Abstract:
The present invention provides synthetic RNA aptamers that bind RDX. In various embodiments, the synthetic RNA aptamers may include one or more aptamers selected from the group consisting of SEQ ID 1-12. The synthetic RNA aptamers that bind RDX provide an inexpensive, in situ method for testing for RDX, which may be used for both soil and water samples.

Description:
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT 
       [0001]    The invention described herein was made by an employee of the United States Government and may be manufactured and used by the Government of the United States of America for governmental purposes without the payment of any royalties thereon or therefore. 
     
    
     INCORPORATION OF SEQUENCE LISTING 
       [0002]    Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 2,854 Byte ASCII (Text) file named “COE-686_RNA_SEQ.txt,” created on Jan. 29, 2015. 
       BACKGROUND OF THE INVENTION 
       [0003]    1. Field of Invention 
         [0004]    This invention relates to the field of chemistry and more specifically to testing for RDX with a ligand-binding assay. 
         [0005]    2. Description of Related Art 
         [0006]    Since World War II, an explosive known as C-4 has been widely used for military and civilian operations, such as excavation and demolition. C-4 contains an environmental contaminant known 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX). RDX can migrate through soil and contaminate underlying groundwater aquifers and may be harmful to humans at relatively low levels. The EPA has established a lifetime health advisory guidance level of 0.002 milligrams per liter (mg/L) for RDX in drinking water. The EPA has identified more than thirty RDX contaminated sites on its list of national clean-up priorities. 
         [0007]    There are several problems known in the art for testing for the presence of RDX to make determinations relevant to a potential need for remediation. RDX concentrations are discrete particles that are irregularly dispersed throughout the soil. The concentration of samples from adjacent areas may vary considerably. Current RDX testing methods are intended to provide data about precise quantities of RDX using highly sensitive, off-site instrumentation to separately test each sample. This type of high-sensitivity off-site testing is not appropriate for wide scale EPA and private environmental remediation projects, and often does not yield the necessary type of data for evaluating dispersal patterns over potentially contaminated site. 
         [0008]    For purposes of planning and remediation, it is important to be able to test many samples to determine the presence or absence of contaminants over a dispersed area and patterns of dispersal. Current high-sensitivity testing methods performed off-site are costly and prone to delay because they cannot be performed in situ. 
       BRIEF SUMMARY OF THE INVENTION 
       [0009]    This invention provides synthetic RNA aptamer(s) that bind 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX). 
         [0010]    This invention also provides a method for detecting RDX involving the steps of admixing a buffered solution of a synthetic RNA aptamer that binds RDX with a sample in need of testing for RDX, and assaying the sample for RDX. 
         [0011]    This invention also provides a biosensor apparatus for RDX. The apparatus for RDX is made of a plurality of synthetic RNA aptamers that bind RDX. The synthetic RNA aptamers are modified to link to an electrode. The surface electrode is linked to the plurality of synthetic RNA aptamers. 
     
    
     
       BRIEF DESCRIPTION OF SEVERAL VIEWS OF THE DRAWING(S) 
         [0012]      FIG. 1  is a schematic illustrating an exemplary embodiment of how a synthetic RNA aptamer binds to RDX. 
           [0013]      FIG. 2  is a graph illustrating the binding affinity of various embodiments of synthetic RNA aptamers for testing the presence of RDX. 
           [0014]      FIG. 3  is a graph illustrating the percent of total RDX bound by synthetic RNA aptamers as a function of time for clones 4 and 12. 
           [0015]      FIG. 4  is a schematic of an exemplary embodiment of a synthetic RNA aptamer electrical-chemical signal transducer. 
       
