Final Manuscript

Alpha-Synuclein RNA Aptamers: Tools for Diagnostics and Therapeutics in Parkinson’s Disease

Cori Booker
11/30/2011
Fall 2011
R50 RNA pool
Alpha-Synuclein
Abstract:
Alpha-Synuclein (AS) is a protein that is expressed most abundantly in the brain and other nerve tissues. More is known about the dysfunction of AS than the normal function. (1) This protein is associated with up to 11 different gene mutations that can adversely affect the conformation of the protein and proteins it may interact with.(6) Genetic or environmental factors can cause AS to aggregate and form buildups of the protein in neuronal cell bodies, away from the cell membrane; the aggregations of AS are called Lewy bodies. These structures were originally thought to be the cause of the death of dopaminergic neurons characteristic of Alzheimer’s Disease. (6,11,13) More recent research suggests, however, that the pathogenic form of the protein is the five part oligomer that, when associated with cell membranes, forms a pore-like structure; the going theory is that the Lewy Bodies are the cell’s defense mechanism against the pore-like oligomer.(14)
Specific Aim 1: This research will seek to identify an RNA aptamer with an affinity for the functional monomer of the AS protein, Figure 1 below. Single stranded RNA aptamers will be selected from a pool of random RNA sequences through repeated rounds of selection in a "process of elimination" type assay. An aptamer could functionally inhibit the monomer, preventing it from forming the toxic oligomer. Adding a fluorescent tag to the aptamer would prove useful for helping to further research of how and why the protein misfolds to form the Lewy bodies by allowing for direct observation.(4)
Specific Aim 2: It would be doubly useful to perform simultaneous rounds of selection against samples of the aggregate forms of AS (see Figure 1) including negative selections in order to increase the in vivo affinity and specificity of the respective aptamers. An aptamer that could bind to the aggregated Lewy bodies would be integral in early diagnostics by adding visible tags to the aptamer.(8) Since Lewy body formation is also often associated with decreased proteosome effectiveness, an aptamer that was tagged with ubiquitin could be used in therapeutics to aid the cell in proper destruction of the aggregations. (5, 9,12)
These aptamers could be a stepping stone to better understanding the cause and nature of many Lewy body-associated diseases. AS is available for reorder from rPeptide (678-753-0747) for $300 per 0.5ng, cat # S-1001-1.


