Nucleic Acids - Science topic

I was wondering whether there are any chemical or enzymatic methods to remove a single nucleotide from the end of DNA. Analogous to Edman degradation but instead of a terminal amino acid it removes a single nucleotide.

It could be either 3 or 5 prime end

It is fine if the nucleotide gets chemically modified, the ejected nucleotide is not of any concern.

The use of exonuclease might remove more than one base which can be a problem.

Can I predict the interaction between nucleic acid structure (eg. G-quadruplex) and protein structure (eg. G-quadruplex helicase) based on their 3D sturcture (*PBD files)? Wether the "AutoDock" can handle the question?

Dear all,

I would like to know if any of you have experience in dephosphorylation of proteins using Shrimp Alkaline Phosphatase. I am currently buying lambda phosphatase, but since I had SAP in the lab I tried it and had nice results. But... What does these results actually mean?? That's the real question here!

SAP is supposed to dephosphorylate nucleic acids, but I am not sure if it also dephosphorylates proteins, and if it does, in which aminoacids (Tyr, Thr, Ser).

I'm working with a Ras-related protein, which could be bound to GDP or GTP, SAP could be dephosphorylating these molecules, but as far as I understand, in a reducing western blot they should be released from the protein, am I right?

Thanks all!

P.D.: the results are from a PhosTag gel.

Dear all,

I am now working on in vitro transcription but struggled with low yield. One of my friends told me that the quality of plasmid, especially the proportion of supercoiled plasmids, has great to do with the IVT efficiency[1][2]. Thus I am now working on improving the quality of my plasmid template. However, I ran electrophoresis several times but the bands seemed weird to me:

(1) There is always a smear above the main band of the plasmid. Although I tried to purify twice with the column, the smear remains. Is that contamination from genome DNA? After linearization, the smear disappeared.

(2) The size of the circular plasmid is always larger than the largest ladder (10kb). Much larger than it should be.

(3) The linearized DNA always has the right size (single cut). However the circular plasmids are larger than the size of linearized DNA. As far as I know, the supercoiled DNA should run faster on the electrophoresis gel. Is that because the plasmids were nicked?

Could anyone explain my result? I am using GeneJET Plasmid Miniprep Kit (K0502)from Thermo Fischer Scientific. How can I improve my quality of my plasmid? Or how to improve the proportion of plasmid?

Thanks a lot for your attention.

Best.

[1]S. Hirose, Y. Suzuki, In vitro transcription of eukaryotic genes is affected differently by the degree of DNA supercoiling., Proc. Natl. Acad. Sci. U.S.A.

85 (3) 718-722,

https://doi.org/10.1073/pnas.85.3.718 (1988).

[2Piao X, Tang Y, Li X, et al. Supercoiled DNA percentage: A key in-process control of linear DNA template for mRNA drug substance manufacturing. Mol Ther Nucleic Acids. 2024;35(2):102223. Published 2024 May 20. doi:10.1016/j.omtn.2024.102223]

G-quadruplex structures of nucleic acids have been a focus of study for anticancer or other diseases therapy for long time. Nonetheless, there is still no G4-targeting drugs available for clinical use. Now, researchers have developed a lot of fundamental knowledge on G4s and many G4-targeting small-molecules. What we are actually lacking and what we need in order to get into another milestone in the future?

I would like to run the FAM labelled oligo DNA on a agarose gel and detect it with Biorad Chemidoc MP, it has "Nucleic acid gels" option, "Protein Gels" and "Blots" Fluorescein channel. Which should I choose as my gel is not stained with anything but only the DNA is labelled with FAM, I wonder if I should still choose nucleic acid gels option.

molecular biology and molecular genetics laboratories. It is a reagent designed for the removal of ribonucleases (RNases) and other nucleic acid contaminants, such as RNA, that can degrade nucleic acid samples, such as DNA.