    
    
     TERMS OF ART 
       [0016]    As used herein, the term “assay” is a test or testing for the quantity, presence or absence of a substance. 
         [0017]    As used herein, the term “synthetic RNA” refers to a RNA molecule that does not occur naturally. 
         [0018]    As used herein, the term “synthetic RNA aptamer” refers to a RNA molecule that includes nucleotides having the chemical structure that binds a substance. 
       DETAILED DESCRIPTION OF THE INVENTION 
       [0019]      FIG. 1  is a schematic illustrating how an exemplary embodiment of a synthetic RNA aptamer  10  binds to RDX  20 . In this exemplary embodiment, synthetic RNA aptamer  10  binds to RDX  20  by the formation of secondary structures. The combination of synthetic RNA aptamer  10  secondary structures and three-dimensional tertiary structures enables synthetic RNA aptamer  10  to bind target RDX  20 . The combination of synthetic RNA aptamer  10  and RDX  20  forms a binding complex  30 . 
         [0020]    In the exemplary embodiment, synthetic RNA aptamer  10  is a 76 base-pair synthetic RNA aptamer including a thirty base pair binding region flanked by T7 primer binding sites. In the exemplary embodiment shown, the use of T7 primer binding sites simplifies the amplification steps during systematic evolution of ligands by exponential enrichment (SELEX) and sequencing. However, in alternate embodiments, other primer binding sequences may be used. The exemplary synthetic RNA aptamer  10  illustrated is developed by preparing a library of synthetic RNA sequences containing a thirty nucleotide variable region. This library was then subjected to multiple rounds of SELEX, to enrich for sequences that bind RDX  20 . 
         [0021]    Table 1 illustrates specific synthetic aptamer sequences capable of binding RDX  20 . The RNA sequence of the twelve synthetic aptamers form structures that have binding characteristics that allow them to bind to RDX  20 . It should be noted that the sequence of synthetic RNA aptamer(s)  10  can be modified by one skilled in the art to change, delete or add nucleotides to obtain synthetic RNA aptamer(s)  10  that form structures that have binding characteristics that allow synthetic RNA aptamer(s)  10  to bind to RDX  20 . For example, the synthetic RNA aptamers  10  shown in Table 1 differ in as much as 50 percent homology, but still have the desired binding characteristics that allow them to bind to RDX  20  and to form binding complex  30 . 
         [0000]    
       
         
               
             
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Sequences of RDX binding synthetic RNA aptamers 
               
             
          
           
               
                 Clone 
                 Sequence 
               
               
                   
               
               
                  1 
                 UAGGGAAGAGAAGGACAUAUGAUCGGACGAGGAGCAAUUGA 
               
               
                   
                 GAUAUGCGCAAAUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 1 
               
               
                   
               
               
                  2 
                 UAGGGAAGAGAAGGACAUAUGAUUGACUAGUACAUGACCAC 
               
               
                   
                 UGAAAGGGCGAAUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 2 
               
               
                   
               
               
                  3 
                 UAGGGAAGAGAAGGACAUAUGAUAGCCCCAGUGUGCGGCAA 
               
               
                   
                 AUGGGGACAAUGUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 3 
               
               
                   
               
               
                  4 
                 UAGGGAAGAGAAGGACAUAUGAUCACUUGACUAGUACAUGA 
               
               
                   
                 CCACUGAAAGGGUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 4 
               
               
                   
               
               
                  5 
                 UAGGGAAGAGAAGGACAUAUGAUCACUUGAUUGACUAGUAC 
               
               
                   
                 AUGACCCUUGAUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 5 
               
               
                   
               
               
                  6 
                 UAGGGAAGAGAAGGACAUAUGAUAUGAUGACACCGUUGACA 
               
               
                   
                 UCCGGGUCAAUUUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 6 
               
               
                   
               
               
                  7 
                 UAGGGAAGAGAAGGACAUAUGAUCACUUGAACUGAUGACUA 
               
               
                   
                 GUACAUACCACUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 7 
               
               
                   
               
               
                  8 
                 UAGGGAAGAGAAGGACAUAUGAUAUCGUUAUCCGGUCGCGG 
               
               
                   
                 UCGAGGCCCUGCUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 8 
               
               
                   
               
               
