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

Samra Obeid; Anna Baccaro; Wolfram Welte; Kay Diederichs; Andreas Marx

doi:10.1073/pnas.1013804107

New Research In

Edited by Jack W. Szostak, Massachusetts General Hospital, Boston, MA, and approved October 29, 2010 (received for review September 14, 2010)

Abstract

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.

The 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 (11–20). 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 modifications are accepted by a DNA polymerase is not at all understood. This is largely due to the absence of suitable structural data.

Here, we present unique crystal structures of a DNA polymerase caught while processing two different C5 modified dNTPs, respectively. 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 (24–31). We compared two dNTP analogs—namely dT^spinTP and dT^dendTP (Fig. 1A). It was already shown that these nucleotides are able to replace natural dTTP in DNA polymerase-catalyzed reactions (22, 23). In the case of dT^spinTP, the nitroxide modification is attached to the C5 position of the nucleobase via a rigid and short acetylene linker that is to ensure direct monitoring of DNA dynamics by EPR (electron paramagnetic resonance) spectroscopy. The dendron-modified substrate dT^dendTP is a flexible and sterically demanding modification. The branched architecture that is connected to the nucleobase via a propargylamide linker is considered to explore the size limits of modifications tolerated by DNA polymerases and to introduce multiple functional groups in a single incorporation step. In this study we employed these analogs as models for C5 modified dNTPs because their structure resembles those dNTPs used for other purposes.

Fig. 1.

Comparison of dT^spinTP and dT^dendTP in single incorporation experiments. (A) Chemical structure of dT^spinTP and dT^dendTP. (B) Single nucleotide incorporation of dT^RTP for 5, 10, 30, 60, 120, 180, or 300 sec, respectively, using KlenTaq. The respective dT^RTP is indicated. In each case, the first lane shows the labeled primer. (C) Competition experiment: single nucleotide incorporation in presence of dT^spinTP and dT^dendTP. The ratio of dT^spinTP/dT^dendTP was varied from 1/1 to 100/1 (1/1, 2/1, 4/1, 10/1, 20/1, 50/1, 100/1). The first lane shows the labeled primer.

Results

Single Nucleotide Incorporation of C5 Modified dNTPs.

To investigate the acceptance of the modified nucleotides by KlenTaq primer extension studies of single nucleotide incorporation opposite a templating dA was conducted with dTTP and the two modified thymidine analogs in a time-dependent manner. The reaction products of the modified dT^RTP migrate slower than the elongated primer in the presence of dTTP in denaturing polyacrylamide gel electrophoresis (PAGE) due to the additional bulk of the modification (Fig. 1B). Similar effects have been reported before (17, 22, 23). Interestingly, these experiments (Fig. 1B) show the preferential incorporation of the sterically more demanding dT^dendTP compared to dT^spinTP. The competition experiment, which is performed in present of the two modified triphosphates with an increasing ratio of dT^spinTP, shows more obviously that KlenTaq favors dT^dendTP over dT^spinTP (Fig. 1C).

Quantification of these findings by pre-steady-state kinetics confirmed that indeed dT^dendTP is about 20 times more efficiently (k_pol/K_D) incorporated compared to dT^spinTP (Table 1 and Figs. S1 and S2). Interestingly, the smaller dT^spinTP shows higher binding affinity (apparent K_D) to the enzyme as compared to dT^dendTP, whereas its incorporation rate (k_pol) is significantly more impaired.

View this table:

Table 1.

Transient kinetic parameters for nucleotide incorporation by KlenTaq wild type

Structure of KlenTaq in Complex with DNA and C5 Modified dNTP.

To reveal the structural basis for the ability of DNA polymerases to process an artificial substrate we crystallized KlenTaq as ternary complex bound to a primer/template duplex and a respective C5 modified triphosphate in the incoming position. The crystals were obtained by a strategy previously used for KlenTaq bound to unmodified substrates (24–26, 28). By incorporation of ddCMP at the primer terminus a primer/template duplex lacking a 3′-terminal hydroxyl group is formed to terminate the primer extension reaction. The structures were solved by difference Fourier techniques and provide snapshots of incorporation of C5 alkyne modified triphosphates at resolutions of 1.9–2.0 Å (Table S1).

Structure of KlenTaq in Complex with DNA and dT^spinTP.

