Direct Detection and Sequencing of Damaged DNA Bases
© Clark et al; licensee BioMed Central Ltd. 2011
Received: 10 November 2011
Accepted: 20 December 2011
Published: 20 December 2011
Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications.
KeywordsDNA Damage Modified Bases Sequencing
DNA is under constant stress from both endogenous and exogenous sources. As the carrier of genetic information, DNA relies on the maintenance and repair of existing molecules and is the only biological molecule to do so. The bases exhibit limited chemical stability and are vulnerable to chemical modifications through different types of damage, including oxidation, alkylation, radiation damage, and hydrolysis. DNA base modifications resulting from these types of DNA damage are wide-spread and play important roles in affecting physiological states and disease phenotypes (reviewed in [1–3]). Examples include 8-oxoguanine, 8-oxoadenine (oxidative damage; aging, Alzheimer's, Parkinson's), 1-methyladenine, 6-O-methylguanine (alkylation; gliomas and colorectal carcinomas), benzo[a]pyrene diol epoxide (BPDE), pyrimidine dimers (adduct formation; smoking, industrial chemical exposure, UV light exposure; lung and skin cancer), and 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, and thymine glycol (ionizing radiation damage; chronic inflammatory diseases, prostate, breast and colorectal cancer).
Currently, methods for detecting these and other products of DNA damage are limited to bulk measurements including chromatographic techniques, polymerase chain reaction assays, the Comet assay, mass spectrometry, electrochemistry, radioactive labeling and immunochemical methods (reviewed in ). To our knowledge, the integration of DNA damage detection into a high-throughput DNA sequencing technique has not been reported. Because base damage can occur at random DNA template positions, sequencing capabilities reaching the level of individual DNA molecules are highly desirable.
Recently, single-molecule, real-time (SMRT) DNA sequencing has been described for the direct detection of methylated and hydroxymethylated DNA bases . In SMRT sequencing, the progression of single molecules of DNA polymerase is monitored in real time during base incorporations using fluorescent phospholinked nucleotides [6, 7]. The dynamics of DNA polymerization is thereby recorded in the form of a train of fluorescent pulses. The length of time that the polymerase retains a nucleotide bound in its active site (pulse width, PW), and the time interval between successive nucleotide-bound states (interpulse duration, IPD) are the principal pulse metrics used in the analysis to ascertain that the polymerase kinetics was altered in the modification-containing template when compared to an unmodified control template . Because the DNA polymerase is in contact with the modified base over a region of ~11 bases , the kinetic effects are not necessarily restricted to the nucleotide incorporation opposite of the modified base. The magnitude and extent of the kinetic signature is dependent on the type of the base modification and the local sequence context. This results in distinct, more complex kinetic signatures that can be used to discriminate between different chemical base modifications .
Here, we apply SMRT DNA sequencing towards the direct detection of damaged DNA bases. Using synthetic DNA templates, we survey several common products of DNA damage for their kinetic effects on the polymerase kinetics in SMRT sequencing. We show that this method can readily detect damaged DNA bases with single-base resolution and discriminate between different types of DNA damage products through distinct kinetic signatures observed for different damaged bases.
Results and Discussion
To investigate the effect of products of DNA damage in SMRT sequencing, we designed synthetic SMRTbell™ templates  carrying two instances of a particular chemical base modification that can occur as a result of DNA damage (Additional File 1). The DNA templates were subjected to standard SMRT DNA sequencing  and analyzed for their effects on the polymerase kinetics, as compared to a control DNA template of identical sequence but lacking the two instances of chemical base modifications and containing the unmodified canonical bases at those positions. In the simplest form of analysis, the ratio of averaged kinetic values between the modified and the control template is calculated for each template position. A deviation of IPD or PW from a ratio of unity indicates the presence of a modified nucleotide . For the characterization of products of DNA damage in the synthetic templates studied here, we employed this ratio analysis.
The kinetic signature of 8oxoA (Figure 1b) was overall similar to 8oxoG, but with a stronger, ~10fold increased IPD at the modification position, and additional signals one to two bases prior to the modification position. In the region five to seven nucleotide incorporations after the 8oxoA position, strong additional kinetic signals were observed, exhibiting similar magnitudes compared to the modification position IPD ratio. Pulse widths were slightly increased in this region. The observed kinetic signature for 8oxoA differs from the previously described kinetic signature for adenine methylation ; N6-methyladenine (6mA) exhibited kinetic signals at the zero position of ~5fold, i.e. half the signal observed for 8oxoA, and a weak signal at the +5 position of ~2fold. These differences can be used to discriminate between different chemical base modifications that occur on the same base type.
Replicative DNA polymerases have evolved to move along DNA templates, synthesizing a complementary DNA strand, with remarkable efficiency, speed and fidelity . The presence of various forms of DNA damage in the template strand can lead to transient stalling, misincorporation, or even termination of DNA polymerization, depending on the type of damage [3, 10, 17]. Taking advantage of this exquisite sensitivity of polymerases towards changes in the DNA template, we have investigated the ability of SMRT DNA sequencing to detect products of DNA damage through an analysis of the polymerase kinetics that is recorded in real time by this method. We have demonstrated the detection of several common forms of DNA damage while performing the regular sequencing protocol, and without the need for special upfront sample preparation steps.