                  9 
                 UAGGGAAGAGAAGGACAUAUGAUGGGUAUGCACACAUCAGC 
               
               
                   
                 GACAACUGGCCGUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 9 
               
               
                   
               
               
                 10 
                 UAGGGAAGAGAAGGACAUAUGAUCCGGAUCCGGAAGGCAAU 
               
               
                   
                 CCCUCCGCGAGGUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 10 
               
               
                   
               
               
                 11 
                 UAGGGAAGAGAAGGACAUAUGAUCCCCACUCCUAUUAUCAU 
               
               
                   
                 UCUGUGCCAGGUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 11 
               
               
                   
               
               
                 12 
                 UAGGGAAGAGAAGGACAUAUGAUGCAGUCAACUGUACGGGG 
               
               
                   
                 UUAGUCUUGCGGUUGACUAGUACAUGACCACUUGA 
               
               
                   
                 SEQ ID NO. 12 
               
               
                   
               
             
          
         
       
     
         [0022]    One skilled in the art can prepare RNA oligonucleotides shown in Table 1 by enzymatic transcription or automated solid-phase synthesis. Enzymatic synthesis can produce relatively long transcripts in significant quantities, while commercial non-enzymatic RNA chemical synthesis can produce RNAs that are 40-80 nucleotides in length. Industrial scale production of RNA may by chemical synthesis, by fermentation or by any other method known in the art for producing synthetic RNA. 
         [0023]    Synthetic RNA aptamers  10  shown in Table 1 can be used to detect RDX  20  in soil and water samples. The sample tested for RDX  20  can include soil or water. Synthetic RNA aptamers  10  shown in Table 1 have binding characteristics that allow them to bind to RDX  20 . These binding characteristics include high affinity and specificity for RDX  20 . Affinity refers to the tendency of a ligand molecule to bind to a biological molecule. 
         [0024]      FIG. 2  is a graph illustrating the binding affinity of various embodiments of synthetic RNA aptamers  10  for testing the presence of RDX  20 . Synthetic RDX aptamers  10  display high affinity for RDX  20  with several clones capable of achieving almost 100% of the theoretical binding capacity. 
         [0025]      FIG. 2  assumes that there is a 1:1 molar ratio between the aptamer and target and that one aptamer will bind one molecule of RDX  20 . In the exemplary embodiment shown, the percent of theoretical binding capacity ranges from approximately 30 to approximately 100 percent. In other embodiments, the percent of theoretical binding capacity ranges from approximately 80 to approximately 100 percent. 
         [0026]    Table 2 shows the percent of theoretical maximum binding capacity for each clone. 
         [0000]    
       
         
               
               
               
             
               
               
               
             
           
               
                   
                   
               
               
                   
                   
                 Percent of  
               
               
                   
                   
                 theoretical 
               
               
                   
                   
                 maximum  
               
               
                   
                 Clone 
                 binding capacity 
               
               
                   
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 1 
                 58.0% 
               
               
                   
                 2 
                 40.0% 
               
               
                   
                 3 
                 46.0% 
               
               
                   
                 4 
                 31.0% 
               
               
                   
                 5 
                 73.0% 
               
               
                   
                 6 
                 82.5% 
               
               
                   
                 7 
                 88.3% 
               
               
                   
                 8 
                 61.4% 
               
               
                   
                 9 
                 57.5% 
               
               
                   
                 10 
                 86.6% 
               
               
                   
                 11 
                 98.7% 
               
               
                   
                 12 
                 98.2% 
               
               
                   
                   
               
             
          
         
       