Hi

Has anyone got any experience of using the above kit without vacuum extraction? I was talking to someone last week who was adamant they have done this and without any impact on DNA yield. Worried it seems too good to be true, but wondered if anyone was doing it and had troubleshooted this method?

FOI - i am vacuumless!

Thanks

I'm purifying the phi29 DNApolymerase, but the protein activity is always low and it's accompanied by very serious nucleic acid contamination. I once purified a batch of highly active protein, but now can not repeat it, the method and operation is almost no difference.

Hello everyone,

I'm in the initial stages of conducting a study involving the ddPCR (Bio-Rad QX200, QX600) and I ran into some problems involving recovery % calculations using direct quantification. I'm spiking a nucleic acid that essentially ends up being detected (and amplified) as a 100bp ssDNA template, and I get a concentration reading from the ddPCR of about 800 copies/uL. My issue is that by calculation, with 2.5pM final spiking concentration, I should get about 3 x 10^7 copies per 20 uL. This is of course not reflected in the results and above the actual detection capabilities of the instrument. Further dilutions down to 500 fM still show this issue. In most of the papers I've read, initial copies spiked in are determined empirically. Am I missing something in my calculations or is determining copy number by weight before spiking the only way? Thanks in advance!

pI of my protein is 4.1. I am using Ni coumn to purify it . Which binding buffers will be good?

Even the pI is low can it still bind to nucleic acid? How do I know?

Hello everyone,

I am looking for any dye that can be used to determine the flow of liquid in a tube. Therefore, it should not affect tissues and cells or bind to nucleic acids or proteins. Additionally, it should be easy to wash off.

Any suggestions would be greatly appreciated.

Cheers

I want to covert RNA aptamer to DNA aptamer.

I try this process by Discovery studio.

This software includes the "Build and Edit Nucleic Acid tool".

I could modify the sugar easily.

However, I edit the 5H to methyl in U to convert T with manually process. It is very time-consuming.

Do you have a good idea to convert U to T easily?

Dear virologists; What is the PCR technique used in virology to detect viral nucleic acids? The steps involved.

I'd also like to know, since some viruses have a single strand of DNA and RNA, how does amplification work in this case?

Kind regards

Hi Everybody,

I am planning on working with packaging and envelope plasmids (Pax2 and VSVG) and cell lines engineered to express Cas9. The biosafety committee in our institution is expecting experimental evidence of the lentivirus used in our experiment. Briefly, I was asked to test the supernatant of my cells to be sure that there are no viral particles, or better, evidence of non replicative potential. Does anyone know the best approach for providing this evidence. I was planning on using the supernatant of my cells (1 day post infection) and extract the nucleic acids. However, what is the best downstream application I could use to show the virus is non replicative and safe to use for injecting infected cells into murine models?

I tried to use RNAase to study protein and I have tried to digest protein to get nucleic acid also. The problem is yield is low and RNA is fragmented. I am trying to purify both of them in functional form. Can anyone please guide me with it? Thanks a lot.

I have red poultry mite samples which have been stored in ethanol. Now I need to perform RNA and DNA extraction followed by shotgun metagenomic sequencing. I would like to know if there is a way to successfully extract the nucleic acids so that I have no inhibition or problems during the sequencing run. You opinion and experience is highly appreciated.

I routinely perform pulldowns in order to purify a protein of interest, and afterwards I digest linear nucleic acids attached to my bait protein using micrococcal nuclease (MNase). So far I have performed digestions after eluting my protein of interest from the resin, with satisfactory results.

I now plan to perform a in-resin MNase digestions, without previous elution of my target protein. Has anyone used MNase in-resin? I wonder how much the digestion efficiency could be affected by the resin itself, which can be critical in order to obtain reproducible results. Any tips regarding how to optimize the reaction?

Thanks.

Dear all,

I would like to kindly ask to help me answer on this question.

As far as I understand, for secondary structure it would be:

- canonical base pairing

while for tertiary structure it would be:

- base stacking

- non canonical base pairing

But it seems that the list is incomplete.

