MALDI-TOF was used to characterize fragments obtained from the reactivity between oxidized RNA and the exoribonuclease Xrn-1. The present protocol describes a methodology that can be applied to other processes involving RNA and/or DNA.
RNA is a biopolymer present in all domains of life, and its interactions with other molecules and/or reactive species, e.g., DNA, proteins, ions, drugs, and free radicals, are ubiquitous. As a result, RNA undergoes various reactions that include its cleavage, degradation, or modification, leading to biologically relevant species with distinct functions and implications. One example is the oxidation of guanine to 7,8-dihydro-8-oxoguanine (8-oxoG), which may occur in the presence of reactive oxygen species (ROS). Overall, procedures that characterize such products and transformations are largely valuable to the scientific community. To this end, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry is a widely used method. The present protocol describes how to characterize RNA fragments formed after enzymatic treatment. The chosen model uses a reaction between RNA and the exoribonuclease Xrn-1, where enzymatic digestion is halted at oxidized sites. Two 20-nucleotide long RNA sequences [5'-CAU GAA ACA A(8-oxoG)G CUA AAA GU] and [5'-CAU GAA ACA A(8-oxoG)(8-oxoG) CUA AAA GU] were obtained via solid-phase synthesis, quantified by UV-vis spectroscopy, and characterized via MALDI-TOF. The obtained strands were then (1) 5'-phosphorylated and characterized via MALDI-TOF; (2) treated with Xrn-1; (3) filtered and desalted; (4) analyzed via MALDI-TOF. This experimental setup led to the unequivocal identification of the fragments associated with the stalling of Xrn-1: [5'-H2PO4-(8-oxoG)G CUA AAA GU], [5'-H2PO4-(8-oxoG)(8-oxoG) CUA AAA GU], and [5'-H2PO4-(8-oxoG) CUA AAA GU]. The described experiments were carried out with 200 picomols of RNA (20 pmol used for MALDI analyses); however, lower amounts may result in detectable peaks with spectrometers using laser sources with more power than the one used in this work. Importantly, the described methodology can be generalized and potentially extended to product identification for other processes involving RNA and DNA, and may aid in the characterization/elucidation of other biochemical pathways.
MALDI-TOF1,2,3 is a widely used technique for the characterization and/or detection of molecules of varying sizes and characteristics. Some of its uses include diverse applications such as detecting tannins from natural resources4, imaging metabolites in food5, discovery or monitoring of cellular drug targets or markers6, and clinical diagnostics7, to name a few. Of relevance to the present work is the use of MALDI-TOF with DNA or RNA, with its use on oligonucleotides dating back to over three decades8, where several limitations were noted. This technique has now evolved to a reliable, commonly used means to characterize both biopolymers9 and identify/understand chemical and biochemical reactions, e.g., characterization of platinated sites in RNA10, identification of RNA fragments following strand cleavage11,12, or formation of protein-DNA cross-links13. Thus, it is valuable to illustrate and highlight important aspects of using this technique. The basics of MALDI-TOF have been described in video format as well14 and will not be further elaborated herein. Furthermore, its application in a DNA or protein context has been previously described and illustrated in the said format15,16,17.
The protocol for detecting RNA fragments formed after enzymatic hydrolysis is reported herein. The experimental model was chosen based on a recent finding published by our group18, where MALDI-TOF was used to determine the unique reactivity between the exoribonuclease Xrn-1 and oligonucleotides of RNA containing the oxidative lesion 8-oxoG. The 20-nucleotide long strands were obtained via solid-phase synthesis19, [5'-CAU GAA ACA A(8-oxoG)G CUA AAA GU] and [5'-CAU GAA ACA A(8-oxoG)(8-oxoG) CUA AAA GU], while Xrn-1 was expressed and purified following the previously described report20. In brief, Xrn-121 is a 5'-3' exoribonuclease with various key biological roles that degrade multiple types of RNA, including oxidized RNA22. It was found that the processivity of the enzyme stalls upon encountering 8-oxoG, which led to RNA fragments containing 5'-phosphorylated ends [5'-H2PO4-(8-oxoG)G CUA AAA GU], [5'-H2PO4-(8-oxoG)(8-oxoG) CUA AAA GU], and [5'-H2PO4-(8-oxoG) CUA AAA GU]18.
Finally, it is important to note that mass spectrometry is a powerful method that, through various methodologies, can be adapted to other purposes23,24; thus, choosing the right ionization method as well as other experimental set up is of utmost importance.
RNase-free ultra pure water (Table 1) was used for the present study.
1. Concentration determination of RNA solution
2. Hydrolysis of oligonucleotides of RNA by Xrn-1
3. Desalting of RNA solution, MALDI-TOF plate spotting
4. Data acquisition and processing
NOTE: In general, THAP requires higher laser power to achieve ionization. Additionally, oligos can be difficult to ionize without fragmenting. Thus, it is usually necessary to use as low laser power as possible and raise detector gains and/or lower laser frequency to maximize detection and minimize fragmentation.
