Effects of unpaired bases on the conformation and stability of three-arm DNA junctions

Programmable one-pot multistep organic synthesis using DNA junctions

A system for multistep DNA-templated synthesis is controlled by the sequential formation of DNA junctions. Reactants are attached to DNA adapters which are brought together by hybridization to DNA template strands. This process can be repeated to allow sequence-controlled oligomer synthesis while maintaining a constant reaction environment, independent of oligomer length, at each reaction step. Synthesis can take place in a single pot containing all required reactive monomers. Different oligomers can be synthesized in parallel in the same vessel, and the products of parallel synthesis can be ligated, reducing the number of reaction steps required to produce an oligomer of a given length.

Stabilization of three-way junctions of DNA under molecular crowding conditions

We examined the effects of molecular crowding conditions on the structures and thermodynamics of three-way junctions (TWJs) of DNA. Structural analysis utilizing gel electrophoresis and circular dichroism spectroscopy showed that the designed DNAs folded into TWJ structures in the presence of Na(+) and Mg(2+) under both dilute and molecular crowding conditions with polyethylene glycol 200 (PEG 200). From the thermodynamic parameters evaluated by UV melting techniques in the absence and presence of 5 mM Mg(2+) under dilute and molecular crowding conditions, it was clear that Mg(2+) stabilized all TWJs under the dilute condition, although the extent of stabilization depended on the stacking partners of TWJs. For example, thermodynamic stability (-DeltaG(o) (37)) of A/B-stacked TWJs (A, B, and C are the three helices of TWJ, and among these helices, A and B are stacked together) increased from 3.7 to 5.6 kcal/mol by the addition of 5 mM Mg(2+), while that of A/C-stacked TWJs (A and C are stacked together) increased only from 3.0 to 3.7 kcal/mol. Molecular crowding with PEG 200 destabilized the whole TWJ consisting of a junction point and three helical duplex arms. Crowding agents such as PEG 200 can affect the stability of DNA by modulating its hydration. To explore the crowding effects on the junction point, we evaluated the number of water molecules associated with the whole TWJ as well as the individual arms, and we found that the number of water molecules taken up by the whole TWJ was significantly smaller than the sum of the individual arms. These results show the dehydration from the junction point of the TWJ structure. Therefore, molecular crowding should be favorable for the junction point of TWJ structure and unfavorable for the duplex structure. To prove this concept, we designed truncated TWJ structures that folded into a bimolecular duplex under the dilute condition. With increasing concentrations of PEG 200 from 0 to 30 wt %, the fraction of truncated TWJ structures gradually increased, and that of the bimolecular duplex structure decreased, even in the absence of Mg(2+). We concluded that a cell-mimicking condition, in which the activity of water decreases and hydration becomes less favorable, might facilitate the formation of junction structures in comparison with duplexes.

Optimizing the interfacial binding and activity of a bacterial phosphatidylinositol-specific phospholipase C

The phosphatidylinositol-specific phospholipase C from Bacillus thuringiensis can be activated by nonsubstrate interfaces such as phosphatidylcholine micelles or bilayers. This activation corresponds with partial insertion into the interface of two tryptophans, Trp-47 in helix B and Trp-242 in a loop, in the rim of the alphabeta-barrel. Both W47A and W242A have much weaker binding to interfaces and considerably lower kinetic interfacial activation. Tryptophan rescue mutagenesis, reinsertion of a tryptophan at a different place in helix B in the W47A mutant or in the loop (residues 232-244) of the W242A mutant, has been used to determine the importance and orientation of a tryptophan in these two structural features. Phosphotransferase and phosphodiesterase assays, and binding to phosphatidylcholine vesicles were used to assess both orientation and position of tryptophans needed for interfacial activity. Of the helix B double mutants, only one mutant, I43W/W47A, has tryptophan in the same orientation as Trp-47. I43W/W47A shows recovery of phosphatidylinositol-specific phospholipase C (PC) activation of d-myo-inositol 1,2-cyclic phosphate hydrolysis. However, the specific activity toward phosphatidylinositol is still lower than wild type enzyme and high activity with phosphatidylinositol solubilized in 30% isopropyl alcohol (a hallmark of the native enzyme) is lost. Reinserting a tryptophan at several positions in the loop composed of residues 232-244 partially recovers PC activation and affinity of the enzyme for lipid interfaces as well as activation by isopropyl alcohol. G238W/W242A shows an enhanced activation and affinity for PC interfaces above that of wild type. These results provide constraints on how this bacterial phosphatidylinositol-specific phospholipase C binds to activating PC interfaces.