Could you tell me please what I am missing?

Thank you for any input,

Best regards,

Aliaksei

I want to see if Nucleic acid (NA) is still bound to my Protein sample after anion exchange. Should I mix Cyber Safe (fluorescent nucleic acid stain) together with protein and SDS loading dye in the same sample before loading it on the SDS PAGE gel, or should I first dilute Cyber Safe in water to visualize nucleic acids after gel electrophoresis and then subsequently stain the gel with Coomassie Brilliant Blue (CBB) to visualize proteins for a more accurate result? (As I am unable to distinguish protein and DNA from IEX peaks and Absorbance at 260nm 280nm 220nm)

Thanks

I used Biotek Epoch 2 nanoplate reader for quantification of my nucleic acid samples. I do not understand what does the above mentioned statement signify.

Hi ResearchGate community,

I am interested in using chemical flocculation to concentrate water samples for eDNA analysis. This is basically to avoid having to filter water.

I have come across interesting papers on this subject, however, people use chemical flocculation for the precipitation of entire cells (bacterial communities). I am wondering if this method can also work when we are dealing with environmental samples (cells + mitochondria + free floating extracellular DNA + mucous + fecal matter, etc). I would appreciate if anyone with experience with this could comment. I am interested in knowing what is the % recovery of this method.

Thanks

Hello. I am learning about different types of cell transfection methods, and I can't find out why protocols and descriptions only explain DNA transfection with calcium phosphate and not RNA or other nucleic acids. What is the reason for this? Thanks.

Hello all,

I am preparing a diagnostic kit for the detection of viral nucleic acid and testing them using Taqman probes. I am getting initial rise of the curves by around 1000 RFU and then suddenly dropping to zero to give rise to a foxtail-like appearance and thereafter the curves started rising again. This happens in low as well as in high copy number viral nucleic acid samples and in internal control curves as well. How to solve this problem as it is affecting the quantitative values interpretation also. Please help in solving it. I have attached a screenshot of one of the curves obtained.

I have heard from ThermoFisher that the removal of RNAlater from fixed cells followed by a resuspension in PBS is recommended to improve RNA extraction yields.

In the past I have always replaced freezing/fixative with PBS prior to nucleic acid extractions, but could somebody explain to me exactly why the salts in these solution can interfere with extractions?

Thanks all!

I used a Kit for purify a gel band of pBAD vector (digested), and after the elution of the sample using firstly the binding buffer and afterwards the elution buffer, but missing the step of the adding the washing buffer in between.

Do you think it is still possible to "wash" the flow-through I still have for a correct purification using the washing buffer I didn't use?

I am thinking about doing this since I don't have more sample left, and the result of the measurements of the current sample in the NanoDrop have still a high ratio of impurities (not Nucleic Acid), and I can't trust the resulting concentration.

Thank you in beforehand for your time,

Javier

P.S : I attach a picture of the results I have obtained so far measuring the current sample.

I am trying to coarse-grain nucleic acid chain usng martini tutorial. Whicle doing so ther is message which says "This is a beta of Martini-nucleotide and should NOT be used for production runs."

What does this means?

Can't we use RNA martini tutorial for proper MD simulations?

Calrimatric LAMP technique i am not getting result on 65C temperature in water bath but i am not sure nucleic acid extracted or not becoue using bromo cresol purple pH indicator dye no colour change in postive contyrol?

Hi,

Except humic acid existence in soil samples, are there other reasons to dilute DNA or cDNA concentrations of soil samples prior to performing qPCR assay? And after dilution and qPCR assay, how we can calculate a gene/transcript expression? To clarify what I meant, for example, if we dilute DNA concentration by 5:1, after getting the raw number from qPCR machine, should we multiply the received number by 5 to reach exact gene expression copy number?

Appreciate

Mehrdad

We have #picodrop in our lab for nucleic acid measurement but for the last few months, it is giving a problem. Thus, we are thinking to replace it with #Nanodrop

Looking for suggestions and reviews...........