KlenTaq in complex with spin-labeled triphosphate dT^spinTP (henceforth termed KlenTaq_spin) adopted an overall conformation very similar to the one in a ternary complex of the enzyme bound to DNA and ddTTP (PDB ID: 1QTM, henceforth termed KlenTaq_1QTM) described earlier (rmsd for Cα 0.392 Å, Fig. S3A and Fig. S4). In KlenTaq_1QTM ddTTP was bound to the active site due to the applied crystallization strategy (24–26, 28). A zoom into the active site shows that the dT^spinTP is located opposite to adenine of the template strand, forming Watson–Crick base pairing interactions to the templating base (Fig. 2A) and undergoes π stacking interactions to the 3′-terminus of the primer strand (Fig. S5). The distance from the primer 3′-terminus to the α-phosphate of dT^spinTP is slightly larger (0.5 Å) than the one in KlenTaq_1QTM (Fig. 2C). Furthermore, the O helix of the finger domain packs against the nascent base pair forming an active and closed complex similar as with ddTTP. However, Arg660, located at the N terminus of the O helix, shows a different orientation than in KlenTaq_1QTM and is positioned in a way to make room for the nitroxide modification (Fig. 2). Arg660 has been suggested to stabilize the closed and active conformation via hydrogen-bonding interaction to the phosphate backbone of the primer 3′-terminus (26, 28). This interaction is exclusively observed in the closed conformation and may act as a clamp between the finger domain and the bound DNA duplex (26, 28). The interaction of Arg660 with the primer 3′-terminus is hindered by the rigid nitroxide modification connected to the nucleobase and thereby prevents the stabilization of the closed conformation. As a result of the loss of the hydrogen-bonding interaction, Arg660 shows a high flexibility (B-factor of the amino acide side chain is 81 Å²), and the O helix is slightly shifted (Fig. S6). The missing clamp, between the finger domain and the primer/template duplex, may account for the observed 2,500-fold decrease in incorporation efficiency of dT^spinTP compared with the natural dTTP.

Fig. 2.

Structure of KlenTaq in complex with dT^spinTP (KlenTaq_spin). (A) The close-up view of KlenTaq_spin (blue) shows the incoming dT^spinTP (magenta), the O helix with amino acid side chain R660, the primer and template strand. The dashed line highlights the Watson–Crick base pairing interactions. (B) Superimposition of KlenTaq_spin and KlenTaq (green, PDB: 1QTM) highlights the different orientation of the amino acid side chain R660. (C) The distance (shown in dashed lines) of the α-phosphate to the primer 3′-terminus is indicated for KlenTaq_spin. (D) The distance of the α-phosphate to the primer 3′-terminus (dashed line; 3.5 Å) and the interaction of R660 with the phosphate-backbone of the primer 3′-terminus is indicated in dashed line (3.4 Å) for KlenTaq. No such interaction is found in KlenTaq_spin (see C) due to displacement of R660 by the modification.

Structure of KlenTaq in Complex with DNA and dT^dendTP.

The structure of KlenTaq in complex with primer/template duplex and dendron-modified triphosphate dT^dendTP (henceforth termed KlenTaq_dend) was determined with a resolution of 1.9 Å. In comparison with KlenTaq_1QTM the overall conformation of KlenTaq_dend is very similar, resulting in a low rmsd for Cα 0.250 Å (Fig. 4 and Fig. S3B). The dT^dendTP is captured in the active site waiting for insertion (Fig. 3A). We observe a closed and active complex very similar to KlenTaq_1QTM and KlenTaq_spin (Fig. 3B). The same stabilizing factors that are described above such as Watson–Crick base pairing and π stacking interaction are observed (Fig. S5). Even the distance from the primer 3′-terminus to the α-phosphate of the dT^dendTP is similar to the observed distance in KlenTaq_1QTM (Fig. 3C). Only partial electron density could be observed for the dendron structure due to the high flexibility of the entity (Fig. 3D and Fig. S4). The rigid propargylamide linkage is well defined, whereas the two flexible branches of the dendron are located outside the active site (Fig. 4). To some extent, one branch reaches in the major groove of the primer/template duplex, indicated by some electron density in this region. The zoom into the active site shows that the finger domain by the O helix packs against the nascent base pair, resulting in a complex poised for catalysis (Fig. S7). Interestingly, in this case the amino acid Arg660 interacts with the phosphate-backbone of the primer 3′-terminus as well as with amide functionality of the propargylamide linkage. Although the described interaction pattern may stabilize Arg660, we observe a high B-factor of the amino acid side chain 97 Å², indicating that the position of Arg660 is tenuous. The geometric freedom of Arg660 may explain the 137-fold reduced incorporation efficiency of dT^dendTP compared to natural dTTP. In addition, the propargylamide linkage is interacting with the phosphate backbone of the primer 3′-terminus via hydrogen-bonding interactions (Fig. 3). Furthermore, we observe a second hydrogen bond formed between the carbonyl group of an amide in the dendron moiety and the nucleobase of the primer 3′-terminus (Fig. 3D). These hydrogen-bonding interactions might support a nucleotide position and conformation better suited for incorporation compared to dT^spinTP and more similar to dTTP.

Fig. 3.

