Fig. 1. Protein-protein interactions between gp32 and gp59 on fDNA. (A) The fluorescence from individual molecules of fDNA with the proteins bound in the order as indicated at the side of each row. The gp32 protein is labeled with A488 (gp32 D ) and the gp59 protein is labeled with A555 (gp59 A ). The filter sets are described in Experimental Methods: F1 is for A488 emission, F2 for FRET between A488 and A555, and F3 for A555 emission. (B) Ensemble FRET studies of Oregon-green-488-maleimide-labeled gp59 titrated into a solution of 400 nM CPM-labeled gp32 and 100 nM fDNA. The fluorescence spectra of 400 nM CPM-gp32 alone (black line), the endpoint of the titration at 1 M Oregon-green-488-maleimide-gp59 (dark gray line), and several intermediate spectra (light gray lines) are shown. (C) Analysis of the donor quenching and acceptor sensitization plotted against the gp59 concentration determines the stoichiometry among gp32, gp59, and fDNA to be 1:1:1 with a calculated binding constant of Ϸ40 nM. The gp32 protein is labeled with A488 (gp32 D ), the gp59 protein is labeled with A555 (gp59 A ), and the gp41 protein is unlabeled. MgATP␥S (500 M) is present for the sample in row 2, and 500 M MgATP is present for the sample in row 3. (B) The gp32 protein is unlabeled, the gp59 protein is labeled with A555 (gp59 A ), and the gp41 is labeled with A488 (gp41 D ). MgATP␥S (500 M) is present for the sample in row 2, and 500 M MgATP is present for the sample in row 3 (5 min after addition of gp41 and nucleotide) and in row 4 (30 min after addition of gp41 and nucleotide). The filter sets are described in the legend to Fig. 1. RNA ͉ tertiary interactions ͉ heterogeneity ͉ time-correlated single photon counting T he discovery that RNAs can catalyze biological reactions has led to intensive effort aimed at identifying additional biological functions for RNA. More than 20 years later, we now know that RNAs play critical functional roles in metabolism, replication, regulation, and development in cells. Extensive biochemical and biophysical studies have led to a better understanding of the molecular mechanisms by which RNAs achieve their biological function, highlighting the important roles of both structure and dynamics. In this regard, single-molecule methods have recently emerged as particularly powerful tools. The folding dynamics of various functional RNAs have been investigated by single-molecule FRET experiments, which probe dynamics under equilibrium conditions via observation of the stochastic fluorescence trajectories as a function of time (1-6). These techniques offer a unique glimpse into subpopulations of a system and, in some cases, have identified conformational heterogeneity or the presence of intermediates that would otherwise be undetectable by ensemble methods (3-5, 7, 8).Unlike the highly cooperative, all-or-none, folding process observed for most protein domains, RNAs generally fold in a noncooperative manner, where the secondary structure forms independently of the tertiary structure. The thermodynamics for f...

The GAAA tetraloop-receptor is a commonly occurring tertiary interaction motif in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop-receptor interaction makes to the folding properties of an RNA. To investigate the kinetics and thermodynamics for the isolated interaction, a GAAA tetraloop domain and receptor domain were connected by a singlestranded A 7 linker. Fluorescence resonance energy transfer (FRET) experiments were used to probe intramolecular docking of the GAAA tetraloop and receptor. Docking was induced using a variety of metal ions, where the charge of the ion was the most important factor in determining the concentration of the ion required to promote docking ([Co(NH 3 . Analysis of metal ion cooperativity yielded Hill coefficients of ≈ 2 for Na + -or K + -dependent docking versus ≈ 1 for the divalent ions and Co(NH 3 ) 6 3+ . Ensemble stopped-flow FRET kinetic measurements yielded an apparent activation energy of 12.7 kcal/mol for GAAA tetraloopreceptor docking. RNA constructs with U 7 and A 14 single-stranded linkers were investigated by single-molecule and ensemble FRET techniques to determine how linker length and composition affect docking. These studies showed that the single-stranded region functions primarily as a flexible tether. Inhibition of docking by oligonucleotides complementary to the linker was also investigated. The influence of flexible versus rigid linkers on GAAA tetraloop-receptor docking is discussed.RNA is an essential biological molecule that functions in numerous cellular processes, including catalyzing such critical reactions as protein synthesis and RNA splicing (1-3). To achieve its various functions, RNAs must adopt complex, well-defined three-dimensional structures, and determining how these RNA structures are formed and stabilized is critical to understanding their biological function. The process by which RNAs fold to these threedimensional structures is complex. Unlike most protein folding, RNA folding often proceeds by a hierarchical pathway, where the secondary structure forms prior to and independently of the tertiary structure, and the tertiary structure is stabilized by interactions between the secondary structural elements (4). † This work was supported in part by grants from: NIH (AI 33098), NSF, NIST and the W. M. Keck Foundation initiative in RNA science at the University of Colorado, Boulder. CDD was also supported in part by Biophysics Training Grant NIH (GM 65103).*To whom correspondence should be addressed. E-mail: arthur.pardi@colorado.edu, Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309. Phone (303) NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptA variety of RNA tertiary interaction motifs have been identified, including loop-loop interactions between hairpin or internal loops, A-minor interactions, and pseudoknots (5-10).One...

