A New 1,5-Disubstituted Triazole DNA Backbone Mimic with Enhanced Polymerase Compatibility

1992 ◽

Vol 50 (1) ◽

pp. 450-451

Author(s):

David P. Bazett-Jones ◽

Mark L. Brown

Keyword(s):

Transcription Factor ◽

Dna Sequences ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Phosphorus Content ◽

Spectroscopic Imaging ◽

Electron Spectroscopic Imaging ◽

Dna Backbone ◽

Two Parameters ◽

High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

Download Full-text

DNA backbone conformation in cis-syn pyrimidine[]pyrimidine cyclobutane dimers

Biopolymers ◽

10.1002/bip.1980.360190913 ◽

1980 ◽

Vol 19 (9) ◽

pp. 1695-1701 ◽

Cited By ~ 18

Author(s):

S. Broyde ◽

S. Stellman ◽

B. Hingerty

Keyword(s):

Backbone Conformation ◽

Cyclobutane Dimers ◽

Dna Backbone ◽

In Cis

Download Full-text

Interactions of the Streptococcus pneumoniae Toxin-Antitoxin RelBE Proteins with Their Target DNA

Microorganisms ◽

10.3390/microorganisms9040851 ◽

2021 ◽

Vol 9 (4) ◽

pp. 851

Author(s):

Inmaculada Moreno-Córdoba ◽

Wai-Ting Chan ◽

Concha Nieto ◽

Manuel Espinosa

Keyword(s):

Streptococcus Pneumoniae ◽

Self Regulation ◽

Mrna Translation ◽

Dna Supercoiling ◽

Bacterial Toxin ◽

Type Ii ◽

Cellular Functions ◽

Dna Backbone ◽

Different Strains ◽

Palindromic Sequences

Type II bacterial toxin-antitoxin (TA) systems are found in most bacteria, archaea, and mobile genetic elements. TAs are usually found as a bi-cistronic operon composed of an unstable antitoxin and a stable toxin that targets crucial cellular functions like DNA supercoiling, cell-wall synthesis or mRNA translation. The type II RelBE system encoded by the pathogen Streptococcus pneumoniae is highly conserved among different strains and participates in biofilm formation and response to oxidative stress. Here, we have analyzed the participation of the RelB antitoxin and the RelB:RelE protein complex in the self-regulation of the pneumococcal relBE operon. RelB acted as a weak repressor, whereas RelE performed the role of a co-repressor. By DNA footprinting experiments, we show that the proteins bind to a region that encompasses two palindromic sequences that are located around the −10 sequences of the single promoter that directs the synthesis of the relBE mRNA. High-resolution footprinting assays showed the distribution of bases whose deoxyriboses are protected by the bound proteins, demonstrating that RelB and RelB:RelE contacted the DNA backbone on one face of the DNA helix and that these interactions extended beyond the palindromic sequences. Our findings suggest that the binding of the RelBE proteins to its DNA target would lead to direct inhibition of the binding of the host RNA polymerase to the relBE promoter.

Download Full-text

Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes

International Journal of Molecular Sciences ◽

10.3390/ijms22020947 ◽

2021 ◽

Vol 22 (2) ◽

pp. 947

Author(s):

Mitsuki Tsuruta ◽

Yui Sugitani ◽

Naoki Sugimoto ◽

Daisuke Miyoshi

Keyword(s):

Molecular Crowding ◽

Dna Duplexes ◽

Crowding Effect ◽

Backbone Flexibility ◽

Cpg Dinucleotides ◽

Key Factor ◽

Dna Backbone ◽

A Cell ◽

Stabilization Effect ◽

And Function

Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.

Download Full-text

Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction

Nucleic Acids Research ◽

10.1093/nar/gkab227 ◽

2021 ◽

Author(s):

Cyong-Ru Jhan ◽

Roshan Satange ◽

Shun-Ching Wang ◽

Jing-Yi Zeng ◽

Yih-Chern Horng ◽

...

Keyword(s):

Hot Spot ◽

Hydration Shell ◽

Repeat Motif ◽

Dna Duplex ◽

Base Pairs ◽

Dna And Rna ◽

Detailed Structural Analysis ◽

Small Molecule Compound ◽

Dna Backbone ◽

Locomotor Deficits

Abstract The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.

Download Full-text

Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures

Nature Communications ◽

10.1038/s41467-020-20258-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Shih-Chi Luo ◽

Hsin-Yi Yeh ◽

Wei-Hsuan Lan ◽

Yi-Min Wu ◽

Cheng-Han Yang ◽

...

Keyword(s):

Functional Analysis ◽

Structural Analysis ◽

Md Simulation ◽

Structural Basis ◽

High Fidelity ◽

Dna Dynamics ◽

Genomic Integrity ◽

Mismatched Dna ◽

Dna Backbone ◽

Loop 2

AbstractBoth high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.

Download Full-text