Oligonucleotide Puns

Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics.

What is the purpose?

Oligonucleotides, or oligos, are short single strands of synthetic DNA or RNA that serve as the starting point for many molecular biology and synthetic biology applications! From genetic testing to forensic research and next-generation sequencing, an oligo may very well be the starting point.

What is the size?

Oligonucleotides are small molecules 8–50 nucleotides in length that bind via Watson-Crick base pairing to enhance or repress the expression of target RNA.

Who was Rosalind Elsie Franklin?

Rosalind Franklin, in full Rosalind Elsie Franklin, (born July 25, 1920, London, England—died April 16, 1958, London), British scientist best known for her contributions to the discovery of the molecular structure of deoxyribonucleic acid (DNA), a constituent of chromosomes that serves to encode genetic information. Franklin also contributed new insight on the structure of viruses, helping to lay the foundation for the field of structural virology.

Franklin attended St. Paul’s Girls’ School before studying physical chemistry at Newnham College, University of Cambridge. After graduating in 1941, she received a fellowship to conduct research in physical chemistry at Cambridge. But the advance of World War II changed her course of action: not only did she serve as a London air raid warden, but in 1942 she gave up her fellowship in order to work for the British Coal Utilisation Research Association, where she investigated the physical chemistry of carbon and coal for the war effort. Nevertheless, she was able to use this research for her doctoral thesis, and in 1945 she received a doctorate from Cambridge. From 1947 to 1950 she worked with Jacques Méring at the State Chemical Laboratory in Paris, studying X-ray diffraction technology. That work led to her research on the structural changes caused by the formation of graphite in heated carbons—work that proved valuable for the coking industry.

In 1951 Franklin joined the Biophysical Laboratory at King’s College, London, as a research fellow. There she applied X-ray diffraction methods to the study of DNA. When she began her research at King’s College, very little was known about the chemical makeup or structure of DNA. However, she soon discovered the density of DNA and, more importantly, established that the molecule existed in a helical conformatio

We have to run gels on the degradation of some very short, single stranded (max. 16 bases, degradation products obv. shorter) oligonucleotides.

We have the thermofischer precast, denaturing PAGE gels here - and the separation seems not amazing, with blurry bands and often no separation.

The highest % gel fischer has is 20% for native and 15% for denaturing which has our oligos eluting very fast.

Anyone has experience/tips for that or a source for higher % gels ?

Hello All,

I am rusty with my biology and I'm wondering if someone can unpack this question I've been tasked with solving?

https://preview.redd.it/w1g0xij5w5m71.png?width=468&format=png&auto=webp&s=dfa8931dbc69076affe62d5932a95b7c49ff9d9a

Is this just asking what is the complimentary strand of DNA? or is it somehow referring to the RNA that would be formed. Both would obviously have different answers, one with Thymine and the other with Uracil in its place.

Is oligonucleotide just a certain type of nucleotide? and what doe they mean with antisense again?

Thanks!

Hello! I am working on some alternatives to radiation for an experiment to detect labeled oligonucleotides. I started off by using a biotin labeled primer and am trying to detect the labeled nucleotides in ssDNA by southern blot, transferring on to a membrane and using a HRP tagged streptavidin antibody. After the transfer is complete, the transferred bands weirdly disappear once immersed in blocking solution even after UV cross linking (I'm using non fat milk, not casein). Does anyone have experience working with this detection technique. Would appreciate any help! Thanks!

I ordered two ssDNA aptamers (30-mer and 80-mer), and much to my surprise, the results I am getting from them are identical. Per the literature, these aptamers have pretty different K_d values (like 150 nM versus 15 nM), and they should give very different results (LoD difference of ~10^6 nM). I can replicate the results of the 80-mer from literature, but I'm not getting anywhere near close to the 30-mer's expected results. The LoD is the same as the 80-mer.

I am wondering if the vendor just synthesized the 80-mer twice...

If I email the vendor, would they have anything in their QC data to indicate whether or not the oligos are indeed correct? (Input from anyone working in oligo synthesis appreciated!)

Alternatively, is there anyway I can check this in-house? We only have the equipment for agarose gels, not PAGE or CE, but I don't think I could separate oligos this short on an agarose gel (correct me if wrong!).

Update: Ran an agarose gel and saw two differently sized bands about where they should be. Also tried SYBR green on plate reader and got two different intensities for the same molarity. Looks like I just can’t replicate the published results! Thanks for the help guys!