Structure of KlenTaq in complex with dT^dendTP (KlenTaq_dend). (A) The close-up view of KlenTaq_dend (orange) shows the incoming dT^dendTP (purple), the O helix with amino acid side chain R660, the primer and template strand. The interaction network is indicated in dashed lines as well as the Watson–Crick base pairing interaction between dT^dendTP and adenine of the template strand. R660 is orientated to allow interaction with the primer 3′-terminus. The amine group of the propargyl-amine-linkage shows an additional interaction to the primer 3′-terminus. (B) Superimposition of KlenTaq_dend and KlenTaq (green, PDB: 1QTM) highlights the different orientation of the amino acid side chain R660. (C) The interaction pattern of the phosphate backbone at the primer 3′-terminus with R660 and the propargylamide linkage is shown in dashed lines. The distance of the α-phosphate to the primer 3′-terminus is 3.7 Å (highlighted in dashed lines). (D) Interaction network of dT^dendTP with the primer 3′-terminus toward the phosphate backbone and the nucleobase is indicated with dashed lines. The final refined model map 2mFo-DFc at 1σ is shown for dT^dendTP.

Fig. 4.

Structure of KlenTaq_dend ternary complex. (A) The overall structure of KlenTaq_dend and the Connolly surface is shown. The incoming dT^dendTP is highlighted in sticks and indicated with a red arrow. (B) The close-up view of the incoming dT^dendTP illustrates that the dendrimer structure is placed in a cleft between the protein and primer/template duplex.

Discussion

Hitherto, structural data of DNA polymerases processing C5 modified pyrimidines that could serve as a guide for structure design of suitable nucleotide modifications was lacking. We present two crystal structures of KlenTaq processing differently modified nucleotide analogs. The protein structures in KlenTaq_spin and KlenTaq_dend exhibit the incoming nucleotide in a position poised for catalysis similar to the structures reported for KlenTaq bound to primer/template and a nucleotide with natural nucleobase (26, 28). Only subtle differences in terms of alignment of the incoming nucleotides, magnesium ions, and water molecules are observed (Fig. S7). This suggests that the enzyme follows similar mechanisms to promote catalysis. However, the structures mainly differ in the position of amino acid side chain Arg660. In KlenTaq_spin the modified dT^spinTP obviates Arg660 to undergo stabilizing interactions with the primer. In contrast, hydrogen-bonding interactions of the enzyme with dT^dendTP via the amide functionality of the propargylamide linker are observed in KlenTaq_dend. The propargylamide linkage as present in dT^dendTP offers the opportunity to stabilize the closed complex poised for catalysis, which may have beneficial effects on the incorporation efficiency. Amino acid sequence alignment of several DNA polymerases that belong to the same sequence family as KlenTaq (i.e., A-family) discloses that the respective arginine is within motif B (32) and is conserved in bacteria (Fig. S8). Thus, it is likely that the depicted mechanism to stabilize the enzyme/substrate complex applies to other DNA polymerases in this sequence family as well.

The results suggest that the modifications are better tolerated by a DNA polymerase if they are attached via linkers that have hydrogen-bonding capability with the enzyme at the depicted positions. In fact, several examples of dNTPs that are processed by DNA polymerases and modified via a C5 propargylamide linker have been reported (1–3, 5, 6, 8, 10–14, 16, 17, 21, 23). These insights suggest that implementing of functionalities with hydrogen binding capability at the discussed position in modified dNTPs may improve their substrate properties. These design guidelines for the development of new modified dNTPs, in combination with directed evolution of DNA polymerases (33–35), will spur the development of future applications.

Materials and Methods

Adducted Protein, Nucleotides, and Oligonucleotides.

Protein expression and purification were conducted as described (25–28, 30, 31). Modified thymidine-5′-triphosphates dT^RTPs were synthesized as described previously. Unmodified dNTPs are commercially available (Roche).

DNA oligonucleotides for enzyme kinetics were synthesized on an Applied-Biosystems 392 DNA/RNA synthesizer and purified by reversed phase HPLC (DMT-ON) and afterwards by preparative PAGE on a 12% polyacrylamide gel containing 8 M urea (DMT-OFF). DNA primer oligonucleotides were labeled with [γ-³²P] ATP using T4 polynucleotide kinase (Fermentas) according to the procedure recommended by the manufacturer.

Single Nucleotide Incorporation Assay.

Incorporation opposite dA: 15 μl of the KlenTaq reactions contained 50 nM primer (5'-GTG GTG CGA AAT TTC TGA CAG ACA), 75 nM template (5′-GTG CGT CTG TCA TGT CTG TCA GAA ATT TCG CAC CAC), 200 μM dNTPs in buffer (20 mM Tris HCl pH 7.5, 50 mM NaCl, and 2 mM MgCl₂) and 200 nM of KlenTaq polymerase. Reaction mixtures were incubated at 37 °C. Incubation times are provided in the respective figure legends. Primer was labeled using [γ-³²P]-ATP according to standard techniques. Reactions were stopped by addition of 45 μl stop solution (80% [v/v] formamide, 20 mM EDTA, 0.25% [w/v] bromophenol blue, 0.25% [w/v] xylene cyanol) and analyzed by 12% denaturing PAGE. Visualization was performed by phosphoimaging.

