What is the difference between adenine and guanine

This allows to follow the mechanism over time and to calculate thermodynamic and kinetic properties. So, the processes that involve the DNA and RNA nucleic acids are frequently studies at molecular level and they are object of many investigations using computational methods Watson and Crick, Solvation methods Cramer and Truhlar, ; Tomasi et al.

Classical molecular dynamic MD simulations Alder and Wainwright, are a useful method to study the processes at the molecular level, but now the solvent is considered as a discrete medium. The steered molecular dynamic SMD technique Izrailev et al.

Adenine and guanine are associated to form the adenine—thymine and guanine-cytosine base pairs. The most stable structures for the adenine base are the amine and imine forms, whereas in guanine there are the keto and enol tautomeric forms Figure 1.

Both bases have been studied in gas and solution phases. The interaction of adenine base with water and oxygen donor molecules has been the subject of studies, because this base can be converted into guanine base and can participate in spontaneous mutation which will be the subject of this work. Specifically, one water molecule attacks the carbon linked to amine group of adenine base to form hypoxanthine and ammonia molecules.

Then hipoxanthine oxidation occurs assisted by an oxygen donor molecule formic acid in this work to give a xanthine molecule. Finally, the NH 3 molecule released in the first process attacks by the carbonyl group new to give the guanine base. The hydrolytic deamination reaction mechanism of adenine has been theoretically investigated with the DFT method by Zhang et al. They found that the deamination may proceed in a stepwise mechanism.

The study shows that the deamination with one water molecule does not take place because of a higher barrier. However, it may be possible if several water molecules are considered, because one molecule can act as a catalyst and the others act as assistant molecules.

This is agreement with the experimental results. In other similar work, the adenine deamination was studied by Zhu and Meng by four different mechanisms using the DFT method. The activation barriers are high, and it is difficult for this process to happen with such high activation barriers.

Later, Zheng and Meng studied the hydrolytic deamination mechanism of adenine using several water-assistant molecules and the density functional method at the DFT method. When the first water molecule attack to adenine base a tetrahedral intermediate is formed. Then, two different intermediates were studied. In A-pathway, the second water molecule acts as a bridge to transfer the hydrogen atom.

In B-pathway, the second water molecule is not involved in the formation of the transition structure and only acts as a aqueous medium. Energy barriers of the two processes are Deamination of protonated adenine to produce hypoxanthine has also been studied by Wang and Meng in acid medium and assisted with a water molecule, using the DFT method. Because adenine could be protonated on different nitrogen atoms, four pathways were investigated.

The pathway where the nitrogen closer to the NH 2 amine group is protonated presents the lowest energy barrier of The first step and rate-determining is the nucleophilic attack of water molecule to form a tetrahedral structure.

The results show that adenine deamination under acidic medium is more favorable than in neutral conditions. Alrawashdeh et al. The effect of aqueous solvent was computed using the PCM model. The oxidation mechanism of hypoxanthine has been investigated by Tafasse This theoretical study aimed to predict the transition state structure in the mechanism of oxidation with xanthine oxidase XO enzyme. The process was exothermic and with a high energy barrier. The process was assisted by a Zn-metalloenzyme and two residues Glutamate 55 and Aspartate The proposed mechanism is initiated by a proton transfer from a Zn-bound water molecule to protonate Asp The protonated Asp can perform the proton transfer to the guanine, facilitating the nucleophilic attack on the nitrogenous base.

The residue Glu55 then perform the proton transfer from the Zn-hydroxide to the amino group of the intermediate. Optimized geometries of all species were determined at different levels of theory and the Gibbs free energies were also determined. The formalism used in this work has been the same as the one used in previous studies by our research group, so for more detailed information it can be consulted in the work of cytosine to thymine conversion Tolosa et al.

Here we will only mention the methods used and some specific considerations of the simulated system. The initial geometry of the Adenine-Water-Formic complex denoted hereafter as A-W-F system , with the formic acid and water reactants about 2. Long-range electrostatic interactions were considered by the Ewald summation Ewald, and the Jarzynski's equality Jarzynski, was used to calculate Gibbs energy differences between two equilibrium states.

The activation and reaction energies were determined through the evolution of the process, as has been shown in several works Tolosa et al. The initial structure of the A-W-F system is shown in Figure 3. The initial configuration between water and formic acid assistant molecules and adenine base is that where these molecules were oriented and positioned to look for the ideal situation to start the first step of the mechanism. The conversion mechanism considered in this work is described in three processes.