Hi

My setup consists of protein-RNA complex. I am able to coarse grain protein structure in my complex by simply following RBCG tutorials in VMD. I am unable to coarse grain RNA chain (nucleic acid). I need to coarse-grained parameters compatible to NAMD.

Anyone please help me if there is any workaround of doing RNA coarse-graining.

Regards

-Manoj

Hi there.

My protein was found to have a high nucleic acid peak when it was further purified by exclusion chromatography. How can I remove the nucleic acids when purifying my protein?

Is there any kit available for labeling the nucleic acid ( or analogue of nucleic acid ) with fluorescence for the new beginners conveniently ?

I worked on ligand -Nucleic acid (DNA) interaction for this I have done UV-Visible Spectroscopy of my synthetic chemical compound (Ligand) with the DNA. I did titration of the ligand with increasing concentration of DNA. Data shows (in attachment) the highest absorbance/Peak around 463 nm or 413 nm in the case of ligand only (A-0). In contrast, when the DNA was titrated with increasing concentration from A1 to A5, the intensity of peat at 463 nm and 413 nm decreased while the peak increased around 260 nm. However, no absorbing peak was found at 260 nm in the case of ligand only. What could be the significance of this blue shift and what could be the possibility of decreasing peak intensity at 463 and 413 nm? Does this shift indicate the ligand-DNA interaction?

In another experiment, I titrated different conformation of DNA with the same compound in which only the blue shift was observed, however, no change was found at 463 and 413 nm. Please explain this difference also. Does the ligand-DNA interaction happen in this condition also?

in all experiments, the baseline was subtracted and prior to the addition of DNA in increasing concentration I added a corresponding buffer to the ligand also and peak overlap to A-0 (ligand only peak)

Please find the attached graph for your kind reference.

I have a pdb file where I have substituted hydrogens on nucleic acidswith substituents (e.g. nitrogen base---phenol) using Avogadro. I saved the pdb file and then loaded it into Autodock Tools to prepare the ligand. All works fine, and I saved the resulting .pdbqt file via Ligand->output->save pdbqt.

However when I load the ligand again I find out the substituents are not bonded to the nucleic acid anymore, e.g. the phenols are suspended in space with no bond to the nitrogen base. That information seems to be lost in the pdbqt file. How could this be solved?

My Lab is working on nucleic acids extraction from different pathogens, we have observed dramatic differences in the results of the viral load when we use viral kit in comparison to the universal one. What is mostly the difference between them? Are the buffers completely different? Is there a specific chemical in one or all of the buffers that could make such difference?

Thanks in Advance.

Hi,

I wonder if anyone knows how to use sample release reagent from Sansure Biotech ?

Nucleic acid extraction using magnetic beads is showing protein contamination. How can i limit or remove the protein contamination from extraction???

Long story short, I need to degrade 30ug of RNA and i need to do it at 4C. I want to use only as much RNAse A as necessary.

So if performing the reaction at 4C, how long of incubation time and how much RNAse A would i need to degrade 30ug of RNA?

For example, would 1ug of RNAse A(20ug/ml conc.) for 15min at 4C be enough?

What DNA or RNA binding dyes absorb strongly at 220nm? I want to sensitively detect nucleic acids using a 220 nm detector.

I know that DNA adsorption to plastic container surfaces (like polypropylene) can result in loss of sample, but I wanted to know specifically how much. I know this depends on several factors, like time, temperature, formulation, etc.. I was hoping I could get some ballpark numbers.

Can anyone point me to a paper or in the direction of where to look up the actual quantity of nucleic acid (ssDNA and dsDNA in particular) adsorption to different plastic polymers and/or silica types?

The best I found was this reference: Gaillard, Claire, and François Strauss. "Avoiding adsorption of DNA to polypropylene tubes and denaturation of short DNA fragments." Technical Tips Online 3.1 (1998): 63-65.

