ben Berkhout% l. u' F8 m( ?' u, u
14   Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway1 _  r  p# h3 @, K" L% \) @
to Clinical Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4 T" }* |2 o2 d, A. . . . .     259
0 D: a$ p, U2 a* nDonald D. Rao, Neil Senzer, Zhaohui Wang, Padmasini Kumar, Chris M. Jay, and John Nemunaitis
) d0 k( t% J- L7 b15  Design and Chemical Modification of Synthetic Short shRNAs$ V$ P0 y+ P+ ~+ ~$ r9 s
as Potent RNAi Triggers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Anne Dallas and Brian H. Johnston0 F  E" X9 P% O: s3 y
16  Production and Application of Long dsRNA in Mammalian Cells . . . . . . . . . .    291( L0 m6 q  r# [! x' i; J+ K
Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda" H9 r4 H' k" q1 I: u( ]
17   Design of RNAi Reagents for Invertebrate Model Organisms
; \$ }# E2 Q  F8 d% aand Human Disease Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Thomas Horn and Michael Boutros: ]5 J1 g1 y1 o9 l- R0 i2 K% N7 ?. \
18  Construction of shRNA Expression Plasmids for Silkworm Cell
; f; ]9 y4 i0 J7 a6 YLines Using Single-Stranded DNA and Bst DNA Polymerase. . . . . . . . . . . . . .     347. E8 Q& Z: ~  u+ e* S
Hiromitsu Tanaka9 r! p, o& L4 m! a. O) h" }) E
19  Designing Effective amiRNA and Multimeric- m7 D! t) l' H6 M; ], F
amiRNA Against Plant Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . w$ E  O9 v, j$ n1 ]* D
.    357
& @- j+ s3 Q2 vMuhammad Fahim and Philip J. Larkin
/ p0 K1 }8 D5 i9 e3 m$ U( b" z20  Downregulation of Plant Genes with miRNA-Induced Gene Silencing . . . . . .   3796 t% ~, u/ y  N  [0 n5 m
Felipe Fenselau de Felippes
0 O& B! E. ?. X6 _+ s; L8 m/ B/ z" aIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 n6 b% @, k' p6 ~
. . . . . . . . . . . .     389
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