A Analogs

Nucleotide Analog Interference Mapping (NAIM) is a chemogenetic approach that makes it possible to simultaneously, yet individually, probe the contribution of a particular functional group at almost every RNA nucleotide position in a single experiment1,2. The method utilizes a series of 5'-O-(1-thio)nucleoside analog triphosphates in a modification interference procedure that is as simple as RNA sequencing. In a NAIM experiment the smallest mutable unit is not the base pair, but rather the individual functional groups that comprise the nucleotides. Because the modification or deletion of a particular functional group within an RNA can severely affect its activity, this approach makes it possible to efficiently determine the chemical basis of RNA structure and function.

NAIM utilizes nucleotide analogs, each of which includes an incremental chemical alteration in the base or ribose sugar. The most completely developed set of analogs are those of adenosine, for which eight different analogs have been utilized in NAIM.3 Five analogs modify the nucleotide base and three modify the ribose sugar. The base analogs include purine riboside (PuraS), N6-methyladenosine (m6AaS), tubercidin (7dAaS), diaminopurine riboside (DAPaS), and 2-aminopurine riboside (2APaS). The ribose sugar analogs all modify the 2'-OH group and include 2'-deoxyadenosine (dAaS), 2'-deoxy-2'-fluoroadenosine (FAaS), and 2'-O-methyladenosine (OMeAaS). All of the analogs can be randomly incorporated into an RNA transcript at an ideal 5% level of efficiency using either the wild-type T7 RNA polymerase or a Y639F RNA polymerase point mutant4. Each of these analogs provides specific information about the chemical basis of RNA activity at almost every incorporated position in the transcript.
Item Catalog No. Pack Price ($)
Adenosine α-thiotriphosphate (0.5mM) (ATTPaS)
80-3000-01 0.1mL 100.00
7-Deaza-Adenosine α-thiotriphosphate (10mM) (7-DATTPaS )
80-3303-01 0.1mL 100.00
N6-Me-Adenosine α-thiotriphosphate (4mM) (N6-Me-ATTPaS)
80-3302-01 0.1mL 100.00
2,6-Diaminopurine riboside α-thiotriphosphate (0.25mM) (DTTPaS )
80-3305-01 0.1mL 100.00
2-Aminopurine riboside α-thiotriphosphate (10mM) (2-AP-TTPaS )
80-3304-01 0.1mL 100.00
Purine riboside α-thiotriphosphate (20mM) (PR-TTPaS )
80-3301-01 0.1mL 100.00
2'-deoxyAdenosine α-thiotriphosphate (15mM) (2'dATTPaS )
80-1000-01 0.1mL 100.00
2'-OMe-Adenosine α-thiotriphosphate (20mM) (2'-O-Me-ATTPaS )
80-1101-01 0.1mL 100.00
2'-Fluoro-Adenosine α-thiotriphosphate (10mM) (2'-F-ATTPaS)
80-1102-01 0.1mL 100.00

α-Thiotriphosphates are sodium salts in TE buffer, pH7, 10X concentrates. The concentrations shown are optimal for incorporation during polymerase reactions.

Intellectual Property

Products for Nucleotide Analog Interference Mapping (NAIM) are supplied under license.


  1. S. A. Strobel and K. Shetty, Proc. Natl. Acad. Sci. U.S.A., 1997, 94, 2903-2908.
  2. G. Gish and F. Eckstein, Science, 1988, 240, 1520-1522.
  3. L. Ortoleva-Donnelly, A. A. Szewczak, R. R. Gutell and S. A. Strobel, RNA, 1998, 4, 498-519.
  4. R. Sousa and R. Padilla, EMBO J., 1995, 14, 4609-4621.

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