Figure 1: Specific Aim 1 proposes selection against the “Native monomer” of alpha-synuclein seen on the far left, Specific Aim 2 selects against the “Fibril” on the far left. The oligomer is a toxic intermediate conformation as the protein goes from monomer to fibril. (1, 14)
Introduction and Background:
Aptamers are derived from synthetically produced random sequences of RNA, ssDNA, or dsDNA. They comprise of a short, variable sequence of nucleic acids (usually about 30-60 bases in length) flanked by forward and reverse primers. A researcher will use the target (a protein, virus, or any molecule of interest) to determine which random sequences out of a pool of 1x1014 synthetic, random sequences exhibit binding affinity, by doing rounds of SELEX in vitro. The SELEX cycle consists of several main steps that are integral in discerning possible aptamers; the target is bound to a filter- or bead-type mechanism and the nucleic acid pool is allowed to interact with the target. The sequences that do not adhere to the target with great affinity during this step are washed away and those that bound are put through rounds of PCR amplification and purification. These newly replicated sequences are used in the subsequent round of selection and the process is then repeated; SELEX represents an inexpensive, process of elimination approach to acquiring highly specific nucleic acids (so named “aptamers”) that will not elicit immune response in vivo. The newly found aptamers can have certain tags added to them (such as a fluorescent tag to show visible signs of binding or a PEG tag to enhance cell uptake, etc) and the SELEX process can be modified to alter the affinity, specificity, and potential application of the aptamers found. (10, 8)
Alpha-Synuclein (AS) is a protein that is mostly expressed in the dopamine-related nerve cells of the central nervous system. (1) It is 140 amino acids long (6), weighs 14.46kDa, and has a pI of 4.6. There are many theories about what this protein’s purpose in the cell is, the most prominent being that it is of structural function.(6) This protein is of particular interest to us when it is in a mutated state. AS has been found to mutate and form large, fibrillic, insoluble aggregations of the protein that are deposited in the cell body of neurons called Lewy bodies (shown in Figure 2, below). These structures impede normal nerve function in a similar way that sickle-cell anemia creates obstructions in the bloodstream. (1,2,6) There are many genetic mutations in the AS coding region that have been previously associated with the presence of Lewy bodies and Parkinson’s Disease, these mutations are shown in figure 3, below.(9,7,13)
Figure 2: Lewy Bodies in brain cells. Lewy Bodies are comprised of malformed aggregations of the protein AS. (2) Figure 3: the gene that codes for the AS protein is shown here, along with regions of the gene that correspond to proposed functional domains; further research must be done to verify the claims made by this source. (3)
Most prominent in research involving AS, are discussions of the oligomeric form that acts as the toxic intermediate between the monomer and the fibril. An aptamer that binds with affinity to the monomer form could prevent formation of the pore-like oligomer by inhibiting the mutated AS proteins from interacting with each other. (6, 7) By counteracting the formation of the oligomeric pore the effects of Parkinson’s Disease in any remaining dopaminergic cells could be minimized. (14)
There is a modification that could be included in this array of AS-binders that would be useful not only for research, but for diagnostics and therapeutics. If a fluorescent tag was added to the aptamer, it could show specifically in what areas of the neural tissue the AS monomer and Lewy bodies are forming and provide earlier diagnosis of Parkinson’s Disease.(4) For even earlier detection, an aptamer could be developed to detect the presence of the intermediate conformation.(1) This type of fluorescently-tagged aptamer could be just as useful in determining the steps along the pathway from normal conformation to toxic aggregation formation.(4,13) Figure 4, below shows the process and usefulness of developing a florescent tagged aptamer.
Figure 4: this figure describes pictorially how a visibly tagged aptamer could function, although there are some risks involved in the process of probe addition. (4)
The grand finale of this aptamer could occur in conjunction with ubiquitin, a protein that labels a protein, often a defective or old one, for destruction by the cell proteosome. This is a normal part of the “housekeeping” functions that a cell must perform in order to remain efficient.(5,12) When an AS-binding aptamer is found, a ubiquitin-like peptide could be integrated onto the aptamer to help the cell become its own medicine. By delivering the signal necessary for protein destruction to occur to the correct location, the aptamer may be able to induce the proteosome to destroy the toxic form of AS, thus ridding the cell of its Lewy body. Figure 4, below is a diagram that shares in more detail how ubiquitin interacts with the proteosome to induce degradation.
Figure 4: a diagram explaining how ubiquitin is integral in the interaction of the proteosome with the protein that is meant to be destroyed. (5)
These aptamers are exciting in their potential for major downstream effects, however before any of those in vivo applications can be implemented, the basic aptamers that bind to the wild type and mutated forms of the AS protein must be painstakingly recovered from the vast nucleic acid pool. AS-binding aptamers have been found by other teams, so it is possible that this aptamer could really be useful if the proper conditions are met and the rounds of SELEX are properly enacted. (8) Although there is already a DNA aptamer that has been identified, it is always integral to scientific research that results are constantly reproduced and improved upon in order to validate previous findings.
Experimental Design, Methods, and Materials:
Filter-based SELEX was deemed appropriate for selecting against AS based on the fact that the AS was suspected of being resuspended in TRIS, rendering biotinylation ineffective; the AS available at the start of the project was from an unknown vendor (though available for reorder from a number of vendors). Although the nitrocellulose filters generally require a protein greater than 15 kDa in weight, the filters usually have a negative charge. (10) AS has a pI of 4.6, meaning that in pH environments near or below this value, the protein will accrue more positive charges on its surface. The more positive the protein, the more likely it is to be bound to the negatively charged protein. The selection buffer used was MES (MW 195.2) at pH 5.6 in order to induce more positive charge on the AS protein, allowing the 14.4kDa AS protein to be better retained on the filter than if the filter-selection was performed at physiological pH. The working concentration of salts is crucial to the proper folding of proteins and nucleic acids; the working concentrations of NaCl and MgCl2 were 150mM and 5mM, respectively. Other papers suggested the importance of Ca2+ in determining the folding of AS, this variable was disregarded for simplicity. (6)
Filter SELEX is useful because the nitrocellulose has pores that are too small to allow the passage of RNA-protein complex yet large enough to allow the passage of unbound RNA, allowing the separation of bound and unbound species. The flow-through and eluants obtained after each of the two binding reactions was ethanol precipitated in order to isolate the RNA. The elutions contained the RNA most interesting to the project, this was the RNA that showed affinity to AS. The precipitated RNA was resuspended in 10uL of diH2O and then reverse transcribed so that ssDNA was now present. The ssDNA derived from the eluted filter underwent a large scale PCR so that the effective pool size was increased. This new dsDNA was transcribed in order to convert the DNA back to ssRNA. The RNA was then isolated from the transcription reaction using a denaturing dye in conjunction with a PAGE gel. The RNA was extracted from the gel using the crash soak method and subsequently ethanol precipitated and quantified. This made the RNA available for use as the starting pool for the next round of selection. (10)
Two rounds of selection were performed using the method described above and the arbitrarily selected R50 RNA pool. For the first, an R50 RNA: AS protein ratio of 400pmol:300pmol was used. For the second the R50 RNA: AS protein ratio was 150pmol:120pmol. Both binding reactions used the MES selection buffer and were allowed to incubate for 30 minutes; the first round incubated at 37C and the second at 25C.
