Slow motions in A·T rich DNA sequence

Abstract In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson–Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA–protein assemblies. R1ρ relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using 13C/15 N labelled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A·T base pairs forming the TAA·TTA segment. The abundance of these HG A·T base pairs can be up to 1.2% which is high compared to what has previously been observed. Data analyses support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimising the probability of having one HG base pair in the TAA·TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A·T base pairs in TAA·TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale.

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A DNA Sequence Based Polymer Model for Chromatin Folding

International Journal of Molecular Sciences ◽

10.3390/ijms22031328 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1328

Author(s):

Rui Zhou ◽

Yi Qin Gao

Keyword(s):

Dna Sequence ◽

Cpg Island ◽

Coarse Grained ◽

Chromosome Territories ◽

Base Pairs ◽

Single Chromosome ◽

Power Law Decay ◽

Multiple Length Scales ◽

Spatial Domains ◽

Chromatin Folding

The recent development of sequencing technology and imaging methods has provided an unprecedented understanding of the inter-phase chromatin folding in mammalian nuclei. It was found that chromatin folds into topological-associated domains (TADs) of hundreds of kilo base pairs (kbps), and is further divided into spatially segregated compartments (A and B). The compartment B tends to be located near to the periphery or the nuclear center and interacts with other domains of compartments B, while compartment A tends to be located between compartment B and interacts inside the domains. These spatial domains are found to highly correlate with the mosaic CpG island (CGI) density. High CGI density corresponds to compartments A and small TADs, and vice versa. The variation of contact probability as a function of sequential distance roughly follows a power-law decay. Different chromosomes tend to segregate to occupy different chromosome territories. A model that can integrate these properties at multiple length scales and match many aspects is highly desired. Here, we report a DNA-sequence based coarse-grained block copolymer model that considers different interactions between blocks of different CGI density, interactions of TAD formation, as well as interactions between chromatin and the nuclear envelope. This model captures the various single-chromosome properties and partially reproduces the formation of chromosome territories.

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Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation

Nature Communications ◽

10.1038/s41467-021-21985-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ruifang Guan ◽

Tengfei Lian ◽

Bing-Rui Zhou ◽

Emily He ◽

Carl Wu ◽

...

Keyword(s):

Dna Sequence ◽

Chromosome Segregation ◽

Budding Yeast ◽

Dna Conformation ◽

Dependent Manner ◽

Dynamic Interactions ◽

Nucleosome Core ◽

Dynamic Mechanisms ◽

Nucleosome Formation ◽

Core Histones

AbstractAccurate chromosome segregation relies on the specific centromeric nucleosome–kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.

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Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Archaea ◽

10.1155/2015/241608 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 10

Author(s):

Reema K. Gudhka ◽

Brett A. Neilan ◽

Brendan P. Burns

Keyword(s):

Unknown Function ◽

Energy Production ◽

Extreme Environment ◽

Evolutionary Significance ◽

Base Pairs ◽

Protein Coding ◽

Inorganic Ion ◽

Damage Repair ◽

Genome Analyses

Halococcus hamelinensiswas the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome ofH. hamelinensisconsisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of theH. hamelinensisgenome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome ofH. hamelinensisalso revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes ofH. hamelinensisagainst various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

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One of the tightly clustered genes of the mouse surfeit locus is a highly expressed member of a multigene family whose other members are predominantly processed pseudogenes.

Molecular and Cellular Biology ◽

10.1128/mcb.8.9.3898 ◽

1988 ◽

Vol 8 (9) ◽

pp. 3898-3905 ◽

Cited By ~ 21

Author(s):

C Huxley ◽

T Williams ◽

M Fried

Keyword(s):

Multigene Family ◽

Open Reading Frame ◽

The Other ◽

Base Pairs ◽

Regulation Of Expression ◽

Reading Frame ◽

Processed Pseudogenes ◽

Dna Fragment ◽

Basic Polypeptide

The mouse surfeit locus is unusual in that it contains a number of closely clustered genes (Surf-1, -2, and -4) that alternate in their direction of transcription (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988). The heterogeneous 5' ends of Surf-1 and Surf-2 are separated by 15 to 73 base pairs (bp), and the 3' ends of Surf-2 and Surf-4 overlap by 133 bp (T. Williams and M. Fried, Mol. Cell. Biol. 6:4558-4569, 1986; T. Williams and M. Fried, Nature (London) 322:275-279, 1986). A fourth gene in this locus, Surf-3, which is a member of a multigene family, has been identified. The poly(A) addition site of Surf-3 lies only 70 bp from the poly(A) addition site of Surf-1. Transcription of Surf-3 has been studied in the absence of the other members of its multigene family after transfection of a cloned genomic mouse DNA fragment, containing the Surf-3 gene, into heterologous monkey cells. Surf-3 specifies a highly expressed 1.0-kilobase mRNA that contains a long open reading frame of 266 amino acids, which would encode a highly basic polypeptide (23% Arg plus Lys). The other members of the Surf-3 multigene family are predominantly, if not entirely, intronless pseudogenes with the hallmarks of being generated by reverse transcription. The role of the very tight clustering on regulation of expression of the genes in the surfeit locus is discussed.