Proper assembly of RNA into catalytically active three-dimensional structures requires multiple tertiary binding interactions, individual characterization of which is crucial to a detailed understanding of global RNA folding. This work focuses on single-molecule fluorescence studies of freely diffusing RNA constructs that isolate the GAAA tetraloop-receptor tertiary interaction. Freely diffusing conformational dynamics are explored as a function of Mg(2+) and Na(+) concentration, both of which promote facile docking, but with 500-fold different affinities. Systematic shifts in mean fluorescence resonance energy transfer efficiency values and line widths with increasing [Na(+)] are observed for the undocked species and can be interpreted with a Debye model in terms of electrostatic relaxation and increased flexibility in the RNA. Furthermore, we identify a 34 +/- 2% fraction of freely diffusing RNA constructs remaining undocked even at saturating [Mg(2+)] levels, which agrees quantitatively with the 32 +/- 1% fraction previously reported for immobilized constructs. This verifies that the kinetic heterogeneity observed in the docking rates is not the result of surface tethering. Finally, the K(D) value and Hill coefficient for [Mg(2+)]-dependent docking decrease significantly for [Na(+)] = 25 mM vs. 125 mM, indicating Mg(2+) and Na(+) synergy in the RNA folding process.

Summary Cellular replicases contain a multiprotein ATPase that loads a sliding clamp processivity factor onto DNA. We reveal a new role for a clamp loader: chaperoning of the replicative polymerase onto a clamp newly bound to DNA. We show that chaperoning confers distinct advantages, including marked acceleration of initiation complex formation. We reveal a requirement for the τ form of DnaX complex to relieve inhibition by single-stranded DNA binding protein during initiation complex formation. We propose that, after loading β2, DnaX complex preserves an SSB-free segment of DNA immediately downstream of the primer terminus and chaperones Pol III into that position, preventing competition by SSB. The C-terminal tail of SSB stimulates reactions catalyzed by τ-containing DnaX complexes through contact distinct for the only known contact involving the χ subunit. The chaperoning of Pol III by the DnaX complex provides a molecular explanation for how initiation complexes form when supported by the non-hydrolyzed analog ATPγS.

In Escherichia coli, coordinated activation and deactivation of DnaA allows for proper timing of the initiation of chromosomal synthesis at the origin of replication (oriC) and assures initiation occurs once per cell cycle. In vitro, acidic phospholipids reactivate DnaA, and in vivo depletion of acidic phospholipids, results in growth arrest. Growth can be restored by the expression of a mutant form of DnaA, DnaA(L366K), or by oriC-independent DNA synthesis, suggesting acidic phospholipids are required for DnaA- and oriC-dependent replication. We observe here that when acidic phospholipids were depleted, replication was inhibited with a concomitant reduction of chromosomal content and cell mass prior to growth arrest. This global shutdown of biosynthetic activity was independent of the stringent response. Restoration of acidic phospholipid synthesis resulted in a resumption of DNA replication prior to restored growth, indicating a possible cell-cycle-specific growth arrest had occurred with the earlier loss of acidic phospholipids. Flow cytometry, thymidine uptake, and quantitative polymerase chain reaction data suggest that a deficiency in acidic phospholipids prolonged the time required to replicate the chromosome. We also observed that regardless of the cellular content of acidic phospholipids, expression of mutant DnaA(L366K) altered the DNA content-to-cell mass ratio.