The monomer was the easiest to procure and was the first (and thus far, only) AS protein formation to be selected against. In order to increase the binding specificity of this aptamer, negative selections will need to be performed in order to eliminate background RNA sequences that exhibit affinity for the nitrocellulose filter. (10) Also, the potential AS monomer aptamers will need to be screened against other conformations of AS in order to increase specificity in this regard.
Budget:
At the start of the project, the AS was available in the lab but was from an unknown vendor. AS is available for reorder from rPeptide; 0.5ng of AS costs $300 and would allow for 86.5 rounds of selection at $3.47 apiece in addition to any costs added by any new equipment, etc. The catalog number is S-1001-1 and can be ordered by calling 678-753-0747.
Results and Discussion:
The first observable results for Round 1 came with the cycle course gel. Samples were taken from the reverse transcription reactions of the first and third flow-through (W1 and W3) as well as the elution. During the 72C extension step of PCR, 5uL aliquots of each of the samples were removed from the PCR reaction mix. This step allows the determination of the optimal number of cycles of PCR in relation to pool concentration after selection has occurred. By observing the image of Gel 1, below, it was determined that 11 cycles of PCR would provide a strong amplification of the eluted pool without over amplification. The bands of the gel may appear distorted, this is due to imperfections/lumps in the gel as it solidified, a human error; the streak running through the bottom half of the gel is a scratch on the imaging bed.
Gel 1: Round 1 cycle course gel. This shows that 11 cycles of PCR is sufficient for amplifying R1 RNA.
The next observable data came from the PAGE gel in which the binding species of RNA were separated from the transcription reaction components. The shadow band of RNA observed in the PAGE, rendered in Gel 2, below, was quite small, though dark. The RNA band was cut out of the gel and eluted through 3 washes using the crash-soak method and an ethanol precipitation.
RNA band
denaturing dye
Gel 2: Round 1 PAGE gel. RNA band was small, yet of condensed appearance.
The Nanodrop spectroscopy revealed that the concentration of RNA indeed was low; the round one RNA yield was 5.3uM, which is not enough to start round 2. I performed three more washes of crash-soak and an ethanol precipitation in order to attempt to extract more RNA out of the gel to add to my final sample of RNA. This increased the concentration of round one RNA to 6uM. This was still an extremely low yield. A check on the large scale PCR reaction was run in order to verify that template was indeed present during the transcription reaction. Gel 3, below, is an exhibition of the lsPCR check.
Gel 3: the large-scale PCR check exhibits a well-defined band; there was template provided for transcription. (Ladder is not shown because it was too dilute.)
With a defined band in the PAGE and a successful lsPCR, the only potential causes of the low RNA yield were failed RNA polymerase for the transcription or RNAse contamination. However, in spite of all this, there was still RNA present and round two could be started using the low concentration round one RNA pool using extreme caution and conversely low concentrations of AS protein. The RNA: protein ratio was lowered to 150pmol:120pmol; this amount of RNA constituted of the entire round one yield, so it was a risky pursuit. The first confirmation of whether or not the second round of selection was successful was with the second cycle course gel, gel 4, below. This gel indicates that the low concentration of RNA did not impede the usual binding process and indicates that 9 cycles of PCR are sufficient in order to amplify the second round bound species.
Gel 4: Round 2 cycle course gel indicates success in spite of low round 1 yield. 9 rounds show optimal amplification. (Only eluted binding species run through PCR in order to conserve materials.)
Overall Problems Encountered:
The most obstructive challenge faced with this project was trying to find an effective way to immobilize the AS protein. Thinking at first that the protein was too small, and therefore ineligible, for filter-based SELEX, biotinylation was attempted. However, the buffer that the protein was resuspended in was a mystery as no information was left by the previous AS user as to the details of this protein’s storage. Because of the possibility that the protein was suspended in TRIS, all of the “biotinylated” AS had to be discarded; TRIS compound reacts with biotinylate in the same way that the amino acid lysine does, this could have prevented a majority of the biotinylate from ever reacting with the AS. Without biotinylation, the only other option was filter-based SELEX, which seemed risky as AS was small enough to potentially pass right through the filter pores. This problem was resolved by buffering the selection reaction at a pH of 5.6, near the pI of AS (4.6) in order to make the protein “stick” to the filter for electrochemical reasons as opposed to mechanical reasons. The process of elimination in deciding which method of SELEX to use took several weeks to overcome yet paid off when one and a half successful rounds of selection were easily procured.
Conclusion and Future Work:
The focus of this semester-long project was to identify (or begin to identify) and aptamer that showed affinity for the AS protein that is assigned responsibility for the onset of Parkinson ’s disease. The AS monomer aptamer could have the potential to be a diagnostic and research tool when tagged with florescent compounds and could also be a therapeutic if the binding of the aptamer inhibited the association of one AS protein monomer with another. The one and a half rounds of selection performed in working towards this goal are outlined in Table 1, below.
Table 1: specifics of each round for R50 RNA selection against AS
Future work could include continuing to hone in on the RNA aptamer for the AS monomer and adding the tags to what is found to adapt the aptamer’s function. Once the AS monomer aptamer is found and studied, it would be a useful therapeutic tool to isolate an AS aptamer that binds to the Lewy Body aggregate or the oligomer formation. The AS LB aptamer could be tagged with ubiquitin peptides to aid in the natural destruction of the LB or of the pore-like oligomer.
Student Story:
Though I am not entirely sure of what I will be doing in the next five or ten years, being a part of the FRI has opened up an option for my future by showing me what it is like to perform biological research and the different types of research that are out there. Regardless of whether or not I end up researching aptamer s in the future or if I even end up doing research at all, my time here in the Aptamer Stream was very enriching to my college experience. I am thrilled that I have been placed in the Undergraduate Rotation Program, because now, after two semesters of performing research alongside my schoolwork, I can’t imagine myself not saying “I have to go to lab”; working in the lab has truly become a major part of my academic experience here at UT
I have taken away so much from this process even though my selection is still only in the first few phases. Not only have I developed a greater understanding for Parkinson’s Disease and aptamers, but I have also learned about the triumphs and tribulations of research and how to problem solve through unforeseen issues with a project. I have also discovered things about myself, my preferences as a scholar, and what I would like to consider for a career path. Through designing my experiment and outlining the parameters for the SELEX reactions, I now understand the creativity that scientific research requires. By analyzing solutions to frustrating issues with getting my project started, I was challenged to think outside the box. Through my preliminary research about Parkinson’s Disease and alpha-Synuclein, I experienced the excitement and gratification that comes from knowing that the work I will be doing both now and in the future could have a real impact on people who may know nothing about science but so desperately need its innovations. Before becoming involved in the FRI and beginning my individual research project I was unsure of my capability and zeal for research, but now that I have become a part of the research community at my university I am realizing what an exciting, relevant, difficult, and flexible field biological research can be.