The oligonucleotides used in this work were synthesized, characterized, and quantified prior to use. The concentration of all oligonucleotides was determined via UV-vis spectroscopy recorded at 90 °C to avoid erroneous readings arising from the potential formation of the secondary structures. Figure 3 displays the spectra of the model oligonucleotides of RNA used in this work, taken at room temperature and after applying heat.
The overall procedure, along with the structure of the oxidative lesion that causes Xrn-1 stalling, is illustrated in Figure 4. Oligonucleotide (1) contains one 8-oxoG at position-11 and is where Xrn-1 activity is blocked, resulting in halted hydrolysis of the RNA strand. Importantly, the results depicted in this figure correspond to experiments carried out using solutions containing 200 pmol of the parent strand (1), although only 20 pmol were spotted on the plate. It is important to note that the average mass was used in all of the calculations and that discrepancies varying between 1-3 atomic mass units (amu) were observed. The figure displays two processes, (1) the efficient 5'-phosphorylation of RNA, evidenced by the appearance of only one peak (1') corresponding to the expected product, and (2) the stalling fragment arising from the treatment of the sample mixture with Xrn-1. Control experiments where the parent strand was treated under the same conditions, in the absence of the kinase (PNK), and the ribonuclease (Xrn-1) did not display differences from those shown in Figure 4 (RNA strand 1).
The same results were obtained using a different sequence (3) that contained two oxidative lesions (Figure 5). The corresponding phosphorylation and enzymatic degradation yielded two main products that suggested that the enzyme successively stalls at both sites containing 8-oxoG. As depicted in the mass spectra corresponding to the fragments of interest, a discrepancy upon MALDI-TOF acquisition was observed when taking spectra of the same oligonucleotide on different days. This is illustrated in Figure 4, where two additional atomic units were observed. The results depicted in this figure correspond to experiments carried out with 100 pmol of the parent strand (3). It is important to note that quantitative data may be obtained to assess the overall efficiency of the biochemical process (and complete tracking via MALDI-TOF) by introducing an internal standard on samples before and after enzymatic degradation.
Figure 1: Spotting of RNA solution. (A) Spotting onto the MALDI plate. (B) Illustration of MALDI-plate placement onto the MALDI-spectrometer. Please click here to view a larger version of this figure.
Figure 2: The camera shot illustrating the formation of the sample: matrix crystals spotted onto the plate. Please click here to view a larger version of this figure.
Figure 3: UV-vis spectra of oligonucleotides (1) and (3) recorded at 25 °C and 90 °C, respectively. Please click here to view a larger version of this figure.
Figure 4: Experimental process for oligonucleotide preparation and mass spectra for each step. (A) Overall steps using oligonucleotide (1) are illustrated. The sequence of events corresponds to (B) 5'-phosphorylation in the presence of polynucleotide kinase (PNK), followed by (C) enzymatic hydrolysis in the presence of Xrn-1. The MALDI-TOF spectra obtained before and after both biochemical processes are displayed. Please click here to view a larger version of this figure.
Figure 5: MALDI-TOF spectra, using oligonucleotide (3), obtained before (left)/after (right) treatment with Xrn-1. Please click here to view a larger version of this figure.
Solution | Composition | ||
A | Tris-HCl (700 mM), DTT (50 mM), pH 7.6, T4 polynucleotide kinase buffer | ||
B | NaCl (1 M), Tris-HCl (0.5 M), MgCl2 (0.1 M), DTT (10 mM), pH 7.9 | ||
C | 2,4,6-Tihydroxyacetophenone monohydrate (THAP, 25 mM), ammonium citrate (10 mM) | ||
D | Ammonium fluoride (300 mM in 50 % aq. Acetonitrile) | ||
RNase-free H2O | Ultra-pure water was treated with diethyl pyrocarbonate (DEPC, 1 mL per liter of water), incubated at 37 °C (12 h), and autoclaved (1 h) |
Table 1: Solution compositions used in the study.
Video 1: Demonstration for spotting onto the MALDI plate. Please click here to download this Video.
Video 2: Demonstration outlining the data analyses. Please click here to download this Video.
Supplementary File 1: Step-by-step illustration for handling UV-vis software (step 1.2), MS data acquisition (step 4.1), and MS data processing (step 4.2). Please click here to download this File.