Pre-Steady-State Enzyme Kinetics.

The rate of single turnover, single nucleotide incorporation was determined using rapid quench flow kinetics on a chemical quench flow apparatus (RQF-3, KinTek Corp.) as previously described (36). 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, MgCl₂ 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. For the investigation of dT^RTP incorporation a 24 nt primer (5'-GTG GTG CGA AAT TTC TGA CAG ACA) and a 36 nt template (5′-GTG CGT CTG TCA TGT CTG TCA GAA ATT TCG CAC CAC) were applied. Quenched samples were analyzed on a 12% denaturing PAGE followed by phosphor imaging. For kinetic analysis experimental data were fit by nonlinear regression using the program GraphPad Prism 4. The data were fit to a single exponential equation: [conversion] = A^∗(1- exp(-k_obst)). The observed catalytic rates (k_obs) were then plotted against the dNTP concentration used and the data were fitted to a hyperbolic equation to determine the apparent K_D and k_cat of the incoming nucleotide. The incorporation efficiency is given by k_pol/K_D. The depicted data derived from double repeated experiments.

Crystallization and Structure Determination.

The closed ternary complexes of KlenTaq were obtained by incubating KlenTaq in presence of DNA primer (5′-d(GAC CAC GGC GC)-3′), template (5′-d(AAA AGG CGC CGT GGT C)-3′), ddCTP and one of the 5-modified dT^RTP. Thereby, one ddCMP is incorporated, while the corresponding 5-modified dT^RTP is captured in the position waiting for insertion.

KlenTaq_spin: The crystallization was set up using purified KlenTaq (11 mg/ml; buffer: 20 mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM β-mercaptoethanol), DNA template/primer duplex, ddCTP and dT^spinTP in a molar ratio of 1∶3∶10∶20 and in presence of 20 mM MgCl₂. The crystallization solution was mixed in 1∶1 ratio with the reservoir solution 0.05 M Tris HCl, pH 9, 0.2 M NH₄Cl, 0.01 M CaCl₂, and 26% PEG 4000.

KlenTaq_dend: The crystallization was set up using purified KlenTaq (11 mg/ml; buffer: 20 mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM β-mercaptoethanol), DNA template/primer duplex, ddCTP and dT^dendTP in a molar ratio of 1∶3∶10∶20 and in presence of 20 mM MgCl₂. The crystallization solution was mixed in 1∶1 ratio with the reservoir solution containing 0.05 M sodium cacodylate (pH 6.5), 0.2 M NH₄OAc, 0.01 M Mg(OAc)₂, and 26% PEG 8000.

Crystals were produced by the hanging drop vapor diffusion method, equilibrating against 1 ml of the reservoir solution for 5 d at 18 °C. They were frozen in liquid nitrogen and kept at 100 K during data collection. Data were measured at the beamline PXIII (X06DA) at the Swiss Light Source of the Paul Scherrer Institute (PSI) in Villigen, Switzerland, at a wavelength 1.000 Å and using a Mar225 CCD detector. Data reduction was performed with the XDS package (37, 38). The structures were solved by difference Fourier techniques using KlenTaq wild type (PDB 1QTM) as model. Refinement was performed with PHENIX (39) and model rebuilding was done with COOT (40). The structures were refined to a resolution of 2.0 Å in KlenTaq_spin and 1.9 Å in KlenTaq_dend. Both structures were in the same space group P3₁21, with cell dimensions a, b 109.0 Å, c 91.5 Å for KlenTaq_spin, and a, b 107.8 Å, c 90.2 Å for KlenTaq_dend, respectively. Figures were made with PyMOL (41). The Ramachandran statistics for KlenTaq_spin show that 91.5% of the residues are in the most favored regions, 7.9% in additional allowed regions, 0.4% in generously allowed and 0.2% in disallowed regions as defined PROCHECK (42). For KlenTaq_dend the values are 92.3%, 7.5%, 0%, and 0.2%, respectively.

Acknowledgments

This work was partly funded by the German Excellence Initiative.

Footnotes

¹To whom correspondence should be addressed: E-mail: andreas.marx{at}uni-konstanz.de.
Author contributions: S.O. and A.M. designed research; S.O. performed research; S.O. and A.B. contributed new reagents/analytic tools; S.O., W.W., K.D., and A.M. analyzed data; and S.O., K.D., and A.M. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 3OJU and 3OJS).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1013804107/-/DCSupplemental.

