Melting Of Base Pairs Research Articles

Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes.

Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.

Mechanism of eukaryotic origin unwinding is a dual helicase DNA shearing process.

DNA replication in all cells begins with the melting of base pairs at the duplex origin to allow access to single-stranded DNA templates which are replicated by DNA polymerases. In bacteria, origin DNA is presumed to be melted by accessory proteins that allow loading of two ring-shaped replicative helicases around single-strand DNA (ssDNA) for bidirectional unwinding and DNA replication. In eukaryotes, by contrast, two replicative CMG (Cdc45-Mcm2-7-GINS) helicases are initially loaded head to head around origin double-strand DNA (dsDNA), and there does not appear to be a separate origin unwinding factor. This led us to investigate whether head-to-head CMGs use their adenosine triphosphate (ATP)-driven motors to initiate duplex DNA unwinding at the origin. Here, we show that CMG tracks on one strand of the duplex while surrounding it, and this feature allows two head-to-head CMGs to unwind dsDNA by using their respective motors to pull on opposite strands of the duplex. We further show that while CMG is capable of limited duplex unwinding on its own, the extent of unwinding is greatly and rapidly stimulated by addition of the multifunctional CMG-binding protein Mcm10 that is critical for productive initiation of DNA replication in vivo. On the basis of these findings, we propose that Mcm10 is a processivity or positioning factor that helps translate the work performed by the dual CMG motors at the origin into productive unwinding that facilitates bidirectional DNA replication.

E. Coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity

Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as occurring by the ATPase motors mechanically pulling the DNA duplex across a wedge domain in the helicase, biochemical data show that processive DNA unwinding by E. coli RecBCD helicase can occur in the absence of ssDNA translocation by the canonical RecB and RecD motors. Here we show that DNA unwinding is not a simple consequence of ssDNA translocation by the motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecBΔNucCD) unwinds dsDNA at significantly slower rates than RecBCD, while the ssDNA translocation rate is unaffected. This effect is primarily due to the absence of the nuclease domain since a nuclease-dead mutant (RecBD1080ACD), which retains the nuclease domain, showed no change ssDNA translocation or dsDNA unwinding rates relative to RecBCD on short DNA substrates (≤60 base pairs). Hence, ssDNA translocation is not rate-limiting for DNA unwinding. RecBΔNucCD also initiates unwinding much slower than RecBCD from a blunt-ended DNA. RecBΔNucCD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecBD1080ACD unwinding are intermediate between RecBCD and RecBΔNucCD. Surprisingly, significant pauses in DNA unwinding occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, possibly allosterically and that RecBΔNucCD may mimic a post-chi state of RecBCD.

“Helicase” activity promoted through dynamic interactions between a ssDNA translocase and a diffusing SSB protein

Replication protein A (RPA) is a eukaryotic single-stranded (ss) DNA-binding (SSB) protein that is essential for all aspects of genome maintenance. RPA binds ssDNA with high affinity but can also diffuse along ssDNA. By itself, RPA is capable of transiently disrupting short regions of duplex DNA by diffusing from a ssDNA that flanks the duplex DNA. Using single-molecule total internal reflection fluorescence and optical trapping combined with fluorescence approaches, we show that S. cerevisiae Pif1 can use its ATP-dependent 5'to 3' translocase activity to chemomechanically push a single human RPA (hRPA) heterotrimer directionally along ssDNA at rates comparable to those of Pif1 translocation alone. We further show that using its translocation activity, Pif1 can push hRPA from a ssDNA loading site into a duplex DNA causing stable disruption of at least 9 bp of duplex DNA. These results highlight the dynamic nature of hRPA enabling it to be readily reorganized even when bound tightly to ssDNA and demonstrate a mechanism by which directional DNA unwinding can be achieved through the combined action of a ssDNA translocase that pushes an SSB protein. These results highlight the two basic requirements for any processive DNA helicase: transient DNA base pair melting (supplied by hRPA) and ATP-dependent directional ssDNA translocation (supplied by Pif1) and that these functions can be unlinked by using two separate proteins.

19F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes.