The main challenge in this workflow arose between finalizing the experiments and carrying out the mass spectrometric analyses. Experiments were carried out and completed at the University of Colorado Denver and shipped (overnight) to the Colorado State University facilities. Data acquisition was carried out upon receipt, as per convenience. Several unexpected circumstances led to time delays in the process. In one instance, unexpected instrument malfunctions required the samples to be frozen (one time for 21 days) prior to spotting and acquiring; however, this time delay did not seem to affect the experimental outcome, although degradation of the RNA (leading to decreased signal intensities) cannot be ruled out.
The limitation of the described experiments, in terms of RNA concentration, was that the experiments were carried out with [RNA] higher than what can be obtained in vivo, for a single RNA sequence23,24. We found that when experiments were carried out with 20 pmol of RNA (2 pmol spotted on the plate), or lower amounts, the expected peaks were not observed. The use of spectrometers with improved laser power may likely lead to enhanced signal and lower detection limits.
It is expected that the step where the enzymes are filtered (using a 10 kDa filtering device) to separate the enzymes can be avoided. Experiments carried out without this step led to similar results. However, the filtration step is recommended if samples are to be shipped or stored for a while.
The provided steps may be amenable to characterizing and understanding several biochemical processes. Examples may include the characterization of processes involving damaged DNA25, peptides26,27, or RNA conjugates28, among many others. In general, we speculate that the process illustrated herein may be applicable to various experimental setups involving nucleic acids, proteins, biomaterials, and/or other biopolymers. Furthermore, the development of enhanced spectrometers will lead to enhanced results, and important discoveries, in areas involving the aforementioned biomolecules.
The authors have nothing to disclose.
It is important to note that this work was a collaborative effort between three institutions, two research groups, and one core facility. The distribution and workload were carried out as follows: Protein (Xrn-1) expression was carried out at the University of Denver (Denver, CO). Oligonucleotide synthesis, quantification, and experimentation (mainly enzymatic degradation) were conducted at the University of Colorado Denver (Denver, CO). Optimization was also carried out there. MALDI-TOF spotting, acquisition, and analysis were carried out at the Analytical Resources Core Facility at Colorado State University. (Fort Collins, CO). SS would like to acknowledge a UROP Award (CU Denver) and Eureca grants (CU Denver) for support. E. G. C. acknowledges support from NIGMS, via R00GM115757. MJER acknowledges support from NIGMS, via 1R15GM132816. K. B. acknowledges resource ID: SCR_021758. The work was also supported by a Teacher-Scholar Award (MJER), TH-21-028, from the Henry Dreyfus Foundation.
0.6 mL MCT Graduated Violet | Fisher Scientific | 05-408-127 | |
6’-Trihydroxyacetophenone monohydrate 98% | Sigma Aldrich | 480-66-0 | |
Acetonitrile 99.9%, HPLC grade | Fisher Scientific | 75-05-8 | |
Adenosine triphosphate, 10 mM | New Englang Bioscience | P0756S | |
Ammonium citrate, dibasic 98% | Sigma Aldrich | 3012-65-5 | |
Ammonium Fluoride 98.0%, ACS grade | Alfa Aesar | 12125-01-8 | |
Bruker bacterial test standard | Bruker Daltonics | 8255343 | |
Commercial source of Xrn-1 | New England BioLabs | M0338S | |
Diethyl pyrocarbonate, 97% | ACROS Organics | A0368487 | |
Flex analysis software | Bruker daltonics | FlexAnalysis software version 3.4, Bruker Daltonics | |
Lambda 365 UV-vis spectrophotometer | Perkin Elmer | ||
MALDI plate: MSP 96 ground steel target | Bruker Daltonics | 280799 | |
Mass Spectrometer | Bruker | Microflex LRFTOF mass spectrometer (Bruker Daltonics, Billerica, MA) | |
Mili-Q IQ 7000 | Milipore Sigma | A Mili-Q system was used to purify all water used in this work | |
Nanosep Centrifugal Devices with OmegaTM Membrane 10 K, blue (24/pkg) | Pall Corporation | OD010C33 | filter media, Omega (modified polyethersulfone) 10 K pore size |
NEBuffer 3 | New England Biolabs | B7003S | This is solution B |
Oligo Analyzer tool | IDT-DNA | https://www.idtdna.com/calc/analyzer | |
Pipette tips P10 | Fisher Scientific | 02-707-441 | |
Pipette tips P200 | Fisher Scientific | 02-707-419 | |
RNase Away | Molecular BioProducts | 7005-11 | |
T4 Polynucleotide Kinase | New England BioLabs | M0201S | |
T4 Polynucleotide Kinase Reaction Buffer | New England BioLabs | B0201S | This is solution A |
Triflouroacetic Acid | Alfa Aesar | 76-05-1 | |
Xrn-1 exoribonuclease | Expressed in house | See ref. 20 | |
ZipTip Pipette Tips for Sample preparation | Millipore | ZTC 18S 096 | 10 µL pipette tips loaded with a C18 standard 0.6 µL bed |