References:
1) Paleek, Emil; Ostatná, Veronika; Masaík, Michal; Bertoncini, Carlos; and Jovin, Thomas, Analyst, 2008, 133, 76; DOI: 10.1039/b712812f.
2) Wong, Kondi, Armed Forces Institute of Pathology; 2004 .
3) doi: 10.1096/fj.03-0338rev; April 1, 2004; The FASEB Journal; vol. 18; no. 6 617-626.
4) Jhaveri et.al. 2000b .

5) Hershko, A; Ciechanover,A; and Rose, I; 2004. .

6) Sandal, M; Valle, F; Tessari, I; Mammi, S; Bergantino, E; Musiani, F; Brucale, M; Bubacco, L; Samorì, B; PLoS biology ; Volume: 6 ; ISSN: 1545-7885; 2008 Jan.

7) Bartels, T; Choi, J; and Selko, D; Nature ; Volume:477, Pages:107–110 (01 September 2011).

8) Tsukakoshi K, Harada R, Sode K, Ikebukuro K. Biotechnol Lett; 32(5):643-8. Epub 2010 Jan 29.“Screening of DNA aptamer which binds to alpha-synuclein.”

9) Aging and Longevity Information “Parkinson’s Disease Genetic Facotrs: Hereditary Risk Causes” < http://aginglongevity.com/aging-news/parkinsons-disease-genetic-factors-hereditary-risk> ; 4 Dec 2010.

