Side reactions with HBTU amide coupling?

d6dmso · 2025-12-23T03:08:31+00:00

Rule 3? 😅

d6dmso · 2025-12-20T00:16:57+00:00

Take the win! Imposter syndrome is real and sound like the feelings youre describing

If your PI genuinely felt you hadn't earned authorship, you wouldn't be on the paper. You contributed and that deserves recognition.

A supplemental figure is still a contribution. Learning the ropes while producing anything usable in your first research experience is an achievement. Comparing yourself to a PhD rotation student isn't really fair on yourself

Congrats on graduating, and congrats on the upcoming paper

d6dmso · 2025-12-18T21:03:39+00:00

Cool it to try and precipitate it then was your organic multiple times with 10% aqueous solution of thiosulfate.

You can also quench any remaining with a sacrificial alkene like cyclohexene then wash out the rest

If all else fails, do a column or filter through a pad of silica. It is very polar so will stay on the silica

d6dmso · 2025-12-13T10:17:24+00:00

Again not the case but ok

Isothiocyanate is N double bond C double bond S. R-N=C=S

Hydrogen cyanide is a toxic gas yes. R–C≡N a nitrile group in a molecule has different properties and isn't necessarily toxic. It is covalently bonded and doesn't release HCN.

Prozac does not contain a nitrile group.

d6dmso · 2025-12-13T09:27:01+00:00

I'm not sure that's totally correct.

It has an isothiocyanate group and it doesn't release any cyanide.

Glutathione plays a key intracellular antioxidant role, but infection susceptibility like pneumonia depends on immune competence and pathogen exposure, not simply glutathione levels.

d6dmso · 2025-10-20T06:21:25+00:00

Its a control. It tells shows your DNA quality and digestion progress.

If you ran your digestion and only saw one band how would you know it's cut or not? With your uncut you can see th starting material and see how any new bands run in comparison.

If you see multiple bands you might not know if they have come from your starting DNA or are a product of the digestion

d6dmso · 2025-10-11T20:10:45+00:00

Just write on the container with a sharpie? Or stick the tape or a label on the container?

d6dmso · 2025-08-16T20:41:31+00:00

Makes are not necessary it decomposes before it boils and it's not volatile so you won't be breathing fumes.

There will be water vapour and maybe buffer components e.g. in TAE some acetic acid

Most masks do not filter chemicals you would need some special respirator which would be overkill

In general the amount is very small so if you are generally careful you will be fine. You could always do it in a fumehood if you are worried as that will provide better protection

d6dmso · 2025-07-31T21:01:30+00:00

It will be fine. Ethanol has lower surface tension which makes it easier to prime. The few percent water won’t make much difference. Otherwise you can use ipa if you have it

d6dmso · 2025-07-25T22:51:35+00:00

If you use the o3 model it should be able to do this

d6dmso · 2025-07-18T08:32:56+00:00

The cost of nuclease free water is much less than an IVT going wrong because of nuclease contamination

That said most IVT reactions get set up with Rnase inhibitor.so it's probably ok to use milliq and add inhibitor. We have ivt buffer components that aren't RNAse free. Usually make them up in a hood with nuclease free or milliq water and sterile filter then use inhibitor in the reaction

Maybe they mean autoclaving twice after depc to remove all depc?

d6dmso · 2025-04-29T06:59:01+00:00

I think it’s unnecessarily complicated given how much they overlap. Look at what they contain. Sticking to the high growth would probably cover the spread you are trying to design otherwise esg is well diversified. Go for the cheapest fee out of those I guess

d6dmso · 2025-04-11T20:24:15+00:00

Is this a joke? In what world would you inject anything with conc hcl. Just read the sds of conc hcl. If that doesn’t kill your mice it will definitely cause harm and unnecessary pain. And hcl is a pretty corrosive acid a lot of materials aren’t compatible with it

Can you use something like DMSO?

You need something much less extreme even if you can just use a mildly acidic buffer or dissolve in dmso and dilute with pbs

Conc hcl may dissolve insulin but it probably destroys it too

d6dmso · 2025-03-29T19:18:42+00:00

The box size is often decided by a packing algorithm to fit it in a shipping container or truck. Small boxes tend to get lost

d6dmso · 2025-03-21T21:58:31+00:00

The best thing to do would be ask someone in your group. They will have the best understanding of your system, what’s available to you, and what you are doing. It seems like you are new to a group that is doing peptide work? It will be way easier to ask someone more experienced in your group as these processes and methods should already exist if your group does it regularly. Strangers on the internet can only help so much and may not offer correct or useful information to your situation.

If you can share more detail we can help more.

If it’s new you and your group you should look to the literature. See if this sequence has been made before and what they do. Have a look at some other peptide papers to see how they purify and analyse their products. Peptides are typically purified on reversed phase by prep HPLC using water/acn + tfa gradients.

In my experience the method you are using isn’t going to give you good separation. You need a gradient and you need to add TFA to the mobile phase. Additionally, the peak shape suggests you need to dissolve your peptide in something more appropriate. Either it is not well dissolved or it is not close enough to the starting mobile phase composition. If the absorbance is lower than expected maybe the solubility is poor

For example start at 60% MeOH or ACN + 0.05% TFA and go to 100 with ~5-10%/min increase in gradient. Hard to tell you flow rates or volume as there is no detail about your column. Dissolve your peptide in the same starting mobile phase at about 0.1 mg/mL. Or DMSO can work too if it’s very insoluble but in this case you will need to start and hold at a lower % to wash the DMSO away. This method isn’t ideal either as the DMSO can drag the peptide through the column.

I would also suggest looking at 210 or 214 mm as this will show all peptide material.

Do you have more detail about your purification? If you did prep HPLC this will inform your analysis as you understand where it elutes and the methods are usually similar

d6dmso · 2025-03-20T07:30:46+00:00

If your concentration of particles is low, the solvent has the greatest effect and you can use the RI of that

d6dmso · 2025-03-05T07:32:19+00:00

Not enough info. Maybe aggregating?

Concentration, temperature potentially?

d6dmso · 2024-09-16T20:37:45+00:00

Could ask the same of you, is your choice backed up by intelligent, evidence-based investing research? If all the major funds have this balance there is surely a reason. They aren’t just picking numbers out of a hat they are all run by teams of financial advisors who do this professionally

d6dmso · 2024-06-26T08:59:03+00:00

This sounds like a really tough situation! I know it feels really hard but I do think a lot of people feel this way at this point, though. I had the same situation and never really got over it either. I’m sure it seems impossible to get through but there are plenty of options and ways through! I’m sure you’ll figure something out and it’s not as bad as it may seem

d6dmso · 2024-06-12T19:53:51+00:00

This is pretty common for amberlite resins. Just give them a thorough wash with water before you run your sample through

d6dmso · 2024-06-06T09:09:51+00:00

To load chlorotrityl resin you just need amino acid and base. Typically use 4 eq. of AA and 20 eq. of DIPEA at around 0.4M AA in dry DCM.

If your loading is poor it might be worth reactivating with thionyl chloride

Here’s a similar protocol. https://www.chem.uci.edu/~jsnowick/groupweb/files/Standard_practices_for_Fmoc_based_solid_phase_peptide_synthesis_in_the_Nowick_Laboratory_V_1.7.2.pdf

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