Ribonucleic acid (RNA) plays an important role in the synthesis of proteins, as well as in genetic transcription and translation. Therefore, the secondary structure of RNA is of special interest. The primary structure of RNA is a nucleotide triplet sequence that points to the relative location of the RNA within the protein. The latter refers to the formation of a secondary structure with a recognizable three-dimensional shape. The determination of the secondary structure of RNA is a difficult task.
3D NMR
This method is one of the oldest and most common techniques used to determine the secondary structure of RNA. The intensity of the resulting signal is proportional to the amount of complexity formed between the RNA and the paramagnetic molecules, and the distance between these signals indicates the three-dimensional structure of the RNA.
Electrophoresis
However, it has a few limitations. The first is that it is often not quantitative enough. This means that it does not give a precise number for the amount of RNA or other substances in the sample. The other major problem with this method is that it is often too time-consuming.
Denaturing gradient gel electrophoresis
In this method, the RNA is first separated into fragments of different sizes on a gel. Furthermore, the technique does not give any information about the RNA structure. It only determines the fragmentation pattern, which does not necessarily correspond to the actual three-dimensional structure of the RNA.
Affinity purification
This method is based on the fact that different RNA molecules have different affinities from other molecules. This means that they have different molecular weights and can therefore be separated according to their size. In general, the smaller the RNA fragment, the less molecular weight it has. This means that the affinity purification of RNA can help determine the structure of the molecule.
Unfortunately, affinity purification of RNA is only capable of separating single-stranded RNA fragments. Therefore, the data obtained will only indicate the stability of the single-stranded fragments.
Mass spectrometry
The major advantage of this technique is that it is quantitative and gives accurate data about the relative amounts of RNA in the sample. It can also be used to determine the stability of RNA, as well as the ability of the RNA to form intramolecular and intermolecular bonds.
The major disadvantage of this technique is that it is very complex and therefore only a few laboratories are equipped to perform it. Furthermore, the data obtained is very complicated and requires special expertise to interpret.
Other methods Summary
The secondary structure of RNA is a very important topic in bioinformatics. It has been shown to affect the function of RNA as well as its cellular abundance. Therefore, it is important to understand the different techniques used to determine the structure of this molecule. In this article, we have discussed several of these techniques, as well as their advantages and disadvantages. We hope that this guide will help you to better identify RNA, as well as interpret the data obtained from your experiments.
Quadrupole Mass Spectrometry
Quadrupole mass spectrometers are the most common type of mass spectrometer. The quadrupole is a device with several rods or cones. The quadrupole mass spectrometer is a mass spectrometer that uses a quadrupole as its ion source.
Linear Ion Trap Mass Spectrometry
A linear ion trap mass spectrometer is similar to a quadrupole mass spectrometer, but with a few key differences. The most notable difference is that a linear ion trap mass spectrometer does not have a vacuum between the poles of the ion source and the detector. This means that ions travel in only one direction. The other difference is that a linear ion trap mass spectrometer does not have a deflection chamber.
Time-of-Flight Mass Spectrometry
Time-of-flight mass spectrometers (TOF-MS) are able to separate ions based on their mass to charge ratio as well as by charge. This means that time-of-flight mass spectrometers are able to separate ions based on their charge.
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR-MS) can do even more than time-of-flight mass spectrometers. They are able to separate ions based on their charge, as well as by their ionization degree (the amount of charge they have). This means that FT-ICR-MS can distinguish between ions with the same charge but different amounts of ionization.
Other Types of Mass Spectrometry
Other types of mass spectrometry are ion traps and field ionization. The ions then travel through a magnetic field to neutralize the charge. A field ionization mass spectrometer works differently. It uses an electric field to ionize gases into charged particles.
Summary
Mass spectrometry is a method of analyzing very large amounts of substances at once. There are many different types of mass spectrometry. The most common is called quadrupole mass spectrometry. Other types of mass spectrometry include linear ion traps, time-of-flight mass spectrometry, Fourier transform ion cyclotron resonance mass spectrometry, and more. Each type of mass spectrometry works in a slightly different way. This article explains the different types of mass spectrometry, including their pros and cons, how they are different from each other, and examples of each.