References

↵
1. Bentley DR,
2. et al.
(2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59.
OpenUrl CrossRef PubMed
↵
1. Bowers J,
2. et al.
(2009) Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6:593–595.
OpenUrl CrossRef PubMed
↵
1. Ruparel H,
2. et al.
(2005) Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc Natl Acad Sci USA 102:5932–5937.
OpenUrl Abstract/FREE Full Text
↵
1. Harris TD,
2. et al.
(2008) Single-molecule DNA sequencing of a viral genome. Science 320:106–109.
OpenUrl Abstract/FREE Full Text
↵
1. Guo J,
2. et al.
(2008) Four-color DNA sequencing with 3-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci USA 105:9145–9150.
OpenUrl Abstract/FREE Full Text
↵
1. Pollack JR,
2. et al.
(1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41–46.
OpenUrl PubMed
↵
1. Perou CM,
2. et al.
(2000) Molecular portraits of human breast tumours. Nature 406:747–752.
OpenUrl CrossRef PubMed
↵
1. Seo TS,
2. et al.
(2005) Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Proc Natl Acad Sci USA 102:5926–5931.
OpenUrl Abstract/FREE Full Text
↵
1. Weisbrod SH,
2. Marx A
(2007) A nucleoside triphosphate for site-specific labelling of DNA by the Staudinger ligation. Chem Commun 18:1828–1830.
OpenUrl
↵
1. Mayer G
(2009) The chemical biology of aptamers. Angew Chem Int Edit 48:2672–2689.
OpenUrl CrossRef
↵
1. Thum O,
2. Jäger S,
3. Famulok M
(2001) Functionalized DNA: A new replicable biopolymer. Angew Chem Int Edit 40:3990–3993.
OpenUrl CrossRef
↵
1. Weizman H,
2. Tor Y
(2002) Redox-active metal-containing nucleotides: Synthesis, tunability, and enzymatic incorporation into DNA. J Am Chem Soc 124:1568–1569.
OpenUrl CrossRef PubMed
↵
1. Giller G,
2. et al.
(2003) Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2′-deoxyribonucleoside-5′-triphosphates. Nucleic Acids Res 31:2630–2635.
OpenUrl Abstract/FREE Full Text
↵
1. Jäger S,
2. Famulok M
(2004) Generation and enzymatic amplification of high-density functionalized DNA double strands. Angew Chem Int Edit 43:3337–3340.
OpenUrl CrossRef
↵
1. Anderson JP,
2. Angerer B,
3. Loeb LA
(2005) Incorporation of reporter-labeled nucleotides by DNA polymerases. Biotechniques 38:257–264.
OpenUrl CrossRef PubMed
↵
1. Ohbayashi T,
2. et al.
(2005) Expansion of repertoire of modified DNAs prepared by PCR using KOD Dash DNA polymerase. Org Biomol Chem 3:2463–2468.
OpenUrl CrossRef PubMed
↵
1. Jäger S,
2. et al.
(2005) A versatile toolbox for variable DNA functionalization at high density. J Am Chem Soc 127:15071–15082.
OpenUrl CrossRef PubMed
↵
1. Srivatsan SG,
2. Tor Y
(2007) Fluorescent pyrimidine ribonucleotide: Synthesis, enzymatic incorporation, and utilization. J Am Chem Soc 129:2044–2053.
OpenUrl CrossRef PubMed
↵
1. Čapek P,
2. et al.
(2007) An efficient method for the construction of functionalized DNA bearing amino acid groups through cross-coupling reactions of nucleoside triphosphates followed by primer extension or PCR. Chem-Eur J 13:6196–6203.
OpenUrl
↵
1. Gramlich PME,
2. Wirges CT,
3. Manetto A,
4. Carell T
(2008) Postsynthetic DNA modification through the copper-catalyzed azide-alkyne cycloaddition reaction. Angew Chem Int Edit 47:8350–8358.
OpenUrl CrossRef
↵
1. Hocek M,
2. Fojta M
(2008) Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 6:2233–2241.
OpenUrl CrossRef PubMed
↵
1. Obeid S,
2. Yulikow M,
3. Jeschke G,
4. Marx A
(2008) Enzymatic synthesis of multi spin-labeled DNA. Angew Chem Int Edit 47:6782–6785.
OpenUrl CrossRef
↵
1. Baccaro A,
2. Marx A
(2010) Enzymatic synthesis of organic polymer-grafted DNA. Chem-Eur J 16:218–226.
OpenUrl
↵
1. Korolev S,
2. Nayal M,
3. Barnes WM,
4. Di Cera E,
5. Waksman G
(1995) Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: Structural basis for thermostability. Proc Natl Acad Sci USA 92:9264–9268.
OpenUrl Abstract/FREE Full Text
↵
1. Li Y,
2. Korolev S,
3. Waksman G
(1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17:7514–7525.
OpenUrl CrossRef PubMed
↵
1. Li Y,
2. Kong Y,
3. Korolev S,
4. Waksman G
(1998) Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein 7:1116–1123.
OpenUrl CrossRef
↵
1. Li Y,
2. Mitaxov V,
3. Waksman G
(1999) Structure-based designof Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc Natl Acad Sci USA 96:9491–9496.
OpenUrl Abstract/FREE Full Text
↵
1. Li Y,
2. Waksman G
(2001) Crystal structures of a ddATP-, ddTTP-, ddCTP-, and ddGTP-trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity. Protein Sci 10:1225–1233.
OpenUrl CrossRef PubMed
↵
1. Rothwell PJ,
2. Mitaksov V,
3. Waksman G
(2005) Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases. Mol Cell 19:345–355.
OpenUrl CrossRef PubMed
↵
1. Obeid S,
2. et al.
(2010) Replication through an abasic DNA lesion: Structural basis for adenine selectivity. EMBO J 29:1738–1747.
OpenUrl CrossRef PubMed
↵
1. Betz K,
2. et al.
(2010) Structures of DNA polymerases caught processing size-augmented nucleotide probes. Angew Chem Int Edit 49:5181–5184.
OpenUrl CrossRef
↵
1. Delarue M,
2. Poch O,
3. Tordo N,
4. Moras D,
5. Argos P
(1990) An attempt to unify the structure of polymerases. Protein Eng 3:461–467.
OpenUrl Abstract/FREE Full Text
↵
1. Ramsay N,
2. et al.
(2010) CyDNA: Synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase. J Am Chem Soc 132:5096–5104.
OpenUrl CrossRef PubMed
↵
1. Leconte AM,
2. et al.
(2010) Directed evolution of DNA polymerases for next-generation sequencing. Angew Chem Int Ed 49:5921–5924.
OpenUrl PubMed
↵
1. Staiger N,
2. Marx A
(2010) A DNA polymerase with increased reactivity for ribonucleotides and C5-modified deoxyribonucleotides. ChemBioChem 11:1963–1966.
OpenUrl CrossRef PubMed
↵
1. Di Pasquale F,
2. et al.
(2008) Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. J Am Chem Soc 130:10748–10757.
OpenUrl CrossRef PubMed
↵
1. Kabsch W
(2010) XDS. Acta Crystallogr D 66:125–132.
OpenUrl CrossRef PubMed
↵
1. Kabsch W
(2010) Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D 66:133–144.
OpenUrl CrossRef PubMed
↵
1. Adams PD,
2. et al.
(2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D 58:1948–1954.
OpenUrl CrossRef PubMed
↵
1. Emsley P,
2. Cowtan K
(2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126–2132.
OpenUrl CrossRef PubMed
↵
1. DeLano WL
(2002) The PyMOL Molecular Graphics System (DeLano Scientific, Palo Alto, CA).
↵
1. Laskowski RA,
2. MacArthur MW,
3. Moss DS,
4. Thornton JM
(1993) PROCHECK—a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291.
OpenUrl CrossRef