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The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

Chemistry - A European Journal ◽

10.1002/(sici)1521-3765(19991203)5:12<3581::aid-chem3581>3.0.co;2-y ◽

1999 ◽

Vol 5 (12) ◽

pp. 3581-3594 ◽

Cited By ~ 233

Author(s):

Célia Fonseca Guerra ◽

F. Matthias Bickelhaupt ◽

Jaap G. Snijders ◽

Evert Jan Baerends

Keyword(s):

Hydrogen Bond ◽

Charge Transfer ◽

Base Pairs ◽

Dna Base ◽

Dna Base Pairs

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Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments

Magnetochemistry ◽

10.3390/magnetochemistry4030033 ◽

2018 ◽

Vol 4 (3) ◽

pp. 33 ◽

Cited By ~ 1

Author(s):

Tsuyoshi Konuma ◽

Aritaka Nagadoi ◽

Jun-ichi Kurita ◽

Takahisa Ikegami

Keyword(s):

Dipolar Coupling ◽

Residual Dipolar Coupling ◽

Nmr Relaxation ◽

Relaxation Dispersion ◽

Conformational Exchange ◽

Resonance Effects ◽

Pulse Trains ◽

At Resonance ◽

Selective Inversion ◽

Resonance Relaxation

Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.

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Competition between crystal growth and intracrystalline chain diffusion determines the lamellar thickness in semicrystalline polymers

Nature Communications ◽

10.1038/s41467-021-27752-0 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Martha Schulz ◽

Mareen Schäfer ◽

Kay Saalwächter ◽

Thomas Thurn-Albrecht

Keyword(s):

Decisive Role ◽

Semicrystalline Polymers ◽

Lamellar Thickness ◽

Polarization Microscopy ◽

Polymer Systems ◽

X Ray Scattering ◽

Special Cases ◽

Lamellar Crystals ◽

Nmr Methods

AbstractThe non-equilibrium thickness of lamellar crystals in semicrystalline polymers varies significantly between different polymer systems and depends on the crystallization temperature Tc. There is currently no consensus on the mechanism of thickness selection. Previous work has highlighted the decisive role of intracrystalline chain diffusion (ICD) in special cases, but a systematic dependence of lamellar thickness on relevant timescales such as that of ICD and stem attachment has not yet been established. Studying the morphology by small-angle X-ray scattering and the two timescales by NMR methods and polarization microscopy respectively, we here present data on poly(oxymethylene), a case with relatively slow ICD. It fills the gap between previously studied cases of absent and fast ICD, enabling us to establish a quantitative dependence of lamellar thickness on the competition between the noted timescales.

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Supercoiling DNA locates mismatches

10.1101/130567 ◽

2017 ◽

Author(s):

Andrew Dittmore ◽

Sumitabha Brahmachari ◽

Yasuhara Takagi ◽

John F. Marko ◽

Keir C. Neuman

Keyword(s):

Dna Sequence ◽

Base Pair ◽

Dna Supercoiling ◽

Magnetic Tweezers ◽

Relative Probability ◽

Base Pairs ◽

Damage Sensing ◽

Mismatched Base Pair ◽

Monovalent Salt

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

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Insights into the substrate discrimination mechanisms of methyl-CpG-binding domain 4

Biochemical Journal ◽

10.1042/bcj20210017 ◽

2021 ◽

Author(s):

Hala Ouzon-Shubeita ◽

Lillian Feigang Schmaltz ◽

Seongmin Lee

Keyword(s):

Carbonyl Oxygen ◽

Binding Domain ◽

Dna Glycosylase ◽

Side Chain ◽

Dna Glycosylases ◽

Base Pairs ◽

Thymine Dna Glycosylase ◽

Mismatched Dna ◽

Domain 4

G:T mismatches, the major mispairs generated during DNA metabolism, are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). Mismatch-specific DNA glycosylases must discriminate the mismatches against million-fold excess correct base pairs. MBD4 efficiently removes thymine opposite guanine but not opposite adenine. Previous studies have revealed that the substrate thymine is flipped out and enters the catalytic site of the enzyme, while the estranged guanine is stabilized by Arg468 of MBD4. To gain further insights into mismatch discrimination mechanism of MBD4, we assessed the glycosylase activity of MBD4 toward various base pairs. In addition, we determined a crystal structure of MBD4 bound to T:O6-methylguanine-containing DNA, which suggests the O6 and N2 of purine and the O4 of pyrimidine are required to be a substrate for MBD4. To understand the role of the Arg468 finger in catalysis, we evaluated the glycosylase activity of MBD4 mutants, which revealed the guanidinium moiety of Arg468 may play an important role in catalysis. D560N/R468K MBD4 bound to T:G mismatched DNA shows that the side chain amine moiety of the Lys stabilizes the flipped-out thymine by a water-mediated phosphate pinching, while the backbone carbonyl oxygen of the Lys engages in hydrogen bonds with N2 of the estranged guanine. Comparison of various DNA glycosylase structures implies the guanidinium and amine moieties of Arg and Lys, respectively, may involve in discriminating between substrate mismatches and nonsubstrate base pairs.

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