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发表于 2013-1-5 20:17 |只看该作者 |倒序浏览 |打印

本帖最后由细胞海洋于 2013-1-5 21:07 编辑 ! j# `4 o4 [" N  n; g0 k
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siRNA Design  Methods and Protocols/ m1 \6 \4 [- j0 n7 I: d
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Edited by
Debra J. Taxman
Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center,
University of North Carolina, Chapel Hill, NC, USA
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ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-118-9 ISBN 978-1-62703-119-6 (eBook)+ c6 |$ {5 P  A, v+ g% i
DOI 10.1007/978-1-62703-119-6
Springer New York Heidelberg Dordrecht London6 w0 W0 s! G% _5 ^2 q
Library of Congress Control Number: 2012947406
© Springer Science+Business Media, LLC 2013

Debra J. Taxman (ed.), siRNA Design: Methods and Protocols, Methods in Molecular Biology, vol. 942,
DOI 10.1007/978-1-62703-119-6_1, © Springer Science+Business Media, LLC 2013

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Contents: |  B: r  a# Y6 r4 [: @
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . .       v6 V; ^: e" s( p) j
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .    xi2 l! S. R5 L  _& x
1 What Parameters to Consider and Which Software Tools to Use" M# l. Q6 }5 M7 e( k! w) @6 ~
for Target Selection and Molecular Design of Small Interfering RNAs . . . . . . .       15 i- w% x6 a' {
Olga Matveeva% g; L$ \; y- _# p  j6 W
2  Methods for Selecting Effective siRNA Target Sequences Using
a Variety of Statistical and Analytical Techniques . . . . . . . . . . . . . . . . . . . . . . .
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Shigeru Takasaki2 a- W! b. I4 V7 i1 P. y# S
3 Designing Functional siRNA with Reduced Off-Target Effects . . . . . . . . . . . .    575 Z% P2 U* u5 v( L( ~
Yuki Naito and Kumiko Ui-Tei
4  Design and Screening of siRNAs Against Highly
Structured RNA Targets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . .    69
Neda Nasheri, John Paul Pezacki, and Selena M. Sagan
5 Engineering Small Interfering RNAs by Strategic
Chemical Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . .    87
Jesper B. Bramsen and Jørgen Kjems
6 The Design, Selection, and Evaluation of Highly Specific. f8 m' C- A9 r7 P+ c' N. ^1 m
and Functional siRNA Incorporating Unlocked Nucleobase Analogs . . . . . . . . 1117 l" n- {3 T6 T
Narendra Vaish and Pinky Agarwal
7 The Design, Preparation, and Evaluation of Asymmetric Small; Z! B3 Z9 I6 s9 b$ q% L
Interfering RNA for Specific Gene Silencing in Mammalian Cells . . . . . . . . . . 135
Chanil Chang, Sun Woo Hong, Pooja Dua, Soyoun Kim, and Dong-ki Lee) D& e! n% Z% X. h' G: i8 j9 _
8  Design of Nuclease-Resistant Fork-Like Small Interfering
RNA (fsiRNA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 153
Elena L. Chernolovskaya and Marina A. Zenkova
9 Designing Dual-Targeting siRNA Duplexes Having Two Active
Strands that Combine siRNA and MicroRNA-Like Targeting . . . . . . . . . . . . .    1690 h& l3 z) d4 {% B5 r" g
Pål Sætrom
10  Strategies for Designing and Validating Immunostimulatory siRNAs . . . . . . . . 179
Michael P. Gantier# k! v- k% c: M* C* e7 W) m
11  Designing Efficient and Specific Endoribonuclease-Prepared siRNAs . . . . . . . . 193
Vineeth Surendranath, Mirko Theis, Bianca H. Habermann, and Frank Buchholz
12  Short Hairpin RNA-Mediated Gene Silencing . . . . . . . . . . . . . . . . . . . . . . . . .
205
Luke S. Lambeth and Craig A. Smith
Luke S. Lambeth and Craig A. Smith# A8 m2 w# R' f$ N4 j
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x          Contents, D) ~. R( t+ Q) L4 S' \+ a
13  Design of Lentivirally Expressed siRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Ying Poi Liu and Ben Berkhout' N2 D) N! B* e9 o/ e# |
14 Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway
to Clinical Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . & H& d6 \% J& F0 }3 L9 Q) g
. . . . .    259
Donald D. Rao, Neil Senzer, Zhaohui Wang, Padmasini Kumar, Chris M. Jay, and John Nemunaitis! d* X& F3 f: D: }
15  Design and Chemical Modification of Synthetic Short shRNAs8 Q' T8 Y! Q: |! ^: s0 d4 ^, Q8 ]
as Potent RNAi Triggers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . .    279) [/ [/ h5 q2 p$ b
Anne Dallas and Brian H. Johnston
16  Production and Application of Long dsRNA in Mammalian Cells . . . . . . . . . . 291
Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda
17 Design of RNAi Reagents for Invertebrate Model Organisms
and Human Disease Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ v2 \0 v2 d6 X- a+ X
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Thomas Horn and Michael Boutros
18  Construction of shRNA Expression Plasmids for Silkworm Cell9 w2 z. f) r0 x# {) t
Lines Using Single-Stranded DNA and Bst DNA Polymerase. . . . . . . . . . . . . .    347  p1 x% x2 V2 a3 g  ^
Hiromitsu Tanaka
19  Designing Effective amiRNA and Multimeric5 N7 e+ Q' ?1 R) h, \; T: w0 V
amiRNA Against Plant Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Muhammad Fahim and Philip J. Larkin$ T0 f% t  p7 J* m  T4 G
20  Downregulation of Plant Genes with miRNA-Induced Gene Silencing . . . . . . 379) Q( `& W3 T/ d- F3 N% ^7 E# f
Felipe Fenselau de Felippes
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ k' a2 B* z, Y3 Y4 w& F
. . . . . . . . . . . .    389" f: r9 Y3 W* U. R! s
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