Motions of the Fingers Subdomain of Klentaq1 Are Fast and Not Rate Limiting: Implications for the Molecular Basis of Fidelity in DNA Polymerases

The catalytic mechanism of DNA polymerases involves multiple steps that precede and follow the transfer of a nucleotide to the 3 -hydroxyl of the growing DNA chain. Here we report a singlemolecule approach to monitor the movement of E. coli DNA polymerase I (Klenow fragment) on a DNA template during DNA synthesis with single base-pair resolution. As each nucleotide is incorporated, the single-molecule Fö rster resonance energy transfer intensity drops in discrete steps to values consistent with single-nucleotide incorporations. Purines and pyrimidines are incorporated with comparable rates. A mismatched primer/template junction exhibits dynamics consistent with the primer moving into the exonuclease domain, which was used to determine the fraction of primer-termini bound to the exonuclease and polymerase sites. Most interestingly, we observe a structural change after the incorporation of a correctly paired nucleotide, consistent with transient movement of the polymerase past the preinsertion site or a conformational change in the polymerase. This may represent a previously unobserved step in the mechanism of DNA synthesis that could be part of the proofreading process.Klenow Fragment ͉ polymerase and exonuclease site ͉ single molecule fluorescence ͉ single nucleotide resolution ͉ structural dynamics T he catalytic mechanism of Escherichia coli DNA polymerase I has been rigorously studied for more than 40 years (1, 2). The E. coli DNA polymerase I (Klenow fragment [KF]), an active truncated form of polymerase I, is composed of two domains: a polymerase domain that incorporates nucleotides, and a 3Ј-5Ј exonuclease domain that excises misincorporated nucleotides. The polymerase domain consists of three subdomains: the fingers, the palm, and the thumb. The fingers subdomain is primarily involved in interactions with the singlestranded region of the DNA template and the incoming nucleotide; the palm forms the active site of the polymerase upon interaction with the incoming dNTP; and the thumb is responsible for binding double-stranded DNA. The exonuclease domain, located Ϸ30 Å from the polymerase domain, binds to the 3Ј-terminus of the primer when a mismatched base is incorporated (3).Like other high-fidelity polymerases, KF achieves its extraordinary accuracy through a series of steps that discriminate between a correct and incorrect dNTP. A minimal reaction pathway for KF has been proposed with much of the data obtained from chemical quench experiments (4, 5) (Fig. 1A). The rate-limiting step (k 3 ) that precedes the phosphoryl-transfer step (k 4 ) had been tentatively attributed to a conformational change of the fingers domain (6). A comparison of the crystal structures of the binary polymerase-DNA complexes with those of the ternary polymerase-DNA-dNTP complexes reveals a substantial movement upon nucleotide binding, supporting the model that fingers closing was the rate-limiting step (7). However, recent results have shown this step is much too fast to be rate limiting, suggesting additional noncovalent steps th...

Section: Figsupporting

confidence: 59%

mentioning

confidence: 60%

Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution

Christian

Romano

Rueda

2009

“…For reaction times longer than 5 s manual quenching was performed. In brief, 15 μl of radiolabelled primer/template complex (50 nM) and DNA polymerase (500 nM) in reaction buffer (RQF buffer, Tris HCl pH 7.5 20 mM, NaCl 50 mM, MgCl 2 2 mM) (29) were rapidly mixed with 15 μl of a dNTP solution in reaction buffer at 37°C. Quenching was achieved by 0.3M EDTA solution (pH 7.0) at defined time intervals.…”

Section: Methodsmentioning

confidence: 99%

“…The large fragment of Thermus aquaticus (Taq) DNA polymerase (in short KlenTaq, N-terminally truncated form of Taq polymerase) was chosen as the target because this enzyme class is heavily employed and well characterized on a functional and structural level (24)(25)(26)(27)(28)(29)(30)(31). We compared two dNTP analogsnamely dT spin TP and dT dend TP (Fig.…”