Article Alerts

Email Article

Citation Tools

Request Permissions

Proceedings of the National Academy of Sciences: 107 (50)

Table of Contents

Submit

Article Classifications

Physical Sciences
Chemistry

Biological Sciences
Biophysics and Computational Biology

[1] ↵
Bentley DR,
et al.
(2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59.
OpenUrl CrossRef PubMed

[2] Bentley DR,

[3] et al.

[4] ↵
Bowers J,
et al.
(2009) Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6:593–595.
OpenUrl CrossRef PubMed

[5] Bowers J,

[6] et al.

[7] ↵
Ruparel H,
et al.
(2005) Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc Natl Acad Sci USA 102:5932–5937.
OpenUrl Abstract/FREE Full Text

[8] Ruparel H,

[9] et al.

[10] ↵
Harris TD,
et al.
(2008) Single-molecule DNA sequencing of a viral genome. Science 320:106–109.
OpenUrl Abstract/FREE Full Text

[11] Harris TD,

[12] et al.

[13] ↵
Guo J,
et al.
(2008) Four-color DNA sequencing with 3-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci USA 105:9145–9150.
OpenUrl Abstract/FREE Full Text

[14] Guo J,

[15] et al.

[16] ↵
Pollack JR,
et al.
(1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41–46.
OpenUrl PubMed

[17] Pollack JR,

[18] et al.

[19] ↵
Perou CM,
et al.
(2000) Molecular portraits of human breast tumours. Nature 406:747–752.
OpenUrl CrossRef PubMed

[20] Perou CM,

[21] et al.

[22] ↵
Seo TS,
et al.
(2005) Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Proc Natl Acad Sci USA 102:5926–5931.
OpenUrl Abstract/FREE Full Text

[23] Seo TS,

[24] et al.

[25] ↵
Weisbrod SH,
Marx A
(2007) A nucleoside triphosphate for site-specific labelling of DNA by the Staudinger ligation. Chem Commun 18:1828–1830.
OpenUrl

[26] Weisbrod SH,

[27] Marx A

[28] ↵
Mayer G
(2009) The chemical biology of aptamers. Angew Chem Int Edit 48:2672–2689.
OpenUrl CrossRef

[29] Mayer G

[30] ↵
Thum O,
Jäger S,
Famulok M
(2001) Functionalized DNA: A new replicable biopolymer. Angew Chem Int Edit 40:3990–3993.
OpenUrl CrossRef

[31] Thum O,

[32] Jäger S,

[33] Famulok M

[34] ↵
Weizman H,
Tor Y
(2002) Redox-active metal-containing nucleotides: Synthesis, tunability, and enzymatic incorporation into DNA. J Am Chem Soc 124:1568–1569.
OpenUrl CrossRef PubMed

[35] Weizman H,

[36] Tor Y

[37] ↵
Giller G,
et al.
(2003) Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2′-deoxyribonucleoside-5′-triphosphates. Nucleic Acids Res 31:2630–2635.
OpenUrl Abstract/FREE Full Text

[38] Giller G,

[39] et al.