Damaged DNA bases can impart effects on the polymerase kinetics in several ways. IPDs can be affected by (i) changes in the affinity of binding the incoming nucleotide, or (ii) altered DNA translocation rates following the phospholinked nucleotide incorporation. Variations in PW can be caused from (i) effects on the rates of conformational changes of the enzyme, as well as (ii) the rate of catalysis during the nucleotide incorporation cycle, as the damaged base can distort active site geometries. All of these effects are captured in SMRT sequencing through the real-time monitoring of each nucleotide incorporation event, thereby making the method sensitive to even extremely small changes to relatively subtle chemical modifications, such as 5hC, 5hU or 5hmU. Because of the nature of the SMRTbell DNA template allowing the sequencing of both the forward and the reverse strand of the same DNA molecule during a SMRT sequencing reaction, products of DNA damage can be detected in a strand-specific manner, allowing for the differentiation of hemi- and fully-modified positions ).
Additional File 3: Animation of the DNA polymerase catalytic cycle during SMRT sequencing. The movie shows the binding of a phospholinked nucleotide, incorporation, and release of the pyrophosphate-linker-fluorophore reaction product. A hypothetical damaged DNA base is highlighted in red, and is moved into the active site following the phospholinked nucleotide incorporation and polymerase translocation. The animation highlights the close contact of the polymerase over an extended region with the nucleic acid: the incoming DNA template (positions -3 to zero) and nascent double-stranded DNA (positions +1 to approximately +7). The polymerization dynamics can be altered by the presence of DNA base modifications throughout this region. The animation is based on an in-house crystal structure and pdb structure 2PZS, followed by a brief energy minimization in PyMOL. The dye and linker are modeled solely for indicating their structures and do not reflect their real conformations and positions. (WMV 760 KB)
Besides the sequencing application, the method opens potential paths to increase our understanding about how different types of DNA polymerases are affected by certain types of DNA lesions. The SMRT sequencing assay could potentially be adapted to study the detailed dynamics of lesion-specific polymerases at the single-molecule level, and to combine their activities with replicative polymerases to capture products of DNA damage which are currently resulting in read termination. We anticipate that SMRT sequencing will become a powerful, high-throughput tool for the detection and sequencing of DNA containing damaged bases to improve our understanding of aging, DNA damage-related diseases, DNA polymerase enzymology, DNA repair mechanisms, and chemotherapeutic efficacies. The presented method should also be applicable towards detecting previously unknown base changes in DNA.
Custom oligonucleotides containing modified bases were purchased from Bio-synthesis (Lewisville, TX), Trilink BioTechnologies (San Diego, CA), ChemGenes (Wilmington, MA) and Integrated DNA Technologies (Coralville, IA). A list of the sequences can be found in Additional File 4. All oligonucleotides contained 5' phosphate groups. SMRTbell templates were generated by ligating several synthetic oligonucleotides, one of which contained two instances of a chemical base modification (Additional File 1). Complementary and hairpin oligonucleotides were annealed by heating to 80°C for 2 minutes and slowly cooling to 25°C (0.1°C/sec) in 10 mM Tris (pH 7.5), 100 mM NaCl. Annealed oligonucleotides were ligated using T4 DNA Ligase (NEB; Ipswich, MA) for 60 minutes at 25°C followed by heat kill for 10 minutes at 65°C. Incompletely formed SMRTbell templates were degraded with a combination of Exonuclease III (NEB; Ipswich, MA) and Exonuclease VII (USB; Cleveland, OH) at 37°C for 30 minutes. SMRTbell templates were purified using QIAquick PCR Purification columns (Qiagen; Valencia, CA).
SMRTbell templates were subjected to standard SMRT sequencing using an engineered phi29 DNA polymerase, as described [6, 7]. All templates were run in duplicate on different days, different sequencing instruments, and using different reagent lots to verify the reproducibility of the reported results. Reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol. IPDs were measured as previously described  for all pulses aligned to each position in the reference sequence. Baseline correction was applied by dividing the IPD mean for each position by the average of mean IPDs over all positions in the template, excluding the positions of base modifications and a window of six bases in each direction around such positions. In addition, 5% of outlier values were trimmed from both sides of the IPD distribution at each position before computing the mean. Thereafter, the ratio of mean IPDs was computed between the modified and control template samples for each template position.
where μ1 and μ2 are the average IPD values of the modified and control, s1 and s2 are their standard deviations and n is the lower sequencing coverage of the two samples.
List of Abbreviations Used
benzo[a]pyrene diol epoxide
This work was supported in part by National Institutes of Health grant 1RC2HG005618-01 (NHGRI). We thank M. Boitano, J. Bullard, K. Luong and S. Kamtekar for help with data acquisition and analysis.
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