I am using GROMACS to simulate the molecular dynamics of protein ligand, and intend to use amber14sb force field file.But I only have amber14sb_ parmbsc1 this file.Because I know that this force field package is mainly used for nucleic acid simulation. I don't know whether this package includes protein force field and patch or only patch?Can I use it on protein？

After adding resuspension buffer and lysis buffer to the cell pellet, the next step is the addition of neutralisation buffer which requires immediate mixing. The expected outcome is the formation of large, fluffy and white precipitate. Slight delay in mixing results in the formation of small floating precipitate which remains suspended despite doubling of centrifugation duration, resulting in the decrease of A260:A280 eventually.

What are the remedies to solve this issue and improve the DNA purity? The DNA is plasmid DNA. Thank you.

Im working on a project and need to make sure this rough draft of a protocol is valid. Is this a good outline, am I missing any steps?

Im basing this protocol off this paper:

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae. Reider Apel A, d'Espaux L, Wehrs M, Sachs D, Li RA, Tong GJ, Garber M, Nnadi O, Zhuang W, Hillson NJ, Keasling JD, Mukhopadhyay A. Nucleic Acids Research. 2016 November 28; DOI: 10.1093/nar/gkw1023. PubMed PMID: 27899650.

I have lysed the bacterial cell with methanol and then take the supernatant after centrifugation. After that, I run my lysate through a nucleic acid purification column to separate nucleic acid from the metabolite. Now how can I separate polar and non polar metabolites from this extract?

Hi everyone,

I have a question regarding RNA sample purity. I am currently extracting RNA from primary cultured periodontal cells using Qiagen Mini kit and quantify the RNA concentration using Nanodrop. In the past I used to get 260/280 ratios of around 2. For the last few samples, I have been getting higher 260/280 ratios for example:

Sample 1: Nucleic acid concentration= 333.9 ng/ul, 260 Abs=8.34, 280 Abs= 0.97, 260/280= 8.58, 260/230= -111.75

Sample 2: Nucleic acid concentration= 378.2 ng/ul, 260 Abs= 9.5, 280 Abs= 1.5, 260/280= 6.38, 260/230= 5.31

My question is how can I purify the samples?

Thank you.

Hi everyone,

Does anyone has experience with the extraction of nucleic acid (both RNA and DNA)?

Do you recommend any kit/method with a good recovery?

Regards,

Loreta

Component: Pure water, Bsm buffer, Bsm polymerase, primer, MgCl2, dNTP, DNA Salmonella

Heat 60 Celcius 1h and 80 Celcius inactivation 10min

Sometimes the results from gel electrophoresis appeared DNA bands but sometimes less band intensity. What happen? Not suitable primer or expired chemical?

When run a LAMP reaction, sometimes false positive appeared in agarose gel electrophoresis. What are factors to create contaminations to false positives? What contaminations do in LAMP?

I am to simulate adenosine phosphartes using charmm27 ff. I tried with the force field files available in http://mackerell.umaryland.edu/charmm_ff.shtml for nucleic acids, but is showing different errors.

Can anyone help me find out the correct topologies and parameters for adenosine phosphates or provide guidance as to how to generate them.

I would really appreciate your help.

I am interested in reading about the effects of physiological stress (including near-fatal heat) on the DNA and/or RNA of procaryotes. More specifically about aberration on the structure of nucleic acids (e.g. fragmentation) that can be expelled/released from their cells.

Any references?

Many thanks in advance.

Orange G is also a dye which is used in nucleic acid electrophoretic separation can other dyes like bromophenol blue can also be used? if not why? and which dye can be used in place of orange G.

I have attached below the literature for reference

Does anyone know the chemical composition of the following commercial nucleic acid preservatives:

1. DNA/RNA Shield Reagent from Zymo Research

2. RNA later from Thermo Fisher

Hello, does anyone know of ways to extract Nucleic acids from cell culture lysates without using commercial kits such as the Qiagen blood and Tissue kit?

