Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.
Although current AMBER force fields are relatively accurate for canonical B-DNA, many noncanonical structures are still described incorrectly. As noncanonical motifs are attracting increasing attention due to the role they play in living organisms, further improvement is desirable. Here, we have chosen the Z-DNA molecule, which can be considered a touchstone of the universality of empirical force fields, since the noncanonical α and γ backbone conformations native to Z-DNA are also found in protein-DNA complexes, i-motif DNA, and other noncanonical DNAs. We show that spurious α/γ conformations occurring in simulations with current AMBER force fields, OL15 and bsc1, are largely due to inaccurate α/γ parametrization. Moreover, stabilization of native Z-DNA substates involving γ = trans conformations appears to be in conflict with the correct description of the canonical B-DNA structure. Because the balance of the native and spurious conformations is influenced by nonadditive effects, this is a difficult case for an additive dihedral energy scheme such as AMBER. We propose new α/γ parameters, denoted OL21, and show that they improve the stability of native α/γ Z-DNA substates while keeping the canonical DNA description virtually unchanged, thus representing a reasonable compromise within the additive force field framework. Although further extensive testing is needed, the new modification appears to be a promising step toward a more reliable description of noncanonical DNA motifs and provides the best performance for Z-DNA molecules among current AMBER force fields.
- MeSH
- B-DNA chemie MeSH
- konformace nukleové kyseliny MeSH
- simulace molekulární dynamiky MeSH
- Z-DNA * MeSH
- Publikační typ
- časopisecké články MeSH
Sex chromosomes are an ideal system to study processes connected with suppressed recombination. We found evidence of microsatellite expansion, on the relatively young Y chromosome of the dioecious plant sorrel (Rumex acetosa, XY1Y2 system), but no such expansion on the more ancient Y chromosomes of liverwort (Marchantia polymorpha) and human. The most expanding motifs were AC and AAC, which also showed periodicity of array length, indicating the importance of beginnings and ends of arrays. Our data indicate that abundance of microsatellites in genomes depends on the inherent expansion potential of specific motifs, which could be related to their stability and ability to adopt unusual DNA conformations. We also found that the abundance of microsatellites is higher in the neighborhood of transposable elements (TEs) suggesting that microsatellites are probably targets for TE insertions. This evidence suggests that microsatellite expansion is an early event shaping the Y chromosome where this process is not opposed by recombination, while accumulation of TEs and chromosome shrinkage predominate later.
- MeSH
- A-DNA genetika MeSH
- chromozomy rostlin genetika MeSH
- duplikace genu MeSH
- hybridizace in situ fluorescenční MeSH
- lidé MeSH
- lidský chromozom Y genetika MeSH
- Marchantia genetika MeSH
- metafáze genetika MeSH
- mikrosatelitní repetice genetika MeSH
- modely genetické MeSH
- molekulární evoluce * MeSH
- periodicita MeSH
- Rumex genetika MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- transpozibilní elementy DNA genetika MeSH
- Z-DNA genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
This work is a continuation of our effort to determine the structure responsible for expansion of the (CGG)(n) motif that results in fragile X chromosome syndrome. In our previous report, we demonstrated that the structure adopted by an oligonucleotide with this repeat sequence is not a quadruplex as was suggested by others. Here we demonstrate that (CGG) runs adopt another anomalous arrangement-a left-handed Z-DNA structure. The Z-DNA formation was induced by high salt and millimolar concentrations of Ni(2+) ions and likelihood of its formation increased with increasing number of repeats. In an oligonucleotide in which the CGG runs were interrupted by AGG triplets, as is observed in genomes of healthy individuals, the hairpin conformation was stabilized and Z-DNA formation was hindered. We show here that methylation of the (CGG) runs markedly stabilized Z-DNA formation. We hypothesize that rather than in the expansion process the Z-DNA may be formed by long, expanded (CGG) stretches that become hypermethylated; this would inhibit transcription resulting in disease.
- MeSH
- cirkulární dichroismus MeSH
- fragilní místa na chromozomu genetika MeSH
- konformace nukleové kyseliny MeSH
- lidé MeSH
- lidské chromozomy X genetika MeSH
- sekvence nukleotidů MeSH
- syndrom fragilního X genetika MeSH
- trinukleotidové repetice MeSH
- Z-DNA chemie genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The (3)J(C8-H1'), (3)J(C4-H1'), (1)J(C8-H8), (1)J(C1'-H1'), (1)J(C2'-H2'), and (1)J(C2'-H2'2) indirect scalar coupling constants were calculated with the density functional theory in the deoxyguanosine and riboguanosine molecules. The following geometry descriptors were considered in analysis of the structural dependence of the six J couplings: the glycosidic torsion angle chi and conformation of the hydroxymethyl group at the C4' carbon of sugar mimicking the backbone residue and the sugar pucker (C2'-, C3'-endo). The (3)J(C8-H1') and (3)J(C4-H1') couplings, which are typically assigned to the chi torsion, also depended on the sugar pucker, although the calculated dependence of the latter coupling on sugar pucker was nearly negligible. New parametrization of the Karplus equations, taking into account the stereoinversion effect at the glycosidic nitrogen atom and solvent effects, was calculated for the (3)J(C8-H1') and (3)J(C4-H1') coupling assigned to the chi torsion. The calculated phase shift of chi torsion angle in these new Karplus equations was larger by approximately 10 degrees compared to its commonly accepted value of 60 degrees (Wijmenga, S. S.; van Buuren, B. N. M. Prog. NMR Spectrosc. 1998, 32, 287.). The calculated (1)J(C2'-H2') and (1)J(C2'-H2'2) coupling dominantly depended on the sugar type (deoxyribose or ribose) and its pucker, while the (1)J(C1'-H1') and (1)J(C8-H8) coupling dominantly depended on the glycosidic torsion angle, although quantitatively, all four (1)J couplings depended on both geometry parameters. The dependences of j-couplings on the torsion angle chi calculated in isolated nucleosides were compared with those taking into account the effect of base pairing occurring in the WC/SE RNA base pair family, which appeared to be minor. The calculated (3)J couplings agreed well with available experimental data similarly as the (1)J couplings, although lack of experimental data diminished more reliable validation of the later couplings.
Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.
