Protein binding microarray (PBM) experiments combined with biochemical assays link the binding and catalytic properties of DNA primase, an enzyme that synthesizes RNA primers on template DNA. This method, designated as high-throughput primase profiling (HTPP), can be used to reveal DNA-binding patterns of a variety of enzymes.
DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. The binding of prokaryotic DnaG-like primases to DNA occurs at a specific trinucleotide recognition sequence. It is a pivotal step in the formation of Okazaki fragments. Conventional biochemical tools that are used to determine the DNA recognition sequence of DNA primase provide only limited information. Using a high-throughput microarray-based binding assay and consecutive biochemical analyses, it has been shown that 1) the specific binding context (flanking sequences of the recognition site) influences the binding strength of the DNA primase to its template DNA, and 2) stronger binding of primase to the DNA yields longer RNA primers, indicating higher processivity of the enzyme. This method combines PBM and primase activity assay and is designated as high-throughput primase profiling (HTPP), and it allows characterization of specific sequence recognition by DNA primase in unprecedented time and scalability.
HTPP makes use of DNA binding microarray technology combined with biochemical analysis (Figure 1) to statistically identify specific features of DNA templates that affect the enzymatic activity of DNA primase. Therefore, HTPP provides a technological platform that facilitates a knowledge leap in the field. The classical tools used to determine primase recognition sites do not have the ability to yield massive amount of data, whereas HTPP does.
PBM is a technique routinely used to determine the binding preferences of transcription factors to DNA1,2; however, it is not suitable for detection of weak/transient binding of proteins to DNA. Unlike the universal PBM that provides information about average protein binding specificity to all possible sequences consisting of eight base pairs, HTPP is based on the library of single-stranded DNA templates comprising unique sequence elements. Such DNA sequence elements involve tens of thousands short (few tens of bp) genomic sequences, as well as computationally designed DNA sequences enriched in certain DNA repetitive sequence elements present in the genome, which possess different average GC content. Such a high-throughput approach allows determination of, in a systematic, quantitative, and hypothesis-driven way, the sequence-related properties that are important for primase binding and its enzymatic activity3. In particular, the important link between primase-DNA binding preferences, (modulated by DNA sequences flanking specific tri-nucleotide binding sites) and primase processivity has been identified for this enzymatic system4.
The new technology was applied to revisit our understanding of primase recognition sites even for the T7 DNA primase that has been extensively studied5. Specifically, re-examination of classical concepts, such as DNA recognition sites of T7 DNA primase (which were determined almost four decades ago 6) using protein-DNA binding microarray (PBM) has led to unprecedented insight into features related to the flanking sequence of these recognition sites3. It was expected that the sequences flanking tri-nucleotide recognition site of T7 DNA primase (5'-GTC-3') will be random. Instead, we found that TG-rich flanking sequences increase the chances of T7 DNA primase to synthesize longer RNA primers indicating an increase in processivity.
Other methods that can be used to study DNA-binding properties of proteins in vitro include the electrophoretic mobility shift assay (EMSA)7, DNase I footprinting8, surface-plasmon resonance (SPR)9, and Southwestern blotting10. These are, however, low-throughput methods only applicable to investigating a small number of DNA sequences. In addition, the precision and sensitivity of some of these techniques (e.g., EMSA) is low. On the other hand, in vitro selection11 is a technique that, similarly to PBM, can be used for the identification of numerous binding sequences. However, low affinity sequences are usually excluded in most applications of in vitro selection; therefore, this approach is not suitable for obtaining comparative binding data for all available sequences. The universal PBM1,2 is mainly used to characterize the binding specificities of transcription factors from prokaryotes and eukaryotes as well as specific factors (e.g., presence of certain ligands, cofactors, etc.) that may affect this interaction12.
HTPP expands the PBM application to DNA processing enzymes by combining unprecedented high-throughput statistical power with high precision to provide information on binding sequence context. Such data has not yet been obtained for primases and related enzymes (that have weak/transient binding to DNA) due to aforementioned technical limitations of other available techniques.
1. Design of microarray
NOTE: DNA probes represent custom 36-nucleotide sequences, consisting of the recognition site for T7 DNA primase (GTC) located between two variable flanking regions, followed by a constant 24-nucleotide sequence tethered to a glass slide3. We used a 4 x 180,000 microarray format, which enabled spotting of each DNA sequence in six replicates, randomly distributed on the slide.
