scholarly journals Physicochemical Investigation of Psoralen Binding to Double Stranded DNA through Electroanalytical and Cheminformatic Approaches

2020 ◽  
Vol 13 (6) ◽  
pp. 108
Author(s):  
Douglas Vieira Thomaz ◽  
Matheus Gabriel de Oliveira ◽  
Edson Silvio Batista Rodrigues ◽  
Vinicius Barreto da Silva ◽  
Pierre Alexandre dos Santos
Keyword(s):  
Electric Potential ◽  
Analytical Signal ◽  
Electroanalytical Methods ◽  
Cross Link ◽  
Base Pairs ◽  
Faradaic Current ◽  
Double Stranded Dna ◽  
Physicochemical Investigation ◽  
Dna Strands ◽  
Intercalating Agents

This work showcased the first physicochemical investigation of psoralen (PSO) binding to double stranded DNA (dsDNA) through electroanalytical methods. Results evidenced that PSO presents one non-reversible anodic peak at electric potential (Epa) ≈ 1.42 V, which is associated with its oxidation and the formation of an epoxide derivative. Moreover, PSO analytical signal (i.e., faradaic current) decreases linearly with the addition of dsDNA, while the electric potential associated to PSO oxidation shifts towards more positive values, indicating thence that dsDNA addition hinders PSO oxidation. These findings were corroborated by the chemoinformatic study, which evidenced that PSO intercalated noncovalently at first between base-pairs of the DNA duplex, and then irreversibly formed adducts with both DNA strands, leading up to the formation of a cross-link which bridges the DNA helix, which explains the linear dependence between the faradaic current generated by PSO oxidation and the concentration of DNA in the test-solution, as well as the dependence between Ep and the addition of dsDNA solution. Therefore, the findings herein reported evidence of the applicability of electroanalytical approaches, such as voltammetry in the study of DNA intercalating agents.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

scholarly journals Hoogsteen Base Pairs Increase the Susceptibility of Double-Stranded DNA to Cytotoxic Damage

2021 ◽  
Vol 120 (3) ◽  
pp. 9a
Author(s):  
Akanksha Manghrani ◽  
Yu Xu ◽  
Emily Cannistraci ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Base Pairs ◽  
Double Stranded Dna

scholarly journals The effect of attachment site mutations on strand exchange in bacteriophage lambda site-specific recombination.

Genetics ◽  
1989 ◽  
Vol 122 (4) ◽  
pp. 727-736
Author(s):  
C E Bauer ◽  
J F Gardner ◽  
R I Gumport ◽  
R A Weisberg
Keyword(s):  
Attachment Site ◽  
Strand Exchange ◽  
Segregation Pattern ◽  
Base Substitution ◽  
Base Pairs ◽  
Multiple Mutation ◽  
Attachment Sites ◽  
Dna Strands ◽  
Substitution Mutations ◽  
Overlap Region

Abstract Recombination of phage lambda attachment sites occurs by sequential exchange of the DNA strands at two specific locations. The first exchange produces a Holliday structure, and the second resolves it to recombinant products. Heterology for base substitution mutations in the region between the two strand exchange points (the overlap region) reduces recombination; some mutations inhibit the accumulation of Holliday structures, others inhibit their resolution to recombinant products. To see if heterology also alters the location of the strand exchange points, we determined the segregation pattern of three single and one multiple base pair substitution mutations of the overlap region in crosses with wild type sites. The mutations are known to differ in the severity of their recombination defect and in the stage of strand exchange they affect. The three single mutations behaved similarly: each segregated into both products of recombination, and the two products of a single crossover were frequently nonreciprocal in the overlap region. In contrast, the multiple mutation preferentially segregated into one of the two recombinant products, and the two products of a single crossover appeared to be fully reciprocal. The simplest explanation of the segregation pattern of the single mutations is that strand exchanges occur at the normal locations to produce recombinants with mismatched base pairs that are frequently repaired. The segregation pattern of the multiple mutation is consistent with the view that both strand exchanges usually occur to one side of the mutant site. We suggest that the segregation pattern of a particular mutation is determined by which stage of strand exchange it inhibits and by the severity of the inhibition.

