Ral systems, including RNA folding,3 ribozyme catalysis,4-6 RNA-protein interactions,7, 8 and even in vivo RNA modification. The method can be applied to the study of any nucleic acid that can be functionally selected from among a larger pool of less active variants. Selection schemes have included native gel mobility shifts, nitrocellulose filter binding, selective radiolabeling by RNA ligation, and size selection in a denaturing polyacrylamide gel.3-8 It has been applied toward the study of catalytic RNA reactivity, tRNAsynthetase interactions, mRNA processing, rRNA modification and snoRNA assembly. RNAs successfully studied by NAIM range from less than 50 to almost 1000 nucleotides in size, yet in all cases the data defines the contribution of a specific functional group at the individual nucleotide level.
Interference
In this particular example, the RNA has five A’s and the 2′-OH groups of two of them (1 and 4 shown in red) are important for activity based upon the NAIM experiment with dAS (A). Interference suppression is performed in the same manner as NAIM, but in this case a 2′-OH known to be important for activity is substituted with a 2′-deoxy G nucleotide within all the molecules in the population. This eliminates one of the critical
Suppression
hydrogen bonds (blue circle) and causes all of the molecules in the population to be less active. However, deletion of the second hydrogen bond in the pair has no additional deleterious effect on activity, so it can be removed without significant penalty. In this example, specific suppression of dAS interference is observed at A4, which is evidence that the 2′-OH of A4 and the 2′-OH of the substituted G participate in a hydrogen-bonding interaction.2383117-96-0 Molecular Weight
Interference Suppression
Although NAIM provides a great deal of chemical information about the functional importance of each nucleotide in an RNA sequence, it can be difficult to reach specific conclusions about the tertiary structure from primary interference data alone.1025065-69-3 supplier While a single NAIM experiment can identify all of the important 2′-OH groups and exocyclic amines within an RNA, it does not define how these groups interact within the overall RNA fold. However, such information can be obtained using a variation of NAIM, termed Interference Suppression.9 This method, which combines site-specific analog substitution and interference modification approaches, makes it possible to identify specific tertiary hydrogen-bonding partners within an RNA structure.10 The principle behind the approach is that, if an interaction is disrupted by deletion or alteration of one functional group in an interacting pair, then no additional energetic penalty will result from deletion or alteration of the second functional group in the pair.PMID:29083663 Interference suppression is scored by the reappearance of a specific band on the sequencing gel which showed interference in the context of the initial NAIM experiment (Figure 1B). For example, if every RNA in the population lacks a 2′-OH group that is known to be important for activity, interference will be suppressed at the specific site with the specific functional group that makes a hydrogen bonding interaction with the deleted group. This type of experiment has provided a series of hydrogen bonding structural restraints that have made it possible to construct a detailed model of the group I intron active site (Figure 2).10 Within this catalytic RNA, deletion of the 2′-OH at G22, resulted in suppression of 2′-deoxy and 3-de.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com