The intermediates and transition structures are schematized in Figure 4 and their Cartesian coordinates, obtained from SMD simulations, are given in Table S2. In the first process, the hydrolytic deamination of adenine to hypoxanthine is performed.

The second process is the oxidation of hypoxanthine to xanthine, and the third is the amination of xanthine to guanine base. All of these three processes are described by stepwise mechanisms. In the deamination process, the H 2 O molecule attacks the C5 atom in a plane perpendicular to the adenine base and forms an I1 intermediate with an OH hydroxyl group linked to this carbon.

The other hydrogen of the water molecule is transferred to the amine nitrogen N7 A-pathway or to the imine nitrogen N10 B-pathway. In the next step, an intramolecular proton transfer from the OH group to the N10 nitrogen A-pathway or to the N7 B-pathway is performed. This elongates the C5-N7 bond before it ruptures and forms the hypoxanthine and ammonia molecules I2 system.

In the oxidation process, the formic acid attacks in the same plane to the hypoxanthine molecule by the C11 carbon atom. In the amination process, the ammonia molecule formed in the deamination process attacks perpendicular to the base by C11 carbon atom of the xanthine with the proton transfer to the O18 oxygen from the N7 nitrogen D-pathway or N13 nitrogen E-pathway to form the I5 intermediate. In a second step, the proton transfer from N13 nitrogen to the hydroxyl oxygen D-pathway or N7 nitrogen E-pathway is performed, releasing a water molecule once the CO18 bond is broken I6 system.

Table 3. When the process follows the B-pathway, the first step is less endergonic with respect to the A-pathway but not so the second step. Although both processes have very similar energy profiles, the most thermodynamically favorable is the A-pathway, because the intramolecular proton transfer observed is more exergonic when it is performed on the N10 imine nitrogen A2-step rather than on the N7 amine nitrogen B2-step.

In the second step, the TS2A structure is formed when the H23 atom is 1. The stationary state structures reveals that in the TS3 state, the formic acid and hypoxanthine molecules are in perpendicular planes and that the O18 oxygen is located 1. In the I3 intermediate, these distances were 1. The structure of TS4 shows a four-membered ring where the H12 and O18 atoms involved in the transfers are at 1.

The nucleophilic attack of the ammonia molecule on the C11 atom and the protonation of O18 oxygen 5D-step present a barrier lower that the ones that describe the proton transfer from N13 to O18 oxygen and the break of the OC11 bond 6D-step. Hence, the E-pathway is considered to be the most thermodynamically favorable.

Namely, the second step of this process where the nucleophilic attack of the NH 3 molecule releases a water molecule 6E-step needs less energy than the intramolecular proton transfer 6D-step. The N7 nitrogen of the ammonia molecule approaches at 1.

The H22 hydrogen transferred from the ammonia to the xanthine molecules is at 1. In the second step of this amination process, a TS6 structure is obtained where the H20 hydrogen transferred is at 1. When adenine is a constituent of DNA, with the help of a covalent bond, it is linked to deoxyribose sugar and is called an adenine residue. Purine metabolism including adenine has the metabolic end product known as uric acid.

The kidney, liver, and other internal organs have a high amount of purine. They are also present but in moderate amounts in seafood, beans, meat, mushrooms, and cauliflower. As it is clear that adenine is a vital component of nucleic acids, but it is also a major constituent of ATP. Adenosine triphosphate. In which adenosine is attached with three phosphate groups. ATP is a molecule with energy -rich and is mainly used in biological reactions such as cellular metabolism. Adenine forms many tautomers they are generally compounds that are often considered equivalent and can be rapidly interconverted.

But in isolated conditions such as in an inert gas matrix , tautomer is mainly found in 9H-adenine. W hen it comes to appearance, adenine is crystalline and range from white to light yellow. Among the main nucleobases, guanine is one of them. When it comes to pairing, guanine is paired in DNA with cytosine.

Guanosine is referred to as the guanine nucleoside. Guanine is also a derivate of purine and comprises a ring system of a fused pyrimidine-imidazole along with conjugated double bonds. MLA 8 , Miguel. Name required. Email required. Please note: comment moderation is enabled and may delay your comment. There is no need to resubmit your comment. Notify me of followup comments via e-mail. Written by : Miguel. User assumes all risk of use, damage, or injury. You agree that we have no liability for any damages.

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