siRNA selection criteria – statistical analyses of
applicability and significance

J 2007

siRNA selection criteria – statistical analyses of applicability and significance

BRADÁČ, Ivan, Radka SVOBODOVÁ VAŘEKOVÁ, Michael WACENOVSKY, Michal ŠKRDLA, Martin PLCHÚT et. al.

Základní údaje

Originální název

siRNA selection criteria – statistical analyses of applicability and significance

Autoři

BRADÁČ, Ivan (203 Česká republika), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, garant, domácí), Michael WACENOVSKY (40 Rakousko), Michal ŠKRDLA (203 Česká republika, domácí), Martin PLCHÚT (203 Česká republika) a Martin POLČÍK (203 Česká republika)

Vydání

Biochemical and Biophysical Research Communications, 2007, 0006-291X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.749

Kód RIV

RIV/00216224:14310/07:00051392

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000247257600014

Klíčová slova anglicky

RNAi; mRNA; siRNA selection criteria; Target Patterns; mRNA secondary structure; RISC enzyme

Štítky

AKR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 3. 2012 03:49, doc. RNDr. Radka Svobodová, Ph.D.

Anotace

V originále

RNA interference is a powerful tool for gene silencing, which is mediated by introducing siRNA. In the present study, statistical analyses of published siRNA selection criteria, the interpretation of some criteria and systematic searching for new criteria have been carried out for CGB siRNA and siRecords databases. The results of the analyses are as follows: (i) Our study supports the two-state model of the RNA-induced silencing complex (RISC). (ii) Stable 50-S ends of a siRNA sequence, higher stability of the whole siRNA, and low breaking energy of siRNA duplex occurs in effective siRNA sequences. Also low internal stability of the 50-AS terminus is preferred. (iii) Secondary structure can be successfully used as an RNAi selection criterion. (iv) Several published sequence criteria have been confirmed and also new criteria have been developed. (v) Also a Target Patterns criterion, which is comparable or better than the best known criteria, has been created.

Návaznosti

LC06030, projekt VaV

Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

BRADÁČ, Ivan, Radka SVOBODOVÁ VAŘEKOVÁ, Michael WACENOVSKY, Michal ŠKRDLA, Martin PLCHÚT a Martin POLČÍK. siRNA selection criteria – statistical analyses of applicability and significance. Biochemical and Biophysical Research Communications. 2007, roč. 359, č. 1, s. 83-87. ISSN 0006-291X.

@article{888526,
   author = {Bradáč, Ivan and Svobodová Vařeková, Radka and Wacenovsky, Michael and Škrdla, Michal and Plchút, Martin and Polčík, Martin and Plchút, Martin and Polčík, Martin},
   article_number = {1},
   keywords = {RNAi; mRNA; siRNA selection criteria; Target Patterns; mRNA secondary structure; RISC enzyme},
   language = {eng},
   issn = {0006-291X},
   journal = {Biochemical and Biophysical Research Communications},
   title = {siRNA selection criteria – statistical analyses of applicability and significance},
   volume = {359},
   year = {2007}
}

TY  - JOUR
ID  - 888526
AU  - Bradáč, Ivan - Svobodová Vařeková, Radka - Wacenovsky, Michael - Škrdla, Michal - Plchút, Martin - Polčík, Martin - Plchút, Martin - Polčík, Martin
PY  - 2007
TI  - siRNA selection criteria – statistical analyses of applicability and significance
JF  - Biochemical and Biophysical Research Communications
VL  - 359
IS  - 1
SP  - 83-87
EP  - 83-87
SN  - 0006291X
KW  - RNAi
KW  - mRNA
KW  - siRNA selection criteria
KW  - Target Patterns
KW  - mRNA secondary structure
KW  - RISC enzyme
N2  - RNA interference is a powerful tool for gene silencing, which is mediated by introducing siRNA. In the present study, statistical analyses of published siRNA selection criteria, the interpretation of some criteria and systematic searching for new criteria have been carried out for CGB siRNA and siRecords databases. The results of the analyses are as follows: (i) Our study supports the two-state model of the RNA-induced silencing complex (RISC). (ii) Stable 50-S ends of a siRNA sequence, higher stability of the whole siRNA, and low breaking energy of siRNA duplex occurs in effective siRNA sequences. Also low internal stability of the 50-AS terminus is preferred. (iii) Secondary structure can be successfully used as an RNAi selection criterion. (iv) Several published sequence criteria have been confirmed and also new criteria have been developed. (v) Also a Target Patterns criterion, which is comparable or better than the best known criteria, has been created.
ER  -

BRADÁČ, Ivan, Radka SVOBODOVÁ VAŘEKOVÁ, Michael WACENOVSKY, Michal ŠKRDLA, Martin PLCHÚT a Martin POLČÍK. siRNA selection criteria – statistical analyses of applicability and significance. \textit{Biochemical and Biophysical Research Communications}. 2007, roč.~359, č.~1, s.~83-87. ISSN~0006-291X.

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