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Upon completion of synthesis of an Okazaki fragment, the lagging strand replicase must recycle to the next primer at the replication fork in under 0.1 second to sustain the physiological rate of DNA synthesis. We tested the collision model that posits that cycling is triggered by the polymerase encountering the 5′-end of the preceding Okazaki fragment. Probing with surface plasmon resonance, DNA polymerase III holoenzyme initiation complexes were formed on an immobilized gapped template. Initiation complexes exhibit a half-life of dissociation of approximately 15 minutes. Reduction of gap size to one nucleotide increased the rate of dissociation 2.5-fold and complete filling of the gap increased the off rate an additional three-fold (t½ ∼ 2 min). An exogenous primed template and ATP accelerated dissociation an additional four-fold in a reaction that required complete filling of the gap. Neither a 5′-triphosphate nor 5′-RNA terminated oligonucleotide downstream of the polymerase accelerated dissociation further. Thus, the rate of polymerase release upon gap completion and collision with a downstream Okazaki fragment is 1000-fold too slow to support an adequate rate of cycling and likely provides a backup mechanism to enable polymerase release when the other cycling signals are absent. Kinetic measurements indicate that addition of the last nucleotide to fill the gap is not the rate-limiting step for polymerase release and cycling. Modest (approximately 7 nucleotide) strand displacement is observed after the gap between model Okazaki fragments is filled. To determine the identity of the protein that senses gap filling to modulate affinity of the replicase for the template, we performed photo-crosslinking experiments with highly reactive and non-chemoselective diazirines. Only the α subunit cross-linked, indicating it serves as the sensor.

The DnaX complex (DnaX 3 ␦␦) within the Escherichia coli DNA polymerase III holoenzyme serves to load the dimeric sliding clamp processivity factor, ␤ 2 , onto DNA. The complex contains three DnaX subunits, which occur in two forms: and the shorter ␥, produced by translational frameshifting. Ten forms of E. coli DnaX complex containing all possible combinations of wild-type or a Walker A motif K51E variant or ␥ have been reconstituted and rigorously purified. DnaX complexes containing three DnaX K51E subunits do not bind ATP. Comparison of their ability to support formation of initiation complexes, as measured by processive replication by the DNA polymerase III holoenzyme, indicates a minimal requirement for one ATPbinding DnaX subunit. DnaX complexes containing two mutant DnaX subunits support DNA synthesis at about two-thirds the level of their wild-type counterparts. ␤ 2 binding (determined functionally) is diminished 12-30-fold for DnaX complexes containing two K51E subunits, suggesting that multiple ATPs must be bound to place the DnaX complex into a conformation with maximal affinity for ␤ 2 . DNA synthesis activity can be restored by increased concentrations of ␤ 2 . In contrast, severe defects in ATP hydrolysis are observed upon introduction of a single K51E DnaX subunit. Thus, ATP binding, hydrolysis, and the ability to form initiation complexes are not tightly coupled. These results suggest that although ATP hydrolysis likely enhances ␤ 2 loading, it is not absolutely required in a mechanistic sense for formation of functional initiation complexes. DNA polymerase III holoenzyme (pol III HE)2 exhibits features common to all other cellular replicases. It is a tripartite assembly composed of a replicative polymerase (pol III), a sliding clamp processivity factor (␤ 2 ), and an AAAϩ ATPase that assembles the ␤ 2 clamp around DNA (DnaX complex) (1, 2). The DnaX complex contains three DnaX subunits and one each of ␦, ␦Ј, , and . The DnaX subunit is either the full-length dnaX translation product or a shorter version, ␥, which is generated by translational frameshifting. ␥ lacks two C-terminal domains that bind the replicative helicase and pol III.Current models for clamp loading, largely derived from ␥-only DnaX complexes in the absence of pol III, propose that ATP binds to all three DnaX subunits, increasing the affinity of the clamp loader for ␤ 2 and primed DNA (1, 3). Once a ␤ 2 -primed DNA complex is formed, hydrolysis of the three ATPs places the DnaX complex into a conformation with decreased affinity for DNA, leading to its dissociation from DNA-bound ␤ 2 (3). pol III then associates with ␤ 2 in a downstream step, leading to formation of an initiation complex for processive replication.We have shown that some of the characteristics of initiation complex formation catalyzed by -containing DnaX complexes are different from ␥-only complexes. For example, complex, when bound to pol III, can form initiation complexes in the leading strand half of a dimeric replicase in the presence of the nonhydrolyzed an...