scholarly journals Physicochemical investigation of Psoralen binding to double stranded DNA through electroanalytical and cheminformatic approaches

2019 ◽  
Author(s):  
Douglas Thomaz ◽  
Vinicius Silva ◽  
Pierre Santos ◽  
Matheus Oliveira ◽  
Edson Rodrigues
Keyword(s):  
Double Stranded Dna ◽  
Physicochemical Investigation

scholarly journals Capture of a Transition State Using Molecular Dynamics: Creation of an Intercalation Site in dsDNA with Ethidium Cation

2010 ◽  
Vol 2010 ◽  
pp. 1-4 ◽  
Author(s):  
Regina R. Monaco
Keyword(s):  
External Surface ◽  
Computational Study ◽  
Helical Axis ◽  
Base Pairs ◽  
Bond Rotation ◽  
Double Stranded Dna ◽  
Dna Backbone ◽  
Interaction Measure ◽  
The Creation ◽  
A Site

The mechanism of intercalation and the ability of double stranded DNA (dsDNA) to accommodate a variety of ligands in this manner has been well studied. Proposed mechanistic steps along this pathway for the classical intercalator ethidium have been discussed in the literature. Some previous studies indicate that the creation of an intercalation site may occur spontaneously, with the energy for this interaction arising either from solvent collisions or soliton propagation along the helical axis. A subsequent 1D diffusional search by the ligand along the helical axis of the DNA will allow the ligand entry to this intercalation site from its external, electrostatically stabilized position. Other mechanistic studies show that ethidium cation participates in the creation of the site, as a ligand interacting closely with the external surface of the DNA can cause unfavorable steric interactions depending on the ligands' orientation, which are relaxed during the creation of an intercalation site. Briefly, such a site is created by the lengthening of the DNA molecule via bond rotation between the sugars and phosphates along the DNA backbone, causing an unwinding of the dsDNA itself and separation between the adjacent base pairs local to the position of the ligand, which becomes the intercalation site. Previous experimental measurements of this interaction measure the enthalpic cost of this part of the mechanism to be about −8 kcal/mol. This paper reports the observation, during a computational study, of the spontaneous opening of an intercalation site in response to the presence of a single ethidium cation molecule in an externally bound configuration. The concerted motions between this ligand and the host, a dsDNA decamer, are clear. The dsDNA decamer AGGATGCCTG was studied; the central site was the intercalation site.

The distribution on the shortest distance between random cuts on opposite strands of DNA

1974 ◽  
Vol 11 (2) ◽  
pp. 363-368
Author(s):  
Samuel Litwin
Keyword(s):  
Unit Length ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Shortest Distance

Experiments involving random enzymatic or radioactive multiple cutting of single strands in double stranded DNA will occasionally cut it at pairs of positions on opposite strands that are within about 12 base pairs. In this case the DNA may unravel and come apart. The distribution of closest opposing breaks as a function of λ, the incidence of breaks per unit length, is obtained and graphs of the probability of critical distances as functions ofλare plotted. It is shown that for very largeλthe distance between closest opposite breaks is approximately exponential with parameter ½λ2.

scholarly journals Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates

2019 ◽  
Vol 47 (21) ◽  
pp. 11225-11237 ◽  
Author(s):  
Chaoyou Xue ◽  
James M Daley ◽  
Xiaoyu Xue ◽  
Justin Steinfeld ◽  
Youngho Kwon ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Genetic Disorder ◽  
Protein A ◽  
Base Pairs ◽  
Single Stranded Dna ◽  
Double Stranded Dna ◽  
Blm Helicase ◽  
Dna Replication And Repair ◽  
Regulatory Effects