10) adapted from Aptamer 2011 Stream Protocols, B.Hall.

11) Hoyer W, Antony T, Cherny D, Heim G, Jovin TM, Subramaniam V.“Dependence of alpha-synuclein aggregate morphology on solution conditions”. J Mol Biol. 2002 Sep 13;322(2):383-93
12) King, Michael W, PhD ; “Secreted and Membrane-Associated Proteins”
, Aug 2011.

13) Cookson, Mark R; Annu. Rev. Biochem. Jan 2005. “THE BIOCHEMISTRY OF PARKINSON’S DISEASE”; Cell Biology Section, Laboratory of Neurogenetics, National Institute on Aging
14) Winner, et. al “in vivo demonstration that a-synuclein oligomers are toxic” Jan 2011, Neuroscience.

RNA Aptamer Selection against Bcl-2 to Promote Apoptosis in Cancer Cells

Jessica Beardsley
November 30, 2011
Fall 2011
R50 Pool, RNA, Bcl-2

Abstract
B-cell lymphoma 2 (Bcl-2) is an integral membrane protein found on the outer membrane of mitochondria, the intermembrane of endoplasmic reticulum and the nuclear envelop of most mammals (Yang et al. 1997).  Bcl-2 takes part in the complex apoptosis signaling pathway by preventing cell death without promoting cell proliferation (Chao and Korsmeyer 1998).  Bcl-2 regulates apoptosis by inhibiting c-Myc or p53 activated Bax/Bid proteins, which increase mitochondrial permeability and ultimately result in cell death (Yang et al. 1997).  Cancer cells often have high amounts of Bcl-2 due to an over-expressed BCL-2 gene, a proto-oncogene that can become activated into an oncogene (Gross 2001).  An abundance of Bcl-2 contributes to tumor initiation, progression, metastasis, and treatment resistance (Fernandez et al. 2002, Oltersdorf et al. 2005).
Bcl-2 specific inhibitors- including drugs such as Genasense- have been developed by researchers to promote apoptosis in cancerous cells with high levels of Bcl-2 ("CancerQuest | Oncogenes: Bcl-2" 2011).  In one study, a small molecule labeled YC137 was discovered and used to inhibit the anti-apoptic protein in breast cancer cells.  This was the first Bcl-2 inhibitor that was able to selectively kill cancer cells that over-expressed or relied on the protein for survival, but had no effect on the majority of primary cells.  Some cells did manage to develop resistance against YC137 by becoming less dependent on Bcl-2 for survival and decreasing Bcl-2 levels.  But these resistant breast cancer cells did become more sensitive to chemotherapy (Real et al. 2004).

Specific Aim 1: Selection of RNA aptamers against over-expressed Bcl-2 in cancer cells.

 Using a high affinity and specific binding RNA aptamer would be an ideal approach to studying the potentially therapeutic effects of Bcl-2 inhibitors on malignant tumor cells.  Prohibiting Bcl-2’s intervention of the cell death pathway will likely stimulate cancerous cells with high concentrations of the protein to undergo cell apoptosis.  A potential problem is that successful aptamers, unlike YC137, might bind to Bcl-2 in both cancerous and normal cells, encouraging apoptosis in important, primary cells.  But the possibility of finding a Bcl-2 aptamer could have a positive impact on the lives of those battling cancer by aiding in mutated cell death and allowing chemotherapy, radiotherapy, and hormone treatments to be more successful (Kimball 2011, Oltersdorf et al. 2005).  

Figure 1. The figure above is simplified version of the p53 cell apoptosis pathway, including specific aim one.  If Bcl-2 is inhibited, cancerous cells avoid survival and complete apoptosis.  There are several independent signal transduction pathways (caused by different stimuli) leading to cell death that include Bcl-2.  Adapted from “Nonsmall Cell Lung Cancer (2011).”

50 ug of recombinant, human Bcl-2 protein with a GST tag can be bought from the SignalChem.  The catalog number is H00006531-P01 and the company can be reached at 909-839-7620.  It is optimal to store the protein in 50 mM Tris-HCl buffer at a pH of around 7.5 at -70˚C for up to a year after the shipping date.

Here is the link to my old project proposal over DAT.
Here is the link to Progress Report 1.
Here is the link to my Final Manuscript over Bcl-2.

Submitting the Final Manuscript

Hey guys, I just asked Gwen the exact specifics of submitting the final manuscript and she thought it would be a good idea to share it via the blog. So basically, make sure you turn in a physical copy of the final manuscript, with the old, marked up version attached. Also, update your original blog post with a link to the new and final manuscript.

