Probing Contacts to the DNA Backbone in the trp Repressor−Operator Sequence-Specific Protein−Nucleic Acid Complex Using Diastereomeric Methylphosphonate Analogues

Abstract

Fourteen analogue DNA sequences containing the trp operator sequence and a single diastereomeric methylphosphonate linkage are each prepared from the stereochemically pure nucleoside methylphosphonate dimer building block, prepared as a phosphoramidite. The analogue sequences are shown to be single diastereomers on the basis of HPLC analysis of the digestion mixture; in each case, only a single diastereomeric dimer is present. These analogue sequences can be used effectively to probe for interactions to either of the prochiral phosphate oxygens as illustrated by their use to identify critical interactions in the trp repressor-operator complex. In a number of cases, the pairs of diastereomeric analogue sequences exhibit variable binding affinities that can be used to identify one of the prochiral phosphate oxygens as a critical site for complex-stabilizing interactions. Upon the basis of dissociation constants, apparent incremental binding energies are assigned to specific interactions. In all but one example, these identified sites for interactions to the phosphate backbone can be correlated with contacts implicated by the crystal structure analysis of the trp repressor-operator complex.

Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA–protein complexes

“…The methylphosphonate linkage, where one of the two nonbridging oxygens is replaced by a methyl group, was used to identify phosphate contacts in DNA-protein complexes (Noble et al+, 1984;Botfield & Weiss, 1994;Smith & McLaughlin, 1997)+ However, methylphosphonates have been used only rarely in studies of RNA-protein interactions, because the ribose methylphosphonate linkage is not chemically stable (Hamy et al+, 1993;Pritchard et al+, 1994)+ Although no enzymatic method exists for introduction of a methylphosphonate linkage, deoxynucleoside methylphosphonoamidites can be used to obtain a mixture of the two stereoisomers by chemical synthesis+ This mixture can easily be separated by HPLC when the oligomer is short (Hamy et al+, 1993;Lebedev et al+, 1993;Pritchard et al+, 1994)+ In contrast to the ethylated phosphate, the methylphosphonate modification is nearly isosteric with the phosphodiester linkage and therefore should not introduce any steric clashes with the protein or within the RNA+ Unlike the phosphorothioate substitution, the methylphosphonate linkage is uncharged, which neutralizes a small section of the RNA backbone (Fig+ 1A)+ This change in electrostatic potential can be expected to reduce the local water structure organization (Kulinska et al+, 1997) as well as weaken the ionic attraction between RNA and protein+ Therefore, the methylphosphonate linkage can be expected to be a useful phosphate analog, because the substitution of an oxygen by a methyl group should be drastic enough to disrupt protein-phosphate contacts and yet conservative enough to only locally disturb the RNA-protein interface+…”

Consequences of P‐Chirality in Chimeric 2′‐O‐Methyloligoribonucleotides with Stereoregular Methylphosphonothioate Linkages

“…[7] It was recently demonstrated that modified oligonucleotides can also deliver precise information on protein functions and interactions with DNA provided that detailed information on their intrinsic structure is available. [8][9][10][11] The physicochemical and biological properties of modified oligonucleotides can be widely tuned since numerous procedures have been elaborated that enable various modifications to internucleotide phosphodiester bonds, sugar or base moieties. [12] Modification of the internucleotide phosphorus centre allows the synthesis of oligonucleotides with enhanced affinity towards complementary templates, increased enzymatic stability, and improved membrane permeability.…”

Probing the Interface of the trp Repressor–Operator Complex Using Operator Sequences Containing Isosteric Base-Pair Analogues

“…But even this interaction may only contribute minimally to target recognition since the symmetrical mutations of C ϩ9 ϪG Ϫ9 → G ϩ9 ϪC Ϫ9 has relatively little effect upon repressor binding monitored in vivo (7). A number of direct contacts to the phosphodiester residues are also present in the complex (5) that afford complex stabilization (8). In addition to these direct interactions, a number of water-mediated contacts are present involving both the base residues (5,9,10) and the internucleotide phosphates (5,8).…”

“…A number of direct contacts to the phosphodiester residues are also present in the complex (5) that afford complex stabilization (8). In addition to these direct interactions, a number of water-mediated contacts are present involving both the base residues (5,9,10) and the internucleotide phosphates (5,8). Base analogue studies have assisted in illustrating that such interactions contribute to high affinity binding in this complex (8,10,11).…”

“…In addition to these direct interactions, a number of water-mediated contacts are present involving both the base residues (5,9,10) and the internucleotide phosphates (5,8). Base analogue studies have assisted in illustrating that such interactions contribute to high affinity binding in this complex (8,10,11). But in addition to both the direct and the water-mediated contacts that can be used to specify interactions with individual functional groups present in the operator sequence, there is a large nonspecific (at least in terms of functional group contacts) contact surface on the DNA that is rendered inaccessible to solvent upon binding by the protein (5).…”