Sequence-dependent folding of DNA three-way junctions

Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined by the DNA sequence. In this study we have compared several three-way DNA junctions in order to assess how the arrangement of bases around the branch point affects the conformer distribution. The results show that rearranging the different arms, while retaining their base sequences, can affect the conformer distribution. In some instances this generates a structure that appears to contain parallel coaxially stacked helices rather than the usual anti-parallel arrangement. Although the conformer equilibrium can be affected by the order of purines and pyrimidines around the branch point, this is not sufficient to predict the conformer distribution. We find that the folding of three-way junctions can be separated into two groups of dinucleotide steps. These two groups show distinctive stacking properties in B-DNA, suggesting there is a correlation between B-DNA stacking and coaxial stacking in DNA junctions.

Role of tryptophan residues in interfacial binding of phosphatidylinositol-specific phospholipase C

The phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus thuringiensis exhibits several types of interfacial activation. In the crystal structure of the closely related Bacillus cereus PI-PLC, the rim of the active site is flanked by a short helix B and a loop that show an unusual clustering of hydrophobic amino acids. Two of the seven tryptophans in PI-PLC are among the exposed residues. To test the importance of these residues in substrate and activator binding, we prepared several mutants of Trp-47 (in helix B) and Trp-242 (in the loop). Two other tryptophans, Trp-178 and Trp-280, which are not near the rim, were mutated as controls. Kinetic (both phosphotransferase and cyclic phosphodiesterase activities), fluorescence, and vesicle binding analyses showed that both Trp-47 and Trp-242 residues are important for the enzyme to bind to interfaces, both activating zwitterionic and substrate anionic surfaces. Partitioning of the enzyme to vesicles is decreased more than 10-fold for either W47A or W242A, and removal of both tryptophans (W47A/W242A) yields enzyme with virtually no affinity for phospholipid surfaces. Replacement of either tryptophan with phenylalanine or isoleucine has moderate effects on enzyme affinity for surfaces but yields a fully active enzyme. These results are used to describe how the enzyme is activated by interfaces.

A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes

A general approach is described for controlling the RNA-cleaving activity of nucleic acid enzymes (ribozymes and DNAzymes) via the use of oligonucleotide effectors (regulators). In contrast to the previously developed approaches of allosteric and facilitator-mediated regulation of such enzymes, this approach, called 'expansive' regulation, requires that the regulator bind simultaneously to both enzyme and substrate to form a branched three-way complex. Such three-way enzyme-substrate-regulator complexes are catalytically competent relative to the structurally unstable enzyme-substrate complexes. Using the 8-17 and bipartite DNAzymes and the hammerhead ribozyme as model systems, 20- to 30-fold rate enhancements were achieved in the presence of regulators of engineered variants of the above three enzymes, even under unoptimized conditions. Broadly, using this approach ribozyme and DNAzyme variants that are amenable to regulation by oligonucleotide effectors can be designed even in the absence of any knowledge of the folded structure of the relevant ribozyme or DNAzyme. Expansive regulation therefore represents a new and potentially useful technology for both the regulation of nucleic acid enzymes and the detection of specific RNA transcripts.

A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate

We describe a novel and general strategy for controlling the activity of RNA-cleaving nucleic acid enzymes (ribozymes and DNAzymes) via the use of RNA and DNA effectors. Whereas in conventional heteroallosteric enzymes (including ribozymes) control of catalysis is achieved by the binding of effector molecules to the enzyme, in our strategy DNA and RNA regulators bind to both the enzyme and the substrate. The design of this system permits the control of catalysis even in the absence of a detailed knowledge of the secondary and tertiary structure of the relevant ribozyme or DNAzyme. Here, we utilize the ability of RNA and DNA to form branched three-way junctions to regulate the RNA-cleaving activity of the in vitro selected "10-23" DNAzyme by three orders of magnitude. Control is exercised by the ability of a DNA or RNA "regulator" to induce formation of stable and catalytically competent "three-way" enzyme-substrate-regulator complexes, relative to otherwise unstable and catalytically poor enzyme-substrate complexes. Such expansively regulated "three-way" ribozyme/DNAzyme systems might find utility in vivo to bring about the catalyzed destruction of one RNA transcript contingent on the presence in its immediate environment of another gene transcript.

Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection

The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. The stacking of the unpaired thymidine bases on arm C resembles the folding of hairpin loops. From this data, combined with the reported stacking behavior of 23 other 3HS2 s, two rules are derived that together correctly reproduce their stacking preference. These rules predict, from the sequence of any 3HS2, its stacking preference. The structure also suggests a plausible mechanism for structure-specific recognition of branched nucleic acids by proteins.

DNA binding by single HMG box model proteins

The HMG1/2 family is a large group of proteins that share a conserved sequence of approximately 80 amino acids rich in basic, aromatic and proline side chains, referred to as an HMG box. Previous studies show that HMG boxes can bind to DNA in a structure-specific manner. To define the basis for DNA recognition by HMG boxes, we characterize the interaction of two model HMG boxes, one a structure-specific box, rHMGb from the rat HMG1 protein, the other a sequence-specific box, Rox1 from yeast, with oligodeoxynucleotide substrates. Both proteins interact with single-stranded oligonucleotides in this study to form 1:1 complexes. The stoichiometry of binding of rHMGb to duplex or branched DNAs differs: for a 16mer duplex we find a weak 2:1 complex, while a 4:1 protein:DNA complex is detected with a four-way DNA junction of 16mers in the presence of Mg(2+). In the case of the sequence-specific Rox1 protein we find tight 1:1 and 2:1 complexes with its cognate duplex sequence and again a 4:1 complex with four-way branched DNA. If the DNA branching is reduced to three arms, both proteins form 3:1 complexes. We believe that these multimeric complexes are relevant for HMG1/2 proteins in vivo, since Mg(2+) is present in the nucleus and these proteins are expressed at a very high level.

Three-way and four-way junctions in DNA: a conformational viewpoint

DNA junctions are potential intermediates in various important genetic processes, including mutagenesis and recombination. The quantity of research carried out in this area is rapidly increasing. Examples of three-way and four-way junctions are now relatively well characterized and a few common properties have been recognized, of which the most important is the tendency of junctions to fold into one or more coaxially stacked helical conformations or cross-over structures.

Calorimetry of proteins and nucleic acids

The availability of sensitive calorimetric instrumentation has led to a considerable increase in thermodynamic studies of proteins, nucleic acids, and their interactions. This article reviews some of the recent contributions of calorimetry to characterizing the thermodynamic origins of protein and nucleic acid stability and conformational preferences, as well as the interactions of proteins with each other, with small molecules, and with nucleic acids.

Recognition and cleavage of hairpin structures in nucleic acids by oligodeoxynucleotides

The possibility of designing antisense oligodeoxynucleotides complementary to non-adjacent single-stranded sequences containing hairpin structures was studied using a DNA model system. The structure and stability of complexes formed by a 17mer oligonucleotide with DNA fragments containing hairpin structures was investigated by spectroscopic measurements (melting curves) and chemical reactions (osmium tetroxide reaction, copper-phenanthroline cleavage). A three-way junction was formed when the oligonucleotide was bound to both sides of the hairpin structure. When the complementary sequences of the two parts of the oligonucleotide were separated by a sequence which could not form a hairpin, the oligonucleotide exhibited a slightly weaker binding than to the hairpin-containing target. An oligodeoxynucleotide-phenanthroline conjugate was designed to form Watson-Crick base pairs with two single-stranded regions flanking a hairpin structure in a DNA fragment. In the presence of Cu2+ ions and a reducing agent, two main cleavage sites were observed at the end of the duplex structure formed by the oligonucleotide-phenanthroline conjugate with its target sequence. Competition experiments showed that both parts of the oligonucleotide must be bound in order to observe sequence-specific cleavage. Cleavage was still observed with target sequences which could not form a hairpin, provided the reaction was carried out at lower temperatures. These results show that sequence-specific recognition and modification (cleavage) can be achieved with antisense oligonucleotides which bind to non-adjacent sequences in a single-stranded nucleic acid.

Structure of three-way DNA junctions. 2. Effects of extra bases and mismatches

The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-pairing in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90 degrees between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.