[40] ↵
Jäger S,
Famulok M
(2004) Generation and enzymatic amplification of high-density functionalized DNA double strands. Angew Chem Int Edit 43:3337–3340.
OpenUrl CrossRef

[41] Jäger S,

[42] Famulok M

[43] ↵
Anderson JP,
Angerer B,
Loeb LA
(2005) Incorporation of reporter-labeled nucleotides by DNA polymerases. Biotechniques 38:257–264.
OpenUrl CrossRef PubMed

[44] Anderson JP,

[45] Angerer B,

[46] Loeb LA

[47] ↵
Ohbayashi T,
et al.
(2005) Expansion of repertoire of modified DNAs prepared by PCR using KOD Dash DNA polymerase. Org Biomol Chem 3:2463–2468.
OpenUrl CrossRef PubMed

[48] Ohbayashi T,

[49] et al.

[50] ↵
Jäger S,
et al.
(2005) A versatile toolbox for variable DNA functionalization at high density. J Am Chem Soc 127:15071–15082.
OpenUrl CrossRef PubMed

[51] Jäger S,

[52] et al.

[53] ↵
Srivatsan SG,
Tor Y
(2007) Fluorescent pyrimidine ribonucleotide: Synthesis, enzymatic incorporation, and utilization. J Am Chem Soc 129:2044–2053.
OpenUrl CrossRef PubMed

[54] Srivatsan SG,

[55] Tor Y

[56] ↵
Čapek P,
et al.
(2007) An efficient method for the construction of functionalized DNA bearing amino acid groups through cross-coupling reactions of nucleoside triphosphates followed by primer extension or PCR. Chem-Eur J 13:6196–6203.
OpenUrl

[57] Čapek P,

[58] et al.

[59] ↵
Gramlich PME,
Wirges CT,
Manetto A,
Carell T
(2008) Postsynthetic DNA modification through the copper-catalyzed azide-alkyne cycloaddition reaction. Angew Chem Int Edit 47:8350–8358.
OpenUrl CrossRef

[60] Gramlich PME,

[61] Wirges CT,

[62] Manetto A,

[63] Carell T

[64] ↵
Hocek M,
Fojta M
(2008) Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 6:2233–2241.
OpenUrl CrossRef PubMed

[65] Hocek M,

[66] Fojta M

[67] ↵
Obeid S,
Yulikow M,
Jeschke G,
Marx A
(2008) Enzymatic synthesis of multi spin-labeled DNA. Angew Chem Int Edit 47:6782–6785.
OpenUrl CrossRef

[68] Obeid S,

[69] Yulikow M,

[70] Jeschke G,

[71] Marx A

[72] ↵
Baccaro A,
Marx A
(2010) Enzymatic synthesis of organic polymer-grafted DNA. Chem-Eur J 16:218–226.
OpenUrl

[73] Baccaro A,

[74] Marx A

[75] ↵
Korolev S,
Nayal M,
Barnes WM,
Di Cera E,
Waksman G
(1995) Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: Structural basis for thermostability. Proc Natl Acad Sci USA 92:9264–9268.
OpenUrl Abstract/FREE Full Text

[76] Korolev S,

[77] Nayal M,

[78] Barnes WM,

[79] Di Cera E,

[80] Waksman G

[81] ↵
Li Y,
Korolev S,
Waksman G
(1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17:7514–7525.
OpenUrl CrossRef PubMed

[82] Li Y,

[83] Korolev S,

[84] Waksman G

[85] ↵
Li Y,
Kong Y,
Korolev S,
Waksman G
(1998) Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein 7:1116–1123.
OpenUrl CrossRef

[86] Li Y,

[87] Kong Y,

[88] Korolev S,

[89] Waksman G

[90] ↵
Li Y,
Mitaxov V,
Waksman G
(1999) Structure-based designof Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc Natl Acad Sci USA 96:9491–9496.
OpenUrl Abstract/FREE Full Text

[91] Li Y,

[92] Mitaxov V,

[93] Waksman G

[94] ↵
Li Y,
Waksman G
(2001) Crystal structures of a ddATP-, ddTTP-, ddCTP-, and ddGTP-trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity. Protein Sci 10:1225–1233.
OpenUrl CrossRef PubMed

[95] Li Y,

[96] Waksman G

[97] ↵
Rothwell PJ,
Mitaksov V,
Waksman G
(2005) Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases. Mol Cell 19:345–355.
OpenUrl CrossRef PubMed

[98] Rothwell PJ,

[99] Mitaksov V,

[100] Waksman G

[101] ↵
Obeid S,
et al.
(2010) Replication through an abasic DNA lesion: Structural basis for adenine selectivity. EMBO J 29:1738–1747.
OpenUrl CrossRef PubMed

[102] Obeid S,

[103] et al.