Has anyone successfully done EDC/NHS coupling with amine-modified short oligonucleotides with carboxylic acid-modified magnetic beads? I am having no such luck and don't know what is going on. All I am getting is oligo adsorbing to the surface since I am doing control tests with only beads and oligo (no EDC/NHS) and measuring the same amount of "coupling". I am using MagnaBind carboxy beads. They state that they have ~4.8 nmol of carboxylic acid group per µL of solution. I am using using 4 µL (19.2 nmol) of beads and 2 nmol of amine oligo but only getting like 5% of the oligo simply "sticking" to the beads rather that coupling. I am at a total loss here and have absolutely no idea why this isn't working.

Linking life's molecules: Rapid and site‐selective oligonucleotide bioconjugation via bifunctional oxidative addition complexes (OACs) is reported. These bifunctional OACs react chemoselectively with amine‐modified oligonucleotides to generate isolable oligonucleotide OACs. Within minutes, the oligonucleotide OACs undergo a site‐selective C−S arylation reaction with a broad range of native thiol‐containing biomolecules.

Abstract

Organometallic reagents enable practical strategies for bioconjugation. Innovations in the design of water‐soluble ligands and the enhancement of reaction rates have allowed for chemoselective cross‐coupling reactions of peptides and proteins to be carried out in water. There are currently no organometallic‐based methods for oligonucleotide bioconjugation to other biomolecules. Here we report bifunctional palladium(II)‐oxidative addition complexes (OACs) as reagents for high‐yielding oligonucleotide bioconjugation reactions. These bifunctional OACs react chemoselectively with amine‐modified oligonucleotides to generate the first isolable, bench stable oligonucleotide‐palladium(II) OACs. These complexes undergo site‐selective C‐S arylation with a broad range of native thiol‐containing biomolecules at low micromolar concentrations in under one hour. This approach provided oligonucleotide‐peptide, oligonucleotide‐protein, oligonucleotide‐small molecule, and oligonucleotide‐oligonucleotide conjugates in >80 % yield and afforded conjugation of multiple copies of oligonucleotides onto a monoclonal antibody.

https://ift.tt/38RX8zw

The majority of driving forces causing DNA to be stable in double-stranded form are based on entropy like the driving forces stabilizing proteins right? So why would a small difference in bond strength due to one more H-bond (which doesn't even contribute that much to stabilization energy) have such a big influence on Tm when comparing GC and AT oligonucleotides?

Journal of the American Chemical SocietyDOI: 10.1021/jacs.0c12043

Laurent Knerr, Thazha P. Prakash, Richard Lee, William J. Drury III, Mehran Nikan, Wuxia Fu, Elaine Pirie, Leonardo De Maria, Eric Valeur, Ahlke Hayen, Maria Ölwegård-Halvarsson, Johan Broddefalk, Carina Ämmälä□, Michael E. Østergaard, Johan Meuller, Linda Sundström, Patrik Andersson, David Janzén, Rasmus Jansson-Löfmark, Punit P. Seth, and Shalini Andersson△

https://ift.tt/3dKx78I

Linking life's molecules: Rapid and site‐selective oligonucleotide bioconjugation via bifunctional oxidative addition complexes (OACs) is reported. These bifunctional OACs react chemoselectively with amine‐modified oligonucleotides to generate isolable oligonucleotide OACs. Within minutes, the oligonucleotide OACs undergo a site‐selective C−S arylation reaction with a broad range of native thiol‐containing biomolecules.

Abstract

Organometallic reagents enable practical strategies for bioconjugation. Innovations in the design of water‐soluble ligands and the enhancement of reaction rates have allowed for chemoselective cross‐coupling reactions of peptides and proteins to be carried out in water. There are currently no organometallic‐based methods for oligonucleotide bioconjugation to other biomolecules. Here we report bifunctional palladium(II)‐oxidative addition complexes (OACs) as reagents for high‐yielding oligonucleotide bioconjugation reactions. These bifunctional OACs react chemoselectively with amine‐modified oligonucleotides to generate the first isolable, bench stable oligonucleotide‐palladium(II) OACs. These complexes undergo site‐selective C‐S arylation with a broad range of native thiol‐containing biomolecules at low micromolar concentrations in under one hour. This approach provided oligonucleotide‐peptide, oligonucleotide‐protein, oligonucleotide‐small molecule, and oligonucleotide‐oligonucleotide conjugates in >80 % yield and afforded conjugation of multiple copies of oligonucleotides onto a monoclonal antibody.

https://ift.tt/38RX8zw