The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is emerging as a powerful technique for obtaining structural information about proteins and nucleic acids. In this work, we explored the capability of Mims 19F ENDOR experiments on reporting intermolecular distances in trityl- and 19F-labeled DNA duplexes at three electron paramagnetic resonance (EPR) frequencies (34, 94, and 263 GHz). For spin labeling, we used the hydrophobic Finland trityl radical and hydrophilic OX063 trityl radical. Fluorine labels were introduced into two positions of a DNA oligonucleotide. The results indicated that hyperfine splittings visible in the ENDOR spectra are consistent with the most populated interspin distances between 19F and the trityl radical predicted from molecular dynamic (MD) simulations. Moreover, for some cases, ENDOR spectral simulations based on MD results were able to reproduce the conformational distribution reflected in the experimental ENDOR line broadening. Additionally, MD simulations provided more detailed information about the melting of terminal base pairs of the oligonucleotides and about the configuration of the trityls relative to a DNA end.

RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics.

A plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA’s secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates.

Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting

E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined RecBCD-DNA initiation complexes using thermodynamic and structural approaches. Measurements of enthalpy changes for RecBCD binding to DNA ends possessing pre-melted ssDNA tails of increasing length suggest that RecBCD interacts with ssDNA as long as 17–18 nucleotides and can melt at least 10–11 bp upon binding a blunt DNA end. Cryo-EM structures of RecBCD alone and in complex with a blunt-ended dsDNA show significant conformational heterogeneities associated with the RecB nuclease domain (RecBNuc) and the RecD subunit. In the absence of DNA, 56% of RecBCD molecules show no density for the RecB nuclease domain, RecBNuc, and all RecBCD molecules show only partial density for RecD. DNA binding reduces these conformational heterogeneities, with 63% of the molecules showing density for both RecD and RecBNuc. This suggests that the RecBNuc domain is dynamic and influenced by DNA binding. The major RecBCD-DNA structural class in which RecBNuc is docked onto RecC shows melting of at least 11 bp from a blunt DNA end, much larger than previously observed. A second structural class in which RecBNuc is not docked shows only four bp melted suggesting that RecBCD complexes transition between states with different extents of DNA melting and that the extent of melting regulates initiation of helicase activity.

Mechanistic insights into Lhr helicase function in DNA repair.

The DNA helicase Large helicase-related (Lhr) is present throughout archaea, including in the Asgard and Nanoarchaea, and has homologues in bacteria and eukaryotes. It is thought to function in DNA repair but in a context that is not known. Our data show that archaeal Lhr preferentially targets DNA replication fork structures. In a genetic assay, expression of archaeal Lhr gave a phenotype identical to the replication-coupled DNA repair enzymes Hel308 and RecQ. Purified archaeal Lhr preferentially unwound model forked DNA substrates compared with DNA duplexes, flaps and Holliday junctions, and unwound them with directionality. Single-molecule FRET measurements showed that binding of Lhr to a DNA fork causes ATP-independent distortion and base-pair melting at, or close to, the fork branchpoint. ATP-dependent directional translocation of Lhr resulted in fork DNA unwinding through the ‘parental’ DNA strands. Interaction of Lhr with replication forks in vivo and in vitro suggests that it contributes to DNA repair at stalled or broken DNA replication.

How Does a Helicase Unwind DNA? Insights from RecBCD Helicase.

DNA helicases are a class of molecular motors that catalyze processive unwinding of double stranded DNA. In spite of much study, we know relatively little about the mechanisms by which these enzymes carry out the function for which they are named. Most current views are based on inferences from crystal structures. A prominent view is that the canonical ATPase motor exerts a force on the ssDNA resulting in "pulling" the duplex across a "pin" or "wedge" in the enzyme leading to a mechanical separation of the two DNA strands. In such models, DNA base pair separation is tightly coupled to ssDNA translocation of the motors. However, recent studies of the Escherichia coli RecBCD helicase suggest an alternative model in which DNA base pair melting and ssDNA translocation occur separately. In this view, the enzyme-DNA binding free energy is used to melt multiple DNA base pairs in an ATP-independent manner, followed by ATP-dependent translocation of the canonical motors along the newly formed ssDNA tracks. Repetition of these two steps results in processive DNA unwinding. We summarize recent evidence suggesting this mechanism for RecBCD helicase action.

Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation

Escherichia coli RecBCD is a DNA helicase/nuclease that functions in double-stranded DNA break repair. RecBCD possesses two motors (RecB, a 3′ to 5′ translocase, and RecD, a 5′ to 3′ translocase). Current DNA unwinding models propose that motor translocation is tightly coupled to base pair melting. However, some biochemical evidence suggests that DNA melting of multiple base pairs may occur separately from single-stranded DNA translocation. To test this hypothesis, we designed DNA substrates containing reverse backbone polarity linkages that prevent ssDNA translocation of the canonical RecB and RecD motors. Surprisingly, we find that RecBCD can processively unwind DNA for at least 80bp beyond the reverse polarity linkages. This ability requires an ATPase active RecB motor, the RecB “arm” domain, and also the RecB nuclease domain, but not its nuclease activity. These results indicate that RecBCD can unwind duplex DNA processively in the absence of ssDNA translocation by the canonical motors and that the nuclease domain regulates the helicase activity of RecBCD.

Unravelling the structural plasticity of stretched DNA under torsional constraint.

Regions of the genome are often held under torsional constraint. Nevertheless, the influence of such constraint on DNA–protein interactions during genome metabolism is still poorly understood. Here using a combined optical tweezers and fluorescence microscope, we quantify and explain how torsional constraint influences the structural stability of DNA under applied tension. We provide direct evidence that concomitant basepair melting and helical unwinding can occur in torsionally constrained DNA at forces >∼50 pN. This striking result indicates that local changes in linking number can be absorbed by the rest of the DNA duplex. We also present compelling new evidence that an overwound DNA structure (likely P-DNA) is created (alongside underwound structures) at forces >∼110 pN. These findings substantiate previous theoretical predictions and highlight a remarkable structural plasticity of torsionally constrained DNA. Such plasticity may be required in vivo to absorb local changes in linking number in DNA held under torsional constraint.

The Effect of Local Melting of DNA on DNA Loop Formation

Statistical mechanics of double-stranded DNA (dsDNA) is well described by the wormlike chain model (WLC) which assumes a harmonic bending potential. Such smooth bending potential may no longer be valid for large bending angles to form small loops (< 100 bp). Instead, DNA may rely on rare structural transitions such as local melting (opening) of base pairs to lower the energetic cost. In theory, open base pairs called bubbles can increase the looping probability of short DNA molecules by a few orders of magnitude, but a robust experimental validation of this theoretical prediction is lacking. Here, we investigated the correlation between local melting probability and looping dynamics of dsDNA using single-molecule fluorescence resonance energy transfer (FRET). We designed two groups of short DNA molecules with low and high melting probabilities around their center and measured their looping and unlooping rates in equilibrium. Our data allow rigorous tests of meltable wormlike chain (MWLC) models at short length scales for setting the lower limit for the free energy of bubble formation.

Cooperative base pair melting by helicase and polymerase positioned one nucleotide from each other.

Leading strand DNA synthesis requires functional coupling between replicative helicase and DNA polymerase (DNAP) enzymes, but the structural and mechanistic basis of coupling is poorly understood. This study defines the precise positions of T7 helicase and T7 DNAP at the replication fork junction with single-base resolution to create a structural model that explains the mutual stimulation of activities. Our 2-aminopurine studies show that helicase and polymerase both participate in DNA melting, but each enzyme melts the junction base pair partially. When combined, the junction base pair is melted cooperatively provided the helicase is located one nucleotide ahead of the primer-end. The synergistic shift in equilibrium of junction base pair melting by combined enzymes explains the cooperativity, wherein helicase stimulates the polymerase by promoting dNTP binding (decreasing dNTP Km), polymerase stimulates the helicase by increasing the unwinding rate-constant (kcat), consequently the combined enzymes unwind DNA with kinetic parameters resembling enzymes translocating on single-stranded DNA.