Abstract Bloom helicase (BLM) and its orthologs are essential for the maintenance of genome integrity. BLM defects represent the underlying cause of Bloom Syndrome, a rare genetic disorder that is marked by strong cancer predisposition. BLM deficient cells accumulate extensive chromosomal aberrations stemming from dysfunctions in homologous recombination (HR). BLM participates in several HR stages and helps dismantle potentially harmful HR intermediates. However, much remains to be learned about the molecular mechanisms of these BLM-mediated regulatory effects. Here, we use DNA curtains to directly visualize the activity of BLM helicase on single molecules of DNA. Our data show that BLM is a robust helicase capable of rapidly (∼70–80 base pairs per second) unwinding extensive tracts (∼8–10 kilobases) of double-stranded DNA (dsDNA). Importantly, we find no evidence for BLM activity on single-stranded DNA (ssDNA) that is bound by replication protein A (RPA). Likewise, our results show that BLM can neither associate with nor translocate on ssDNA that is bound by the recombinase protein RAD51. Moreover, our data reveal that the presence of RAD51 also blocks BLM translocation on dsDNA substrates. We discuss our findings within the context of potential regulator roles for BLM helicase during DNA replication and repair.

Frontispiz: Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs

2016 ◽  
Vol 128 (21) ◽  
Author(s):  
Noelia Santamaría-Díaz ◽  
José M. Méndez-Arriaga ◽  
Juan M. Salas ◽  
Miguel A. Galindo
Keyword(s):  
Base Pairs ◽  
Double Stranded Dna

scholarly journals Interrupted amperometry: the new possibilities in electrochemical measurements

2017 ◽  
Vol 89 (10) ◽  
pp. 1459-1469 ◽  
Author(s):  
Ekaterina Semenova ◽  
Daria Navolotskaya ◽  
Sergey Ermakov
Keyword(s):  
Analytical Signal ◽  
Electrical Circuit ◽  
Iron Ions ◽  
Amperometric Determination ◽  
Capacitive Current ◽  
Faradaic Current ◽  
Highly Sensitive ◽  
Current Measuring ◽  
Better Than

AbstractInterrupted amperometry is a new highly sensitive method for diffusion current measuring. The main feature of the proposed technique is the use of capacitive current as the analytical signal together with the faradaic current. The conventional electrical circuit for amperometric measurements is complemented by a switcher that enables periodical interruption of the circuit. The technique was successfully applied for direct amperometric determination of lead, cadmium and iron ions, phenol and hydroquinone; for determination of dichromate ion via titration; for determination of dissolved oxygen in water by Clark-type sensor. In all the mentioned cases the achieved values of analytical characteristics are significantly better than for conventional amperometric methods. There are limitations and perspectives of the proposed technique considered.

scholarly journals Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid

1968 ◽  
Vol 109 (4) ◽  
pp. 543-557 ◽  
Author(s):  
K. J. Thrower ◽  
A. R. Peacocke
Keyword(s):  
Ionic Strength ◽  
Rate Constant ◽  
Base Pairs ◽  
Phage Dna ◽  
Dna Strands ◽  
Entropy Of Activation ◽  
T7 Phage ◽  
Kinetics Of ◽  
Rate Controlling Step ◽  
Adenine Thymine

The kinetics of the renaturation of Escherichia coli DNA in 0·4–1·0m-sodium chloride at temperatures from 60° to 90° have been studied. The extent of renaturation was a maximum at 65° to 75° and increased with ionic strength, and the rate constant increased with both ionic strength and temperature. The energy and entropy of activation of renaturation were calculated to be 6–7kcal.mole−1 and −40cal.deg.−1mole−1 respectively. It has been shown that renaturation is a second-order process for 5hr. under most conditions. The results are consistent with a reaction in which the rate-controlling step is the diffusion together of two separated complementary DNA strands and the formation of a nucleus of base pairs between them. The kinetics of the renaturation of T7-phage DNA and Bordetella pertussis DNA have also been studied, and their rates of renaturation related quantitatively to the relative heterogeneity of the DNA samples. By analysis of the spectra of DNA at different stages during renaturation it was shown that initially the renatured DNA was rich in guanine–cytosine base pairs and non-random in base sequence, but that, as equilibrium was approached, the renatured DNA gradually resembled native DNA more closely. The rate constant for the renaturation of guanine–cytosine base pairs was slightly higher than for adenine–thymine base pairs.

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