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To account for this discrepancy, a modified, branched ratchet model was proposed in which the NTP must also bind to a secondary site on the polymerase in the pre-translocated configuration.
Subsequent experiments revealed that A9 was an allosteric inhibitor, which could bind to a secondary site outside the catalytic cleft of TACE, thus disturbing its ability to bind to the active site [22].
Results from toe-printing assays showed that AS 54-84 did not bind to a secondary site on the RRE, indicating the SHAPE change could be a result of long-range crosstalk.
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While distribution into the SF and/or local trapping is likely to contribute to the decrease in circulating pGSN, pGSN may also be bound to a secondary yet unidentified plasma factor (for example, CRP) that may cause it to remain undetected by our functional assay.
Secondary siRNAs are synthesized by RNA-dependent RNA polymerases (RdRPs), and bind to a number of secondary siRNA-specific Argonaute proteins to bring about target silencing (Yigit et al., 2006).
The other primary antibody was first bound to a biotinylated secondary antibody, followed by coupling to avidin-linked alkaline phosphatase.
In support of this, it was recently shown that eIF4E binds to a specific secondary structure outside of the 5′ UTR of Histone H4 mRNA to promote the translation of this mRNA in an eIF4A-dependent manner (Martin et al, 2011).
The advantage of indirect labeling is the amplification of the signal obtained, since several secondary antibodies may bind to a single primary antibody (Brown and Lemmon [1995]; Marttila and Santén [2007]).
Some of these targets also bind to secondary binding sites of the receptor.
To determine what motifs an algorithm discovers, we compare its output motifs to a large panel of known motifs using the TOMTOM (Gupta et al., 2007) algorithm and use gene expression data from the Gene Expression Atlas (Kapushesky et al., 2010) to determine which TF among TFs with similar DNA-binding affinity may bind to secondary motifs.
These include natural products, such as geldanamycin, radicicol and derivatives; synthetic purine-based inhibitors, such as PU3, PU24FCI and PU29FCI; and compounds that bind to Hsp90 on a secondary ATP-binding site, such as novobiocin and cisplatin [ 6].
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