Tension-Dependent Stability of Torsionally Constrained DNA: Melting Precedes Overwinding

Key genomic processes such as replication and transcription require localized unwinding and base-pair melting of the double-helix. In vivo, however, DNA is often torsionally constrained, presenting a topological barrier to unwinding. While it is known that unwinding can proceed through buckling of such DNA (resulting in plectonemes), this may only occur at low forces (typically below 1 pN). Here, we ask: how can torsionally constrained DNA unwind at higher forces without changing the overall twist?Using a combination of optical tweezers and fluorescence microscopy we map the local changes in twist and base-pair integrity of torsionally constrained DNA as a function of tension and ionic strength. By correlating the second derivatives of force-extension curves of torsionally constrained DNA to the binding of a fluorescently-labeled single-stranded DNA binding protein (Replication Protein A), we identify two tension-dependent structural transitions. In agreement with a previous proposal, we show that at high tension (above 115 pN), unwinding is accompanied by the formation of overwound DNA (termed P-DNA) in a largely cooperative mechanism. Strikingly, we also reveal that for intermediate tensions (60 to 115 pN), localized base-pair melting can occur without changes in DNA twist. This mechanism, which is significantly less cooperative, is referred to here as ‘pre-melting’. We demonstrate that pre-melting is favored by AT-rich sequences and low ionic strength. In contrast, P-DNA is largely stabilized by higher salt concentrations, while also having a preference for AT-rich domains. This supports the hypothesis that P-DNA consists of tightly entwined backbones with exposed bases.These findings provide a new understanding of the interplay between DNA twist, extension and sequence. Moreover, since DNA unwinding can be induced through either tension or applied torque, this work may have strong implications for the metabolism of torsionally constrained DNA in vivo.

Friction and Interactions between Bare DNA Molecules: The Role of DNA Handedness

Cellular DNA is packaged through a range of re-modeling proteins. As a result, disparate regions of the genome may find themselves in close contact with one another. Here, we address an important and emerging issue resulting from this fact: what happens when DNA becomes entangled? Is it possible that the mechanical properties of DNA can influence interactions of the genome even in the absence of proteins? Recent experiments have suggested that the handedness of DNA may affect the stability of DNA-DNA pairs.Using a single-molecule approach, we employ a unique 4-way optical trap to wrap two separate DNA molecules around one another. By displacing optically trapped beads, it is possible to slide one DNA molecule along the other. Using triangulation, we are then able to track the location at which the DNA molecules are entwined. This analysis reveals that a small but clear friction is present only when sliding the DNA molecule through a right-handed wrap. Moreover, when sliding the DNA further, tension is built up and then released, giving rise to an abrupt stick-release force pattern. Strikingly, the latter is once again found predominantly in the case of a right-handed wrap. By staining the DNA molecules with the force-sensitive fluorescent dye Sytox, we are able to both visualize and measure this build-up and release of force. The stick-release behavior occurs only after a force of ∼65 pN has been applied. This suggests that the DNA molecules interact at their point of contact via melting of base-pairs, possibly creating a 3- or 4-stranded complex.The existence of chiral and force dependent interactions between bare DNA molecules has strong implications for the study of DNA in confined environments and raises interesting questions as to their potential importance in vivo.

Thermal Response of DNA Supramolecular Polymers Assembled with Hydrophobic Sticky Ends

We report the self-assembly and thermal dissociation of DNA dumbbell conjugates having a perylenediimide (PDI) linker on each end separated by 6-16 A-T base pairs. In the presence of NaCl these dumbbells form one-dimensional supramolecular assemblies as a consequence of the hydrophobic association of their PDI sticky ends. The dependence of assembly formation on dumbbell concentration, salt concentration, and temperature can be conveniently monitored by UV-vis spectroscopy. The melting of these linear assemblies follows two limiting mechanisms, depending on the length of the dumbbells. Upon heating in the presence of salt, the assemblies formed by the longer dumbbells undergo a sequential transition from assembly to base-paired monomer to random coiled monomer, whereas the assemblies formed by the shorter dumbbells undergo disassembly and base-pair melting cooperatively. In all cases, the intramolecular hydrophobic association of the PDI chromophores is observed at elevated temperature. The thermal behavior of these one-dimensional assemblies is compared to that of other sticky-ended assemblies.