-Umar

No artifact in the N50 pool.

This is the R1 ccPCR for my target protein H1N1 Hemagglutinin and I have found nothing amplified in the NTC. And as a side note, the 100 bp ladders turned out to be very faint and I'm not the only person whose had really faint ladders.


HIV-1 Gag p24 First Progress Report--Camille Alilaen

Camille Alilaen
October 18, 2011
Fall 2011
Pool N34, HIV-1 Gag p24


Abstract and Proposal Link: http://aptamerstream.blogspot.com/2011/08/aptamer-selection-against-hiv-1-gag-p24.html

Progress, Results and Discussion:
            In the week following the completion of the second practice round, the RNA selection process began against the HIV-1 Gag p24 protein. The conditions selected were tailored for the protein itself, and will become more restricted in order to select for the best binding aptamers. Because the protein was tagged with His, nickel-NTA beads were used to incubate the RNA with the protein. This incubation lasted for 25 minutes and was kept at 37*C for its duration, in order to mimic body temperature. Three washes using one volume (100 uL) was used to wash the loose or non-binding RNA from the beads, and the buffer used was Tris at pH 7.3.
            After ethanol precipitation and reverse transcription were performed on the reaction, cycle course was done on the resulting DNA. After withdrawing 5 uL from the E1, W3, and W0 reactions every 6th, 9th, 12th, 15th, and 20th cycle, ethidium bromide was added to each of the 15 tubes. The reactions run for 35 minutes in TBE buffer at 110 V in a 3.8% agarose gel. It was determined that the optimal cycle for running large scale PCR without overamplifying the DNA was 10 cycles, as seen on Figure 1 below.


 Figure 1: PCR gel for R1. The 3.8% agarose gel was run at 110 V for about 35 minutes in TBE buffer. Samples were taken starting at cycle 6 until cycle 15 in 3 cycle increments, then at cycle 20.
            A no template control was made for the cycle course PCR, however, it was not added in with the cycle course samples due to human error. Therefore, it was run the next day by itself in another 3.8% agarose gel for 30 minutes at 105 V in TBE buffer. No bands appeared, therefore, all reagents were free of contaminants (see Figure 2). Large scale PCR was also performed on 6 tubes of 100 uL of DNA for 10 cycles. These reactions were then ethanol precipitated, and transcription was performed on the result.


Figure 2: The no template control was run in a 3.8% agarose gel in TBE buffer at 105 V for 30 minutes alongside the ladder. No bands appeared, and the small dot that appeared was assumed to be caused by human error while taking the picture.

Problems Encountered:
            There were no problems with working with the protein during target immobilization and incubation, and binding and selection as well as ethanol precipitation and reverse transcription went smoothly. However, when the cycle course gel was run, it was noted that an unusual amount of bands appeared in W3. Although this result is not unheard of, it is still undesirable as it shows that there are many loose binders. In addition to this, during large scale PCR it was noticed that instead of 600 uL of reagents, there were about 500 uL after PCR. This change in volume could be due to evaporation or human error (i.e not adding a reagent, which could cause failure while running the PAGE gel).

Additional Work:
            When the lab used up all the 3.8% agarose gel, I helped Austin to prepare more, which was a great learning experience in case no mentors are present and the agarose is needed. I also helped him to aliquot 4 uM of dNTP’s when we ran out of stock.


Conclusion and Future Work:
            Since research on HIV-1 Gag p24 has begun, most of a round of selection has been completed. Cycle course was successful, even though there were more bands in W3 than desirable. The no template control was clear, and all that remains to complete is the PAGE gel and elution of RNA. Over the next weeks I plan to complete this round and about three or four more others, prior to the next progress report.


P.S Gwen sorry for posting so late!!

R50 Selection Against CD105/Endoglin - Progress Report #1 (10/18/11)


Progress, Results and Discussion

Dry protein CD105/Endoglin(1600pmol) was resuspended in PBS buffer to achieve desired working concentration of around 20uM. Aliquots consisted of 3X200pmol (10ul) and 10X100pmol (5ul). Binding reaction (100ul) was made with 400pmol R50 pool and 200pmol target protein. Filter-based selection was designated optimum partioning method for size of protein (61.2kDa).