We try to isolate viral RNA and DNA from bat oral, rectal, stool samples. We tried Zymo Quick-DNA/RNA MagBead and we got minus concentrations. Then we increased the bead-binding time and decreased the elution volume. Again, we could not get good results. Is there anyone who have used this kit before and can you please give us advice about how to increase our yield? Thanks!

TarFisDock is a web-based tool for automating the procedure of searching for small molecule–protein interactions over a large repertoire of protein structures. It offers PDTD (potential drug target database), a target database containing 698 protein structures covering 15 therapeutic areas and a reverse ligand–protein docking program.

It was accessible via http://www.dddc.ac.cn/tarfisdock/ not until I had checked the website few days back. What really happened to such a promising database?

From the screenshot attached, you can see that it is permanently unavailable.

WHAT ARE OTHER PROTEIN TARGET WEB SERVERS AVAILABLE?

Reference: Li H, Gao Z, Kang L, Zhang H, Yang K, Yu K, Luo X, Zhu W, Chen K, Shen J, Wang X, Jiang H. TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W219-24. doi: 10.1093/nar/gkl114. PMID: 16844997; PMCID: PMC1538869.

I have synthesized carbon dots that exhibit fluorescent properties, that are further coated with PEG through EDC. I want to separate them through gel electrophoresis based on the number of PEG attachment. Is the gel electrophoresis for Carbondots any different than gel electrophoresis for nucleic acids ?

Very interested in seeing how people design sequences for nucleic acids such as primers, siRNAs, and sgRNAs other than just looking up previous studies. I'm very interested in learning how to design my own sequences.

We known that Lipofectamine2000 consists of a 3:1 mixture of DOSPA and DOPE, which complexes with negatively charged nucleic acid molecules to allow them to overcome the electrostatic repulsion of the cell membrane. What are the chemical consists of Lipofectamine3000?

What is better to detect nucleic acid integrity.. Bioanalyzer 2100 or Tapestation 4150? in relation quality and price

I am running nucleic acid samples on a 20% Acrylamide, 1X TTE, 7.5M Urea gel overnight and lately I have been getting this weird inconsistency in the gel that seems to be forming sometime in the early morning hours of the gel run. (see attached images)

I am running the gel at a constant voltage of 170v.

Has anyone seen anything like this before and have (hopefully) overcome it? At this point I am thinking it is a problem with the power supply I am using, as it is very old.

Thank you for any input!

Josh

Does anyone buy oligos anywhere but IDT? They have messed up a couple of my orders in the last few months and I am in the market for a new source.

We have tried Sigma in the past, but weren't super happy with the quality.

I have recorded 2D 1H-1H NOESY for RNA. It's a 64 nucleotides RNA and assigning manually in SPARKY is tough. Any software for automated NOE peak assignments

I am working with an automated nucleic acids system based on magnetic particles, but in some of my assays, at the end, when the nucleic acids are on the elution buffer it also contains residual magnetic beads. I would like to have some clues about why it is happening, and get to prevent it.

Regards

I have a MBP fusion protein that is not binding to amylose beads. I have already tried adding glucose to the media (although I did not add it to my starter culture) and I am not using detergents or salts in my buffer. Has anyone found methods to increase binding to the beads? I am wondering if my protein is forming some large complex with nucleic acids (it is known to bind nucleic acids) and other proteins and the MBP tag is obscured.

Hi all,

I’m planning to tag polyarginine(9 consecutive arginin) on the N term of target protein and wondering if it doesn’t impair the transcription or translation level. I found out that polyarginine is mostly tagged on the C term and wonder if tagging on the N term will cause any problem. I think one putative issue might be the degradation of polyarginine by ompT protease, but I’m going to express the protein in BL21(DE3) which lacks theompT protease so I think it would be okay.