[104] ↵
Betz K,
et al.
(2010) Structures of DNA polymerases caught processing size-augmented nucleotide probes. Angew Chem Int Edit 49:5181–5184.
OpenUrl CrossRef

[105] Betz K,

[106] et al.

[107] ↵
Delarue M,
Poch O,
Tordo N,
Moras D,
Argos P
(1990) An attempt to unify the structure of polymerases. Protein Eng 3:461–467.
OpenUrl Abstract/FREE Full Text

[108] Delarue M,

[109] Poch O,

[110] Tordo N,

[111] Moras D,

[112] Argos P

[113] ↵
Ramsay N,
et al.
(2010) CyDNA: Synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase. J Am Chem Soc 132:5096–5104.
OpenUrl CrossRef PubMed

[114] Ramsay N,

[115] et al.

[116] ↵
Leconte AM,
et al.
(2010) Directed evolution of DNA polymerases for next-generation sequencing. Angew Chem Int Ed 49:5921–5924.
OpenUrl PubMed

[117] Leconte AM,

[118] et al.

[119] ↵
Staiger N,
Marx A
(2010) A DNA polymerase with increased reactivity for ribonucleotides and C5-modified deoxyribonucleotides. ChemBioChem 11:1963–1966.
OpenUrl CrossRef PubMed

[120] Staiger N,

[121] Marx A

[122] ↵
Di Pasquale F,
et al.
(2008) Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. J Am Chem Soc 130:10748–10757.
OpenUrl CrossRef PubMed

[123] Di Pasquale F,

[124] et al.

[125] ↵
Kabsch W
(2010) XDS. Acta Crystallogr D 66:125–132.
OpenUrl CrossRef PubMed

[126] Kabsch W

[127] ↵
Kabsch W
(2010) Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D 66:133–144.
OpenUrl CrossRef PubMed

[128] Kabsch W

[129] ↵
Adams PD,
et al.
(2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D 58:1948–1954.
OpenUrl CrossRef PubMed

[130] Adams PD,

[131] et al.

[132] ↵
Emsley P,
Cowtan K
(2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126–2132.
OpenUrl CrossRef PubMed

[133] Emsley P,

[134] Cowtan K

[135] ↵
DeLano WL
(2002) The PyMOL Molecular Graphics System (DeLano Scientific, Palo Alto, CA).

[136] DeLano WL

[137] ↵
Laskowski RA,
MacArthur MW,
Moss DS,
Thornton JM
(1993) PROCHECK—a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291.
OpenUrl CrossRef

[138] Laskowski RA,

[139] MacArthur MW,

[140] Moss DS,

[141] Thornton JM

Main menu

User menu

Search

New Research In

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

Abstract

Results

Single Nucleotide Incorporation of C5 Modified dNTPs.

Structure of KlenTaq in Complex with DNA and C5 Modified dNTP.

Structure of KlenTaq in Complex with DNA and dT^spinTP.

Structure of KlenTaq in Complex with DNA and dT^dendTP.

Discussion

Materials and Methods

Adducted Protein, Nucleotides, and Oligonucleotides.

Single Nucleotide Incorporation Assay.

Pre-Steady-State Enzyme Kinetics.

Crystallization and Structure Determination.

Acknowledgments

Footnotes

References

Citation Manager Formats

Article Classifications

You May Also be Interested in

Similar Articles

Articles

PNAS Portals

Information

Main menu

User menu

Search

New Research In

Physical Sciences

Featured Portals

Articles by Topic

Social Sciences

Featured Portals

Articles by Topic

Biological Sciences

Featured Portals

Articles by Topic

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

Abstract

Results

Single Nucleotide Incorporation of C5 Modified dNTPs.

Structure of KlenTaq in Complex with DNA and C5 Modified dNTP.

Structure of KlenTaq in Complex with DNA and dTspinTP.

Structure of KlenTaq in Complex with DNA and dTdendTP.

Discussion

Materials and Methods

Adducted Protein, Nucleotides, and Oligonucleotides.

Single Nucleotide Incorporation Assay.

Pre-Steady-State Enzyme Kinetics.

Crystallization and Structure Determination.

Acknowledgments

Footnotes

References

Citation Manager Formats

Sign up for Article Alerts

Article Classifications

Jump to section

You May Also be Interested in

Similar Articles

Articles

PNAS Portals

Information

Structure of KlenTaq in Complex with DNA and dT^spinTP.

Structure of KlenTaq in Complex with DNA and dT^dendTP.