Millipore nitrocellulose membrane filter (0.45um) was pre-washed with 100ul 1X PBS SELEX buffer and five total washes executed after addition of binding reaction. RNA was eluted with 400ul elution buffer (5M urea and 25mM EDTA buffer). Ethanol Precipitation of RNA was performed with 1/10th volume 3M NaOAc, 3ul glycoblue, 2.5 volumes 100% ethanol. Reverse transcription achieved with following conditions: incubate at 42°C for 50 minutes and heat inactivate the enzyme at 70°C for 15 minutes. The correct R50 T-7 Forward primer and R50 reverse primer were used to prepare the 100ul PCR reaction with 2ul ssDNA from reverse transcription which was performed on W0, W5, and E1. Reactions were cycled for 20 cycles under following conditions: initial at 94°C for 2 minutes, denature at 92°C for 45 seconds, anneal at 54°C for 45 seconds, elongate at 72°C for 60 seconds. Five ul aliquots were extracted during end of cycles as shown in Figure 1 in orange.


As seen in figure 1, 11 cycles was chosen to be performed during large scale PCR. Ethanol precipitation of PCR yielded dsDNA for subsequent transcription reaction. Five ul precipitated dsDNA was transcribed using the Ampliscribe Transcription Kit from Epicentre and incubated at 37°C for 16 hours. RNA was purified with 8% Polyacrylamide Gel Electrophoresis, 10% APS and TEMED. Denaturing bromophenol blue (2X) dye was used in a 1X TE TBE rig. Visualization of RNA shadow in gel through UV illuminator was very small and faint. Crush soak elution and precipitation was continued with the ssDNA PAGE band. Nanodrop specing revealed 78ng/ul or a concentration of 2.33uM. This concentration was too low to continue on to the next round and steps to address this issue are discussed in following section.



Problems Encountered

Initially, 400pmol of target protein was to be added to 400pmol (20ul) pool to begin selection. However the pool mixture RNA was not denatured before protein was added and the process had to be repeated. With only ~1400pmol left of protein, 200pmol (10ul) was used in consideration of minimal remaining amount. While adding protein (W0), no resistance against filter was observed unlike in pre-wash. The filter was then assumed to contain a hole, but selection was continued and stringency decrease noted. A no-template negative control failed to be performed, but will be in future gels.

Concentration of RNA after one round deemed insufficient to proceed. Possible reasons for low amounts were mainly attributed to small RNA shadow observed in PAGE. Failure during transcription posed as leading cause for low detection. Therefore an agarose gel was run to validate this hypothesis as seen in figure 2.




As seen in Figure 2, the dsDNA band was found to be around equal length to the 100bp. Therefore the problem occurred after large scale PCR and transcription needed to be duplicated with DNA from PCR. Also, the smudging around what should be a clearly defined band was noted and could indicate possible over amplification. Transcription was then repeated with careful precaution to use of reagents and alteration of Ampliscribe Kit then that of the previous used. It was then realized that 0.1M DTT had been used instead of 100mM thus explaining reason for low amplification during first transcription reaction. This new transcription reaction that used 100mM DTT was incubated for 16 hours. When placed in incubator no precipitate or evidence of a nucleotide crashing out was evident however when retrieved the next morning clear evidence of white precipitant was observed. DNA template was still removed and preparation of PAGE in hopes of a still successful transcription reaction.


Conclusion and Future Work

As of October 18th, 2011 one round of selection has been executed using the R50 pool against Endoglin/CD105. However, this round was not completely successful due to insufficient RNA concentration amount of 2.33uM. Error in amount of DTT was concluded to be reason for transcription failure and correct amounts were used in new reaction. PAGE on second transcription reaction will hopefully reveal successful concentrations of RNA to continue on to second round where a negative selection will also be performed. In the next reporting period I hope to accomplish a couple more rounds of selection.


Final Manuscript: https://docs.google.com/document/d/1DRo2m--Hr9V4lYq8MnboE8rvMq-Y5Hyni1zN0zEZ2GU/edit


KRAS R1 Progress Report - Ryan Lannan

Ryan Lannan

October 18, 2011

N58, RNA, KRAS

Progress Report 1

Background information on and justification for a KRAS selection can be found here as an abstract and proposal. The KRAS selection will be performed using the “toggle” technique. This technique involves the use of two different selection methods in order to remove background binders to the different binding mediums. Due to KRAS’s size (50 kDa) a filter-based selection is possible. And as for the other selection method, the His tag attached to KRAS allows for a bead-based selection using nickel beads. The selection will alternate between filter and bead-based selections, starting with a filter selection. The first round of filter-based selection was performed against KRAS with the following conditions:

