Putative HIV and SIV G-Quadruplex Sequences in Coding and Noncoding Regions Can Form G-Quadruplexes

Krafčíková, Petra; Demkovičová, Erika; Halaganová, Andrea; Víglaský, Viktor

doi:10.1155/2017/6513720

Cited by 6 publications

(5 citation statements)

References 49 publications

(72 reference statements)

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“…PQSs are also present in viral genomes [11,12], and emerging evidence suggests that they can be implicated in viral replication and recombination, in the regulation of virulence via gene expression control [13,14], and in key steps in the viral cycles [15]. The presence of putative G4 sequences has been reported in various viral genomes, such as the human immunodeficiency virus (HIV-1) [16,17,18,19,20], the Epstein–Barr virus (EBV) [21,22], or papillomaviruses (HPV) [23,24,25]. In particular, the Epstein–Barr virus encodes the genome replication and maintenance protein EBNA1 that binds G-rich sequences to recruit the replication complex [21].…”

Section: Introductionmentioning

confidence: 99%

Relationship Between G-Quadruplex Sequence Composition in Viruses and Their Hosts

2019

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A subset of guanine-rich nucleic acid sequences has the potential to fold into G-quadruplex (G4) secondary structures, which are functionally important for several biological processes, including genome stability and regulation of gene expression. Putative quadruplex sequences (PQSs) G3+N1–7G3+N1–7G3+N1–7G3+ are widely found in eukaryotic and prokaryotic genomes, but the base composition of the N1-7 loops is biased across species. Since the viruses partially hijack their hosts’ cellular machinery for proliferation, we examined the PQS motif size, loop length, and nucleotide compositions of 7370 viral genome assemblies and compared viral and host PQS motifs. We studied seven viral taxa infecting five distant eukaryotic hosts and created a resource providing a comprehensive view of the viral quadruplex motifs. Overall, short-looped PQSs are predominant and with a similar composition across viral taxonomic groups, albeit subtle trends emerge upon classification by hosts. Specifically, there is a higher frequency of pyrimidine loops in viruses infecting animals irrespective of the viruses’ genome type. This observation is confirmed by an in-depth analysis of the Herpesviridae family of viruses, which showed a distinctive accumulation of thermally stable C-looped quadruplexes in viruses infecting high-order vertebrates. The occurrence of viral C-looped G4s, which carry binding sites for host transcription factors, as well as the high prevalence of viral TTA-looped G4s, which are identical to vertebrate telomeric motifs, provide concrete examples of how PQSs may help viruses impinge upon, and benefit from, host functions. More generally, these observations suggest a co-evolution of virus and host PQSs, thus underscoring the potential functional significance of G4s.

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Section: Introductionmentioning

confidence: 99%

Relationship Between G-Quadruplex Sequence Composition in Viruses and Their Hosts

2019

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“…The isothermal analysis performed at laboratory temperature enables the visualization of the occurrence of native conformers at various concentrations of the ligand. A sequence which occurs in the HIV genome was used for this purpose [ 37 ]. The effect observed in the case of RhG was not recorded with RhB, a result which is probably due to the weak interaction of the ligand with G4.…”

Section: Resultsmentioning

confidence: 99%

Rhodamine 6G-Ligand Influencing G-Quadruplex Stability and Topology

Trizna

Janovec

Halaganová

et al. 2021

IJMS

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The involvement of G-quadruplex (G4) structures in nucleic acids in various molecular processes in cells such as replication, gene-pausing, the expression of crucial cancer-related genes and DNA damage repair is well known. The compounds targeting G4 usually bind directly to the G4 structure, but some ligands can also facilitate the G4 folding of unfolded G-rich sequences and stabilize them even without the presence of monovalent ions such as sodium or potassium. Interestingly, some G4-ligand complexes can show a clear induced CD signal, a feature which is indirect proof of the ligand interaction. Based on the dichroic spectral profile it is not only possible to confirm the presence of a G4 structure but also to determine its topology. In this study we examine the potential of the commercially available Rhodamine 6G (RhG) as a G4 ligand. RhG tends to convert antiparallel G4 structures to parallel forms in a manner similar to that of Thiazole Orange. Our results confirm the very high selectivity of this ligand to the G4 structure. Moreover, the parallel topology of G4 can be verified unambiguously based on the specific induced CD profile of the G4-RhG complex. This feature has been verified on more than 50 different DNA sequences forming various non-canonical structural motifs.

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“…Thermal Difference Spectra (TDS) were obtained by subtracting the UV absorbance spectra of the unfolded form at 95°C from the folded form at 20°C in given sample yield profiles that are characteristic of G4 (i.e., featuring a negative peak at 295 nm and a positive peak at 275 nm) ( Mergny et al, 2005 ; Krafčíková et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

DNA minicircles capable of forming a variety of non-canonical structural motifs

Trizna,

Olajoš,

Víglaský

2024

Front. Chem.

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Although more than 10% of the human genome has the potential to fold into non-B DNA, the formation of non-canonical structural motifs as part of long dsDNA chains are usually considered as unfavorable from a thermodynamic point of view. However, recent experiments have confirmed that non-canonical motifs do exist and are non-randomly distributed in genomic DNA. This distribution is highly dependent not only on the DNA sequence but also on various other factors such as environmental conditions, DNA topology and the expression of specific cellular factors in different cell types. In this study, we describe a new strategy used in the preparation of DNA minicircles containing different non-canonical motifs which arise as a result of imperfect base pairing between complementary strands. The approach exploits the fact that imperfections in the pairing of complementary strands thermodynamically weaken the dsDNA structure at the expense of enhancing the formation of non-canonical motifs. In this study, a completely different concept of stable integration of a non-canonical motif into dsDNA is presented. Our approach allows the integration of various types of non-canonical motifs into the dsDNA structure such as hairpin, cruciform, G-quadruplex and i-motif forms but also combinations of these forms. Small DNA minicircles have recently become the subject of considerable interest in both fundamental research and in terms of their potential therapeutic applications.

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Putative HIV and SIV G-Quadruplex Sequences in Coding and Noncoding Regions Can Form G-Quadruplexes

Cited by 6 publications

References 49 publications

Relationship Between G-Quadruplex Sequence Composition in Viruses and Their Hosts

Relationship Between G-Quadruplex Sequence Composition in Viruses and Their Hosts

Rhodamine 6G-Ligand Influencing G-Quadruplex Stability and Topology

DNA minicircles capable of forming a variety of non-canonical structural motifs

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