I‘m tagging polyarginine to promote electrostatic based nucleic acid binding and given the structure of the protein, it has to be tagged on the N term. Is there any alternatives to polyarginine that can non-specifically bind to nucleic acids and not impair the transcription and translation level? I also looked up the N term of DNA-binding proteins form starved cells(DPS) which contains several lysine residue but I’m not sure if it has strong affinity to nucleic acid.

I would appreciate it if you could give any of your thoughts about the question and thank you in advance:)

Ethanol is commonly used for RNA, DNA and protein isolation. What is the percentage of ethanol to precipitate Nucleic acid and proteins respectively?

Dear researchers

Is it possible to control the amplification by Nanodrop instead of performing an electrophoresis gel? For example, if we know the concentration of DNA added in the Mix (1ng/20ul of the Mix) and taking into account the number of primers and DNTP used, is it possible to know with a nucleic acid assay system (Nanodrop) if the matrix has been amplified or not?

Hey! ;) I was wondering if anyone could help me out on how I could quantify and check the purity of some samples containing inactivated virus particles.

The virus has been inactivated with beta-propiolactone (BPL) so that the nucleic acids have been affected. Therefore, I am not sure a qPCR could work. I do not need to quantify them very precisely but I'd need an estimation so that I could use them for a selection assay. Does anyone have a suggestion of how could I do it? Thank you very much!

Among the plethora of biological modifications of proteins and nucleic acids, why is the phosphorylation process so universally abundant?

That is, compared to a variety of other possible molecular groups, is there a specific reason for biological systems to adopt phosphorus groups to the extent they do?

Is this just because of the abundance and metabolic economy of this group, or are there other considerations involved (e.g., bond energetics, physical properties, solubility etc.)

Or is this question itself misplaced? Please clarify!

Thank you :)

next protocol and how to proceed

I characterized functional groups of EPS using FTIR. Goups of sugars and proteins (e.g., -OH, amide, -COOH) as well as phosphate group of nucleic acid were readily detected. However, peaks of nucleic acid bases were not detected, why?

I want to do standard curves for qPCR with usutu nucleic acid (RNA virus). I've got some nucleic acid stock so do I need to extract the RNA from the stock or can I just do dilutions of the stock I have and use that as the template for the qPCR?

Lab work is quite new to me so I appreciate this is a basic question.

Thank you!

If a protein sample is contaminated with nucleic acid, will these DNA/RNA run on the gel and show bands? (gradient gel, 4-20%, MW-marker: 14.4-116 kDa)

Once I have oligo-GNP conjugates, I need to use them as sensor for my target nucleic acid. Before doing that I need to confirm whether the oligo probe (conjugated to GNP) hybridizes well with my target. What method can I use to test this? Will DLS or FTIR work?

I want to do an electrophoresis of RNA from baker's yeast. However, our lab only has a vertical electrophoresis, while usually electrophoresis of nucleic acid (RNA or DNA) use horizontal electrophoresis with agarose gel. Is it possible to do electrophoresis of RNA in vertical electrophoresis using acrylamide gel or agarose? and how will be the quality compared with the horizontal electrophoresis?

I saw in previous literature the two major species of RNAA seen in the gels have size about 2200 and 3900 nucleotides.

Thank you.

I am doing nucleic acid extraction (manual silica magnetic bead-based) from the serum sample. After the extraction, I have taken the OD 260/280 in UV spec. There is no protein contamination. But the purity of DNA is very low (OD 260: 0.014). So, I tried the two different wash buffers to remove the salt in that solution {Wash Buffer 1 (25 mM Tris-HCl, 1.8 M GuHCl, 75% EtOH, pH 6.6 and Wash Buffer 2 (10 mM Tris-HCl, 100 mM NaCl, 80% EtOH, pH 6.6}. Finally washed with 70% ethanol. But I cannot able to get the purified DNA. Please, anyone, suggest to me a good wash buffer for salt removal and purified DNA.

I'm looking to try and extract nucleic acid from FTA cards, has anyone had trizol extraction to work well?

Thanks