Round One Conditions

Nucleic Acid/Protein Ratio: 400-pmol/400-pmol

Buffer: 1X PBS SELEX with MgCl2 salts (pH 7.4)

Incubation Temperature/Time: 37 degrees C for 40 minutes

Wash Frequency and Volume: Three 100 uL washes

Progress, Results and Discussion

To begin the selection, an RNA binding reaction was prepared with 400 pmol of N58 R0 pool diluted by 1X PBS SELEX buffer. The reaction was then denatured by heating it to 65 degrees C for five minutes. 400 pmol of KRAS was added to the reaction and incubated for 40 minutes at 37 degrees C to allow both nucleic acids and protein to reach a stable equilibrium at physiological temperatures. The nitrocellulose filter was set up and washed three times using 1X PBS SELEX buffer. The 100 uL binding reaction created earlier was then added to the filter and the liquid was pushed through using a syringe, hopefully leaving behind the target and any possible binders. Three 100 uL washes with 1X PBS SELEX buffer were then performed to remove any non-binders. After washing, an elution was performed on the filter using 200 uL Elution buffer (5M urea and 25mM EDTA). The elution reaction was then heated at 90-100 degrees C for five minutes. The elution buffer was then removed and another 200 uL of elution buffer was reapplied and the reaction was reheated. The combined 400 uL was then ran through ethanol precipitation to concentrate the nucleic acids. The pellet produced from ethanol precipitation was resuspended in 10 uL diH2O and an initial reverse transcription solution was performed with 7 uL of the RNA solution, 20 uM of N58 reverse primer and 50 uM dNTPs. This initial mix was incubated for five minutes at 65 degrees C, and allowed to cool. 1X First Strand Buffer, 10 mM Dtt and 1 uL SSII reverse transcriptase were added and the reaction was run using these steps: 42 degrees C for 50 minutes, 70 degrees C for 15 minutes and a cooling step.

To amplify the newly created ssDNA, a PCR reaction had to be performed. In order to determine the optimal number of cycles and troubleshoot possible selection problems, cycle course PCR was run before large-scale PCR. The following reaction was created for E1, 1X PCR buffer, 0.2 mM dNTP, 0.4 uM forward and reverse N58 primer, 2 uL ssDNA, and 0.8 uL Taq DNA polymerase. 5 uL was removed from this PCR reaction at each chosen cycle, and another aliquot was removed from a cycle without template at 18 cycles as a no-template control which came out negative (see Figure 1 below). An agarose gel was run with these 5 uL aliquots (Figure 1).


Looking at band intensity, it was determined that 12 was the optimal number of cycles for lsPCR (in a filter selection there are no other washes, cycle course gels on even rounds will be more informative as they utilize beads and have multiple washes). Large-scale PCR was ran on the remainder of the ssDNA, creating 6 PCR reactions identical to the one described for cycle course. After lsPCR, an ethanol precipitation was performed. The pellet created was resuspended in 20 uL of diH2O. A transcription reaction was then prepared with the following composition: 1X Ampliscribe Transcription Buffer, 10 mM DTT, 7.5 mM of each NTP, 5 uL of ds DNA from lsPCR and 2 uL of T7 enzyme. The reaction was incubated overnight at 37 degrees C. After transcription, a PAGE gel (represented very roughly by Figure 2) was ran to purify the RNA from the transcription components, which was successful (showing a distinct band). Ethanol precipitation was then performed, and the pellet resuspended in 30 uL 1X PBS SELEX buffer.

Figure 2 – KRAS R1, N58

Problems Encountered

During filter selection at the beginning of the round, a hissing noise was noted while washing the filter. This could indicate that a small tear had formed in the filter, causing liquid to flow through without passing through the filter. Seeing as the binding reaction had already been applied, I continued onwards, hoping that the tear was small enough to not cause a significant loss of my binding reaction.

Additional Work

Besides small tasks I have performed such as re-aliquotting protein and glycogen, or processing protein deliveries, I have started helping Oliver with his closed-MBP selection. He is currently cloning his rounds to determine sequences, and I have started to help him by regenerating his R9, R11 and R12 pools to dsDNA.

Conclusion and Future Work

I will continue to help Oliver with his selection, and will soon perform cloning on his (now) dsDNA pools. The concentration of my R1 gold was 1768.4 ng/uL. This is a good number quantity of RNA, but I am hoping to see a decrease in concentration next round indicating that my switching of selection methods has significantly decreased background binders. R2 has already been started with Nickel beads, and I hope to finish the round within the week and start the cloning procedure for Oliver’s selection.