Jahnu:

You may convert the 3' amine of the oligonucleotide into COOH first using Succinic anhydride or maliec anhydride.

While there are a few ways to do this, first you need to consider the functional groups in your peptide. If you have lys, asp or glu side chains you cannot use carbodiimides to link to a carboxyl terminated oligo.

In fact, even just a lysine side chain is going to cause issues with any approach to conjugation, as the lysine will compete with the n-terminal amine. However, if the reaction pH is around 7 or less, you may be able to achieve some degree of selectivity for the reaction at the N terminus because the side chain lys will largely be protonated.

Personally, I would put a cys on the n-terminus during peptide synthesis and react with a maleimide derivatised oligo. Obviously, this requires the peptide to have no other cys residues. If you already have the peptide and oligo, hopefully the side chains are benign.

Nick is right, if you have the exact sequence of the peptide, people can give better answer.

Thank you Guobing Xiang and Nick Gee . At this point I cannot disclose the sequence. But it does not or rather cannot have Cys in the sequence. I am looking for other protocols like converting the C terminus to an aldehyde and promoting conjugation through an imine-forming reaction. The problem here is the reaction needs an acidic pH (~5) which is detrimental to the oligo.

Maybe you should put some click groups on. It’s going to be more expensive, but at least you can use mild conditions.

To conjugate two amines, I suggest using a linker with carboxylic acid groups on each end. Bis-PEG-acid linkers or similar linear linkers would be a natural first choice and are widely commercially available. Aspartic, glutamic, or homo-glutamic acids would be another option, which would also be cheap and easy to derivatise, and possess an additional amine handle; likewise, succinic and glutaric acid would be exceedingly inexpensive. Length, physicochemical properties (eg, solubility), and functionality (eg, amine handle) will depend on the specific project goals.

With a dicarboxylic acid linker, you can protect one end as an ester, activate the other end carboxylic acid with a classic reagent (eg, HATU, PFP TFA), then conjugate one amine. Conjugating the oligonucleotide first would likely mean fewer concerns about orthogonality, but again this depends on your goals and specific substrate. Next, you can deprotect the ester using something mild (eg, LiOH) then activate and conjugate the second amine group. There are synthetic tricks to producing the mono-ester in the first step, or you can buy most dicarboxylic already derivatised to the mono-ester.

Other strategies may be possible (eg, derivatising one primary amine to an isocyanate and forming a urea linkage between the two amines), but since you can't share more about the sequences it's difficult to meaningfully speculate further about these solutions.

My friend published a paper that isn't relevant to your synthetic needs, but does cover some alternative strategies in the introduction and characterisation techniques that may be helpful otherwise:

Article A Platform for Site‐Specific DNA‐Antibody Bioconjugation by ...

Thanks Grant.. that was a great explanation. I will look into it.