Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures

Somkuti, Judit; Molnár, Orsolya; Grád, Anna; Smeller, László

doi:10.3390/biology10111173

Cited by 4 publications

(10 citation statements)

References 65 publications

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“…The genome of the SARS-CoV-2 virus has also been analyzed from this point of view [ 149 ], and some of the predicted viral GQs were experimentally found [ 148 , 150 ]. In my previous papers I analyzed three GQ-forming sequences of the Hepatitis B virus [ 65 , 151 ], and genomic analysis suggested the possible GQ formation of these sequences [ 152 , 153 ]. Using FTIR and FRET measurements, I proved that all these three sequences (called HepB1, HepB2 and HepB3) form GQ structures.…”

Section: Pressure Effect On Some Biomoleculesmentioning

confidence: 99%

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

Smeller

2022

IJMS

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Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.

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Section: Pressure Effect On Some Biomoleculesmentioning

confidence: 99%

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

Smeller

2022

IJMS

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“…This means one must correct the pH shift caused by a pressure or temperature increase. The best way is to make a 3D fit for the obtained T m values, as it was performed by Somkuti et al [ 14 ]. They fitted the T m as the function of pressure and pH, and the ∂ T m /∂p| pH value was obtained from the fitted function.…”

Section: Experimental Methods To Study the Phase Transitions Of Nucle...mentioning

confidence: 99%

“…The pressure behavior of several GQ structures has been investigated [ 14 , 26 , 46 , 51 , 61 , 62 , 63 , 64 , 65 , 66 ]. The studied sequences are listed in Table 1 , while the main results are summarized in Table 2 .…”

Section: Gq and Pressurementioning

confidence: 99%

“…These oligos named HepB1-3 were investigated in our laboratory [ 13 , 14 ] (HepB1: GGC TGG GGC TTG GTC ATG GGC CAT CAG, HepB2: GGG AGT GGG AGC ATT CGG GCC AGG G HepB3: TTG GGT GGC TTT GGG GCA TGG AC). All three of the oligos were proven to be able to form GQ experimentally [ 13 , 14 ]. Their pressure behavior was investigated.…”

Section: Gq and Pressurementioning

confidence: 99%

“…G-quadruplexes are present in viral genomes in both DNA and RNA viruses, and they take part in the key steps of viral infection of the cell from replication to encapsidation [ 10 , 11 , 12 , 13 , 14 , 15 ]. This research was even further accelerated by the recent pandemic: the focus of the research turned to the genome of the SARS-CoV-2 virus [ 15 , 16 , 17 , 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

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Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures

Smeller

2023

IJMS

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Four-stranded folded structures, such as G-quadruplexes and i-motifs in the genome, have attracted a growing interest nowadays since they have been discovered in the telomere and in several oncogene promoter regions. Their biological relevance is undeniable since their existence in living cells has been observed. In vivo they take part in the regulation of gene expression, in vitro they are used in the analytical biochemistry. They are attractive and promising targets for cancer therapy. Pressure studies can reveal specific aspects of the molecular processes. Pressure tuning experiments allow the determination of the volumetric parameters of the folded structures and of the folding–unfolding processes. Here, we review the thermodynamic parameters with a special focus on the volumetric ones, which were determined using pressure tuning spectroscopic experiments on the G-quadruplex and i-motif nucleic acid forms.

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G-quadruplexes in the evolution of hepatitis B virus

Brázda

Dobrovolná

Bohálová

et al. 2023

Nucleic Acids Research

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Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of ‘genetic camouflage’ to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.

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Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures

Cited by 4 publications

References 65 publications

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures

G-quadruplexes in the evolution of hepatitis B virus

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