     
         [0027]    Deriving the data in  FIG. 2  required testing the binding affinity of synthetic RNA aptamers  10  using the following exemplary method. The method dissolved two and a half micrograms of the synthetic RNA aptamer(s)  10  in 100 uL of a binding buffer consisting of 100 mM sodium chloride (NaCl), 5 mM magnesium chloride (MgCl2), and 25 mM Tris-HCl, pH 6. An aliquot of RDX  20  was dried down and resuspended in the aptamer-buffer solution at final concentrations ranging from 1-100 ppm and allowed to react for 1 hour at room temperature with constant stirring. Centrifugation removed synthetic RDX aptamers  10  with bound RDX  20  from solution by and HPLC measured RDX  20  remaining in solution. 
         [0028]    One skilled in the art may use alternative methods to measure bound or unbound RDX  20 . For example, in alternative embodiment, the assay can be an electrochemical assay platform. In another embodiment, synthetic RNA aptamer  10  is modified to covalently link to a detectable label and the detectable label is covalently linked to synthetic RNA aptamer  10 . 
         [0029]      FIG. 3  is a graph illustrating the percent of total RDX  20  bound by synthetic RNA aptamers  10  as a function of time for clones 4 and 12. The exemplary synthetic RNA aptamers  10  illustrate a range of binding times. Even lower affinity synthetic RNA aptamers  10  demonstrate a fast response time, binding over 50% of available RDX  20  in one hour. The specificity in this context refers to the ability of synthetic RNA aptamers  10  to bind to the desired target and not bind similar compounds. Synthetic RNA aptamers  10  showed no affinity to 2-4-dinitroanisole (DNAN) and trinitrotoluene (TNT), which are structurally similar compounds used in explosive compositions. 
         [0030]      FIG. 4  is a schematic of an exemplary embodiment of a synthetic RNA aptamer electrical-chemical signal transducer  400 . Transducer  400  includes a redox probe  410 , a biosensor  420  and an electrode  430 . In the exemplary embodiment shown, biosensor  420  is made of a bio-recognition layer including a plurality of synthetic RNA aptamers  10  that bind RDX  20 . Synthetic RNA aptamers  10 , in this exemplary embodiment, are modified with a 5′ C6 disulfide linker  440  for covalent attachment to the surface of electrode  430 . In the exemplary embodiment shown, synthetic RNA aptamers  10  also have a 3′-amino modification to covalently attach redox probe  410 , such as for example ferrocene (Fc). 
         [0031]    In the exemplary embodiment shown, the addition of RDX  20  causes a conformational change in synthetic RNA aptamers  10 , which changes the distance between redox probe  410  and a surface of electrode  430 , which in turn changes the efficiency of electron transfer (eT). A potentiostat  450  measures the change in current over a voltage gradient. The amplitude of the current corresponds to the concentration of RDX  20 . Potentiostat  450  is an electronic instrument that controls the voltage difference between a working electrode and a reference electrode, 
         [0032]    A biological sensor can detect the existence of the target molecule within a relatively short time period. Biosensors are hybrid analytical devices that amplify signals generated from the specific interaction between a receptor, such as a binding region, and a ligand of interest, through a biophysical mechanism. Biosensors use nucleic acids as receptors, coupled to a physicochemical signal transducer. 
         [0033]    In various embodiments, biological sensors can use chromatographic or enzymatic immunoassay detection techniques. A detectable label allows for the detection of a ligand. A label can be chemically linked or conjugated to the ligand or synthetic RNA aptamer  10 . The detectable label can be a fluorescent label, a radioactive label, an enzyme label, or a redox label. 
         [0034]    In one embodiment, the biosensor is an apparatus to detect RDX  20 . The apparatus is made of a housing configured to receive a sample and to retain synthetic RNA aptamer  10 . Synthetic RNA aptamer  10  with a 3′-amino modification binds to a detectable label such as ferrocene. In this way, the presence of the detectable label in the housing shows RDX  20  is present in the sample. 
         [0035]    It will be understood that many additional changes in the details, materials, procedures and arrangement of parts, which have been herein described and illustrated to explain the nature of the invention, may be made by those skilled in the art within the principle and scope of the invention as expressed in the appended claims. It should be understood that the drawings are not necessarily to scale; instead, emphasis has been placed upon illustrating the principles of the invention.