mentioning

confidence: 99%

Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase

Obeid¹,

Baccaro²,

Welte

et al. 2010

Numerous 2′-deoxynucleoside triphosphates (dNTPs) that are functionalized with spacious modifications such as dyes and affinity tags like biotin are substrates for DNA polymerases. They are widely employed in many cutting-edge technologies like advanced DNA sequencing approaches, microarrays, and single molecule techniques. Modifications attached to the nucleobase are accepted by many DNA polymerases, and thus, dNTPs bearing nucleobase modifications are predominantly employed. When pyrimidines are used the modifications are almost exclusively at the C5 position to avoid disturbing of Watson-Crick base pairing ability. However, the detailed molecular mechanism by which C5 modifications are processed by a DNA polymerase is poorly understood. Here, we present the first crystal structures of a DNA polymerase from Thermus aquaticus processing two C5 modified substrates that are accepted by the enzyme with different efficiencies. The structures were obtained as ternary complex of the enzyme bound to primer/template duplex with the respective modified dNTP in position poised for catalysis leading to incorporation. Thus, the study provides insights into the incorporation mechanism of the modified nucleotides elucidating how bulky modifications are accepted by the enzyme. The structures show a varied degree of perturbation of the enzyme substrate complexes depending on the nature of the modifications suggesting design principles for future developments of modified substrates for DNA polymerases.modified nucleotide | nucleobase modification | functional DNA | X-ray structure | PCR T he capability of DNA polymerases to accept modified 2′-deoxynucleoside triphosphates (dNTPs) is exploited in many important biotechnological applications. These include next-generation sequencing approaches (1-3), single molecule sequencing (4), labeling of DNA and PCR amplificates, e.g., for microarray analysis (5-8), DNA conjugation (9), or the in vitro selection of ligands such as aptamers by SELEX (systematic enrichment of ligands by exponential amplification) (10). Furthermore, utilizing the intrinsic properties of DNA in combination with chemically introduced functionalities provides an entry to new classes of nucleic acids-based hybrid materials (9). In most cases the dNTP modifications were introduced to the nucleobase. In cases where pyrimidines are employed the modifications are almost exclusively at the C5 position to avoid disturbing of Watson-Crick base pairing ability (11)(12)(13)(14)(15)(16)(17)(18)(19)(20). In addition, the C5 modification is well accommodated into the major groove of DNA without perturbing the DNA structure. Mainly C5 alkyne modified dNTPs are used because they are accessible via metal mediated cross coupling reactions (21-23) in a straightforward manner. While many C5 modified dNTP analogs are already applied, because they are processed by DNA polymerases at least to some extent, it is still unpredictable which modification will be accepted (8, 11-23) because the detailed molecular mechanism by which C5 modif...

“…In the homologous T7 RNA polymerase (RNAP) the coding base in a preinsertion site appears to hydrogen bond with the incoming complementary rNTP, thereby forming an "open ternary" complex (11,12). A similar conformation has been proposed, though not observed, to explain the kinetic selection of dNTP by DNAP (13)(14)(15). Following Waksman (15), we refer to such a positioning of the coding base as an "intermediate preinsertion" site conformation (Fig.…”

mentioning

confidence: 94%

DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase

Datta

Johnson

Hippel

2010

Local conformational changes in primer-template (P/T) DNA are involved in the selective incorporation of dNTP by DNA polymerases (DNAP). Here we use near UV CD and fluorescence spectra of pairs of base analogue probes, substituted either at the primer terminus or in the coding region of the template strand, to monitor and interpret conformational changes at and near the coding base of the template in P/T DNA complexes with Klenow fragment (KF) DNAP as the polymerase moves through the nucleotide addition cycle. Incoming dNTPs and rNTPs encounter binary complexes in which the 3′-end of the primer shuttles between the polymerization (pol) and exonuclease (exo) sites of DNAPs, even for perfectly complementary P/T DNA sequences. We have used spectral changes of probes inserted in both strands to monitor this two-state distribution and determine how it depends on the formation of ternary complexes with both complementary ("correct") and noncomplementary ("incorrect") NTPs and on the local sequence of the P/T DNA. The results show that the relative occupancy of the exo and pol sites is coupled to conformational changes in the P/T DNA of the complex that are partially regulated by the incoming NTP. We find that the coding base on the template strand is unperturbed by the binding of incorrect dNTPs, while binding of complementary rNTPs induces a novel template conformation. We conclude that, in addition to its editing function, primer strand occupancy of the 3′-exo site may also serve as a regulatory checkpoint for accurate dNTP selection in DNA synthesis.DNA editing | Klenow DNA polymerase | primer partitioning in DNAP active sites | low energy circular dichroism | base analogues 6-MI and 2-AP