2. Primase DNA binding experiment
NOTE: The day before (or at least 2 h before) the PBM, prepare the blocking solution [2% w/v skim milk in phosphate buffer saline (PBS)] and stir it on a magnetic stirrer. Prior to use, filter the solution with a 0.45 µM filter. To detect the primase binding to the DNA strands, several steps should be performed in the following order.
3. Microarray data analysis
NOTE: All data processing was performed using custom written scripts in MATLAB.
4. Template-directed RNA synthesis catalyzed by T7 DNA primase
This technological advance for mapping the primase binding sites allows the obtaining of DNA binding properties that are difficult, if not impossible, to observe using classical tools. More importantly, HTPP enables the revisiting of the traditional understanding of primase binding sites. Specifically, HTPP reveals binding specificities in addition to known 5'-GTC-3' recognition sequences, which leads to changes in functional activities of T7 DNA primase. Namely, two groups of sequences were identified: strong-binding DNA sequences that contained T/G in the flanks and weak-binding sequences that contained A/G in the flanks (all thymines in the strong-binding templates were replaced by adenines). No primase binding to DNA templates that were missing 5'-GTC-3' within their sequence was detected.
The primase DNA recognition sites that contained specific features, such as T/G-rich flanks, increased primase-DNA binding up to 10-fold, and surprisingly also increased the length of newly formed RNA (up to threefold) (Figure 2 in previous publication3). Importantly, HTPP allowed us to observe and quantify the variability in primer length in relation to the sequence of the DNA template.
Figure 1: Schematic representation of high-throughput primase profiling (HTPP). (A) The slide was incubated with the primase in activity buffer (40 mM Tris-HCl, pH 7.5; 10 mM MgCl2, 50 mM K-glutamate, 10 mM DTT, 100 µM rNTPs). Next, Alexa 488-conjugated anti-his fluorescent antibody was introduced to label the protein. After the mild washing step, the slide was scanned using microarray scanner. Binding affinity was determined according to the median fluorescence signal and DNA sequences were divided into groups accordingly. (B) Biochemical assays were performed to correlate the DNA-binding results obtained from the microarray experiment, with the functional properties of T7 DNA primase. Please click here to view a larger version of this figure.
Figure 2: Comparison of catalytic activity of T7 DNA primase on two groups of DNA templates (strong binding with T/G in the flanks and weak binding with A/G in the flanks) obtained from PBM. (A) RNA primer formation catalyzed by the T7 DNA primase. The reactions contained oligonucleotides with the primase recognition sequence (numbered lanes), 32P-α-ATP, ATP, CTP, UTP, and GTP in the standard reaction mixture. One group of DNA oligonucleotides (dark blue) contained T/G in the flanks, whereas all thymines were replaced with adenines in the second group (light blue). After incubation, the radioactive RNA products were separated by electrophoresis through a 25% polyacrylamide gel containing 7M urea and visualized by autoradiography. (B) Relative length (number of ribonucleotides constituting each RNA primer is unknown) and amount of RNA primers synthesized by T7 DNA primase on two groups of DNA templates (panel A). The plots show that longer RNA primers are synthesized (increased processivity) on DNA templates that primase binds with higher affinity (that contain T/G in the flanks) compared to the templates that are bound with lower affinity (that contain A/G in the flanks). (C) Quantification of the amount of synthesized RNA primers on two groups of DNA templates. The results demonstrate a correlation between the DNA-binding affinity and the amount of synthesized RNA by the T7 DNA primase. AU (arbitrary unit) is the measure of intensity of radioactive signal which directly correlates with the amounts of synthesized RNA primers. Please click here to view a larger version of this figure.
The PBM method has been widely used to investigate binding properties of transcription factors and can also be applied to DNA processing enzymes, such as DNA primase, that bind to DNA with low affinity. However, certain modifications of experimental procedures are required. The microarray experiment involves several steps: design of the DNA library, preparation of the chip, binding of the protein target, fluorescent labeling, and scanning. Mild washing steps are critical, since the long washes with solutions containing detergents cause dissociation of the protein from the DNA template due to the weak/transient mode of binding. Other critical steps include binding conditions (e.g., buffer composition, cofactors) and incubation times that need to be optimized for each specific enzyme.
The results obtained from microarray need to be validated in biochemical assays. Biochemical assays also provide insight into interesting features of DNA processing enzymes such as the correlation between DNA binding affinity and enzymatic activity/processivity. HTPP enabled us to observe the effect of DNA binding on functional properties of T7 DNA primase. For example, it has been observed that if primase exhibits higher binding affinity for the DNA template, it catalyzes the formation of longer RNA primers (increased processivity).