The Primary and Secondary Translocase Activities within E. coli RecBC Helicase Are Tightly Coupled to ATP Hydrolysis by the RecB Motor

Escherichia coli RecBC, a rapid and processive DNA helicase with only a single ATPase motor (RecB), possesses two distinct single-stranded DNA (ssDNA) translocase activities that can operate on each strand of an unwound duplex DNA. Using a transient kinetic assay to detect phosphate release, we show that RecBC hydrolyzes the same amount of ATP when translocating along ssDNA using only its primary translocase (0.81±0.05ATP/nt), only its secondary translocase (1.12±0.06ATP/nt), or both translocases simultaneously (1.07±0.09ATP/nt). A mutation within RecB (Y803H) that slows the primary translocation rate of RecBC also slows the secondary translocation rate to the same extent. These results indicate that the ATPase activity of the single RecB motor drives both the primary and secondary RecBC translocases in a tightly coupled reaction. We further show that RecBC also hydrolyzes the same amount of ATP (0.95±0.08ATP/bp) while processively unwinding duplex DNA, suggesting that the large majority, possibly all, of the ATP hydrolyzed by RecBC during DNA unwinding is used to fuel ssDNA translocation rather than to facilitate base pair melting. A model for DNA unwinding is proposed based on these observations.

RNA Unwinding from Reweighted Pulling Simulations

The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively characterized at the molecular level. In this work, the base opening process was first enforced by atomistic pulling simulations and then analyzed with a novel reweighting scheme, which allowed the free-energy profile along any suitable reaction coordinate, for example, solvation, to be reconstructed. The systematic application of such approach to different base-pair combinations provides a molecular motion picture of helix opening, which is validated by comparison with an extensive set of experimental observations and links them to the enzyme-dependent unwinding mechanism. The RNA intrinsic dynamics disclosed in this work could rationalize the directionality observed in RNA-processing molecular machineries.

Perylenediimide-Linked DNA Dumbbells: Long-Distance Electronic Interactions and Hydrophobic Assistance of Base-Pair Melting

The synthesis and properties of synthetic DNA dumbbells having A-tract base pair domains consisting of 6−16 base pairs connected by perylenediimide (PDI) linkers are reported. The dumbbells were prepared in good yield by chemical ligation of nicked-dumbbell precursors having six or more A-T base pairs. The dumbbell structures have been investigated by a combination of electronic spectroscopy and molecular dynamics simulations. UV−visible spectra are indicative of the formation of monomeric dumbbells at room temperature in aqueous buffer in the absence of added salt. The long-wavelength region of the circular dichroism (CD) spectra is a composite of induced CD of the PDI monomers and intramolecular exciton-coupled CD between the two PDI chromophores. Weak exciton coupled CD can be observed between PDI chromophores separated by 13 base pairs, thus extending the reach of dumbbell molecular rulers. Upon heating, the dumbbells undergo base pair melting and intramolecular PDI−PDI association. Analysis of the temperature-dependent spectral data provides evidence for a three-state model in which base pair melting of the intact dumbbell results in the formation of an intermediate species which is in equilibrium with a collapsed dumbbell having intramolecular PDI−PDI stacking. The low melting temperatures of the shorter dumbbells are attributed to the partial compensation of PDI−PDI association for base pair dissociation.

Thermodynamics of RNA melting, one base pair at a time: FIGURE 1.

The melting of base pairs is a ubiquitous feature of RNA structural transitions, which are widely used to sense and respond to cellular stimuli. A recent study employing solution nuclear magnetic resonance (NMR) imino proton exchange spectroscopy provides a rare base-pair-specific view of duplex melting in the Salmonella FourU RNA thermosensor, which regulates gene expression in response to changes in temperature at the translational level by undergoing a melting transition. The authors observe "microscopic" enthalpy-entropy compensation--often seen "macroscopically" across a series of related molecular species--across base pairs within the same RNA. This yields variations in base-pair stabilities that are an order of magnitude smaller than corresponding variations in enthalpy and entropy. A surprising yet convincing link is established between the slopes of enthalpy-entropy correlations and RNA melting points determined by circular dichroism (CD), which argues that unfolding occurs when base-pair stabilities are equalized. A single AG-to-CG mutation, which enhances the macroscopic hairpin thermostability and folding cooperativity and renders the RNA thermometer inactive in vivo, spreads its effect microscopically throughout all base pairs in the RNA, including ones far removed from the site of mutation. The authors suggest that an extended network of hydration underlies this long-range communication. This study suggests that the deconstruction of macroscopic RNA unfolding in terms of microscopic unfolding events will require careful consideration of water interactions.