Introduction to modification interference studies

The NAIM approach; Nucleotide analogue interference mapping (NAIM) is a specific

and versatile chemogenetic approach which allows to probe the functional consequences of changes as minor as single atom substitutions in the base, sugar or phosphate moiety of nucleic acids. NAIM uses the potential of phosphorothioate modifications as reporters (Fig. 4.3.1, yellow), which permits to specifically cleave the nucleic acid chain by iodine exclusively at the sites of analogue incorporation (Gish & Eckstein, 1998; 3.4.8). Phosphorothioate modifications are obtained by substitution of one of the two non-bridging phosphate oxygen atoms (pro Sp and pro Rp) with sulphur. For synthesis of modified RNA by run-off transcription, Sp-α-thio-NTP’s are used. During polymerisation the phosphate group is converted to the Rp– configuration (Griffiths et al., 1987). The substitution with sulphur may affect the coordination of Mg2+ and the formation of hydrogen bonds while the secondary structure of RNA usually remains unaffected.

At the onset of NAIM studies, a pool of RNA molecules with limited numbers of randomly distributed nucleotide analogues is synthesised. Such a pool of RNAs is then subjected to a selection procedure to separate active variants from those with impaired function due to modification at a particular location. Subsequent comparative analysis of the distribution of modifications in the active RNA fraction and a reference fraction (e.g. the fraction of molecules with impaired function or the original unselected pool) reveals positions critical for function.

The partial modification of RNA is achieved by the presence of nucleoside α- thiotriphosphate analogues during in vitro transcription by T7 RNA polymerase, resulting in the aforementioned pool of RNA molecules, each carrying a low number of randomly Fig. 4.3.1: Phosphorothioate as reporter for modification

distributed modifications. The elegance of the method lies in the capacity to simultaneously screen for the functional contribution of a particular chemical group at almost every A, C, G or U position in an RNA chain. The analogues available for NAIM studies can be divided into three categories (Strobel, 1999), according to their main attribute: (a) if they primarily change the chemical properties of the substitutent, (b) delete a functional group or (c) introduce a bulky substituent.

Depending on the type of modification introduced, NAIM experiments have the potential to reveal the following information:

• An Rp-phosphorothioate (Fig. 4.3.1, yellow) modification per se (AMPαS, GMPαS, CMPαS, UMPαS) may identify crucial coordination sites for Mg2+ ions. Substitution of sulfur for a non-bridging phosphate oxygen essentially abolishes inner-sphere coordination to Mg2+, because Mg2+, a "hard" Lewis acid, prefers to bind oxygen, a "hard" Lewis base, relative to the much more polarisable and thus "softer" sulfur (Pearson, 1963). However, addition of more thiophilic metal ions ("softer" Lewis acids) such as Mn2+ or Cd2+ may restore, to varying extent, metal ion binding to the thiophosphate, leading to a (partial) rescue of the functional defect (Warnecke et al., 1996).

• C7-deaza (the nitrogen marked in red replaced by a C-H group; Fig. 4.3.1) purine analogues (c7-AMPαS, c7-GMPαS) are employed to reveal N7 positions involved in hydrogen binding or metal ion coordination. The latter aspect may be particularly relevant if RNA structure and function is probed in the presence of transition metal ions, such as Mn2+ _{or Zn}2+_{, which form inner-sphere complexes with the N7 of} purines (Sigel & Song, 1996; Rubin et al., 1983).

• 2'-deoxy (removal of the 2’-OH group highlighted in green; Fig. 4.3.1) modifications allow probing of the hydrogen donor and acceptor functions of 2' hydroxyls.

• IMPαS (the amino group highlighted in magenta replaced with hydrogen; Fig. 4.3.1), incorporated by T7 RNA polymerase instead of G nucleotides is suited to probe the role of guanine exocyclic amino groups in hydrogen bonding. For E. coli P RNA, relatively few inosine interference effects were detected in regular helices, suggesting that helix destabilisation by this modification is of minor importance for the function of the RNase P ribozyme (Heide et al., 1999). However, destabilisation of secondary structure can become important if inosines are part of a short intermolecular hybrid helix required to bind the substrate to the ribozyme, particularly under conditions where ribozyme molecules compete for a limited amount of substrate RNAs (Ortoleva–Donnely et al., 1998). For such cases, combined analysis of IMPαS and N2-methyl-GMPαS interfence patterns was reported as a strategy to

differentiate between helix destabilisation and loss of important tertiary interactions as the cause of interference (Strobel, 1999; Ortoleva–Donnely et al., 1998). The N2- methyl group can still form a hydrogen bond with the O2 of cytosine in Watson-Crick base pairs, but has lost its capacity to participate in a bifurcated hydrogen bonding frequently observed in tertiary contacts that involve the 2-amino group of paired G residues (Heide et al., 1999; Ortoleva–Donnely et al., 1998; Cate et al., 1996; Pley et al., 1994).

Nucleotide analogue interference suppression (NAIS) is an extension of NAIM to

determine whether an observed interference effect is caused by disruption of a direct contact between two particular functional groups of two interacting molecules. In NAIS, the partially analogue-modified RNA pool (RNA 1) is analysed for interference effects in two parallel setups: one employing the interacting RNA (RNA 2) in its unmodified form, as in NAIM, and the second one using RNA 2 with a point mutation or a single chemical group altered at a location suspected to interact directly with RNA 1. If a functional group in RNA 2 that normally interacts with the functional group in RNA 1 has been changed by the aforementioned mutation or modification, the interference effect observed in the first experimental setup corresponding to the disruption of this particular interaction should disappear, since the contact has already been abolished by the mutation or modification introduced into RNA 2, and a modification in RNA 1 at the corresponding position remains without effect. A critical point of such NAIS experiments is to adapt the functional assay with the mutant or modified RNA 2 in such a way that the extent of reaction or complex formation is the same as in the reference assay with unmodified RNA 2. For a more detailed description and illustration of NAIM and NAIS, see Cuzic & Hartmann, 2005 and Fedorova et al., 2005.