Overall, the method presented in this article is fast, reliable, and provides the opportunity to simultaneously test binding properties on tens of thousands of diverse DNA sequences in a single experiment in a hypothesis-driven way. Addition of other proteins or metal cofactors to the reaction mixture offers the possibility to investigate their effect on DNA binding properties of primases in a fast, high-throughput manner. On the other hand, the application of this method is limited by relatively high price of microarray slides and the safety precautions required when handling radioactive material for primase activity assays.
It is important to note that different primases require modifications of both microarray binding conditions and buffer conditions for activity assays. For example, primase of Mycobacterium tuberculosis requires substitution of magnesium with divalent manganese in the reaction buffer. Inappropriate metal cofactors or inappropriate reaction buffers may lead to poor primase activity or decreased DNA binding affinity.
As mentioned previously, primases bind to DNA templates with weak affinity; therefore, gentle washing steps are required during microarray binding experiment. Otherwise, they will be washed out from the microarray slide, leading to loss of the florescent signal upon addition of fluorescently labeled antibody.
To summarize, the DNA binding properties of many prokaryotic primases (including the trinucleotide DNA recognition sequence) are still poorly understood, mostly due to the technical limitations of currently available methods. HTPP represents a fast and efficient platform for the discovery of the DNA recognition sites or investigations of other template-related factors (i.e., overall nucleotide composition, GC content, presence of repetitive DNA sequence elements and their symmetry) that affect the binding affinity and activity of ssDNA binding enzymes. In addition, future applications may be directed towards the effects of different proteins or cofactors on DNA binding affinity, recognition patterns, or functional activity of primases and other DNA processing enzymes.
The authors have nothing to disclose.
This research was supported by the ISRAEL SCIENCE FOUNDATION (grant no. 1023/18).
40% acrylamide-bisacrylamide (19:1) solution | Merck | 1006401000 | |
95% formamide | Sigma-Aldrich | F9037-100ML | |
Alexa 488-conjugated anti-his antibody | Qiagen | 35310 | |
Ammonuium persulfate (APS) | Sigma-Aldrich | A3678-100G | |
ATP, [α-32P] – 3000 Ci/mmol | Perkin Elmer | NEG003H250UC | |
Boric acid, granular | Glentham Life Sciences | GE4425 | |
Bovine Serum Albumin (BSA) | Roche | 10735094001 | |
Bromophenol blue | Sigma-Aldrich | B0126-25G | |
Coplin jar | |||
Dithiothreitol (DTT) | Sigma-Aldrich | D0632-25G | |
DNA microarray | Agilent | 4x180K (AMADID #78366) https://www.agilent.com |
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Ethylenediaminetetraacetic acid (EDTA) | Acros Organics | AC118430010 | |
Fujifilm FLA-5100 phosphorimager | FUJIFILM Life Science | ||
Glass slide staining rack | Thermo Scientific | 12869995 | If several slides are used |
Lab rotator | Thermo Scientific | 88880025 | |
Magnesium chloride | Sigma-Aldrich | 63064-500G | |
Microarray Hybridization Chamber | Agilent | G2534A | https://www.agilent.com/cs/library/usermanuals/Public/G2534-90004_HybridizationChamber_User.pdf |
Microarray scanner (GenePix 4400A) | Molecular Devices | ||
Phosphate Buffered Saline (PBS) | Sigma-Aldrich | P4417-100TAB | |
Potassium glutamate | Alfa Aesar | A172232 | |
Ribonucleotide Solution Mix (rNTPs) | New England BioLabs | N0466S | |
Salmon testes DNA | Sigma-Aldrich | D1626-1G | |
Skim milk powder | Sigma-Aldrich | 70166-500G | |
Staining dish | Thermo Scientific | 12657696 | |
Tetramethylethylenediamine (TEMED) | Bio-Rad | 1610800 | |
Tris base (2-Amino-2-(hydroxymethyl)-1,3-propanediol) | Sigma-Aldrich | 93362-500G | |
Triton X-100 | Sigma-Aldrich | X100-500ML | |
Tween-20 | Sigma-Aldrich | P9416-50ML | |
Urea | Sigma-Aldrich | U6504-1KG | |
Xylene cyanol | Alfa Aesar | B21530 |