NMR Studies of Restriction Enzyme−DNA Interactions:  Role of Conformation in Sequence Specificity†

Biochemistry ◽  
2005 ◽  
Vol 44 (13) ◽  
pp. 5065-5074 ◽  
Author(s):  
Cynthia M. Dupureur
1989 ◽  
Vol 22 (2) ◽  
pp. 93-138 ◽  
Author(s):  
Xiaolian Gao ◽  
Dinshaw J. Patel

The intelligent design of new families of DNA-binding antitumour agents must await an understanding at the molecular level of the structure, dynamics and energetics of drug-DNA interactions on currently available systems. Recent progress in this area has been significant and reflects the interplay between footprinting methods that identify the sequence specificity of drug binding, structural approaches that define conformational features in the crystalline and solution states, hydrogen exchange techniques that monitor transient base pair opening and calorimetric methods that partition the enthalpic and entropic contributions to the binding isotherm.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shihang Sun ◽  
Chungen Hu ◽  
Xiujuan Qi ◽  
Jinyong Chen ◽  
Yunpeng Zhong ◽  
...  

AbstractBeta-amylase (BAM) plays an important role in plant resistance to cold stress. However, the specific role of the BAM gene in freezing tolerance is poorly understood. In this study, we demonstrated that a cold-responsive gene module was involved in the freezing tolerance of kiwifruit. In this module, the expression of AaBAM3.1, which encodes a functional protein, was induced by cold stress. AaBAM3.1-overexpressing kiwifruit lines showed increased freezing tolerance, and the heterologous overexpression of AaBAM3.1 in Arabidopsis thaliana resulted in a similar phenotype. The results of promoter GUS activity and cis-element analyses predicted AaCBF4 to be an upstream transcription factor that could regulate AaBAM3.1 expression. Further investigation of protein-DNA interactions by using yeast one-hybrid, GUS coexpression, and dual luciferase reporter assays confirmed that AaCBF4 directly regulated AaBAM3.1 expression. In addition, the expression of both AaBAM3.1 and AaCBF4 in kiwifruit responded positively to cold stress. Hence, we conclude that the AaCBF-AaBAM module is involved in the positive regulation of the freezing tolerance of kiwifruit.


Catalysts ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 39
Author(s):  
Lyudmila V. Parfenova ◽  
Pavel V. Kovyazin ◽  
Almira Kh. Bikmeeva ◽  
Eldar R. Palatov

The activity and chemoselectivity of the Cp2ZrCl2-XAlBui2 (X = H, Bui) and [Cp2ZrH2]2-ClAlEt2 catalytic systems activated by (Ph3C)[B(C6F5)4] or B(C6F5)3 were studied in reactions with 1-hexene. The activation of the systems by B(C6F5)3 resulted in the selective formation of head-to-tail alkene dimers in up to 93% yields. NMR studies of the reactions of Zr complexes with organoaluminum compounds (OACs) and boron activators showed the formation of Zr,Zr- and Zr,Al-hydride intermediates, for which diffusion coefficients, hydrodynamic radii, and volumes were estimated using the diffusion ordered spectroscopy DOSY. Bis-zirconium hydride clusters of type x[Cp2ZrH2∙Cp2ZrHCl∙ClAlR2]∙yRnAl(C6F5)3−n were found to be the key intermediates of alkene dimerization, whereas cationic Zr,Al-hydrides led to the formation of oligomers.


2015 ◽  
Vol 12 (110) ◽  
pp. 20150589 ◽  
Author(s):  
Maria C. Z. Meneghetti ◽  
Ashley J. Hughes ◽  
Timothy R. Rudd ◽  
Helena B. Nader ◽  
Andrew K. Powell ◽  
...  

Heparan sulfate (HS) polysaccharides are ubiquitous components of the cell surface and extracellular matrix of all multicellular animals, whereas heparin is present within mast cells and can be viewed as a more sulfated, tissue-specific, HS variant. HS and heparin regulate biological processes through interactions with a large repertoire of proteins. Owing to these interactions and diverse effects observed during in vitro , ex vivo and in vivo experiments, manifold biological/pharmacological activities have been attributed to them. The properties that have been thought to bestow protein binding and biological activity upon HS and heparin vary from high levels of sequence specificity to a dependence on charge. In contrast to these opposing opinions, we will argue that the evidence supports both a level of redundancy and a degree of selectivity in the structure–activity relationship. The relationship between this apparent redundancy, the multi-dentate nature of heparin and HS polysaccharide chains, their involvement in protein networks and the multiple binding sites on proteins, each possessing different properties, will also be considered. Finally, the role of cations in modulating HS/heparin activity will be reviewed and some of the implications for structure–activity relationships and regulation will be discussed.


Reproduction ◽  
2010 ◽  
Vol 140 (3) ◽  
pp. 411-423 ◽  
Author(s):  
Philippe Arnaud

The cis-acting regulatory sequences of imprinted gene loci, called imprinting control regions (ICRs), acquire specific imprint marks in germ cells, including DNA methylation. These epigenetic imprints ensure that imprinted genes are expressed exclusively from either the paternal or the maternal allele in offspring. The last few years have witnessed a rapid increase in studies on how and when ICRs become marked by and subsequently maintain such epigenetic modifications. These novel findings are summarised in this review, which focuses on the germline acquisition of DNA methylation imprints and particularly on the combined role of primary sequence specificity, chromatin configuration, non-histone proteins and transcriptional events.


1988 ◽  
Vol 8 (2) ◽  
pp. 963-973
Author(s):  
J T Holt ◽  
R L Redner ◽  
A W Nienhuis

To study the role of a nuclear proto-oncogene in the regulation of cell growth and differentiation, we inhibited HL-60 c-myc expression with a complementary antisense oligomer. This oligomer was stable in culture and entered cells, forming an intracellular duplex. Incubation of cells with the anti-myc oligomer decreased the steady-state levels of c-myc protein by 50 to 80%, whereas a control oligomer did not significantly affect the c-myc protein concentration. Direct inhibition of c-myc expression with the anti-myc oligomer was associated with a decreased cell growth rate and an induction of myeloid differentiation. Related antisense oligomers with 2- to 12-base-pair mismatches with c-myc mRNA did not influence HL-60 cells. Thus, the effects of the antisense oligomer exhibited sequence specificity, and furthermore, these effects could be reversed by hybridization competition with another complementary oligomer. Antisense inhibition of a nuclear proto-oncogene apparently bypasses cell surface events in affecting cell proliferation and differentiation.


1993 ◽  
Vol 291 (3) ◽  
pp. 765-771 ◽  
Author(s):  
P R Williamson ◽  
M A Huber ◽  
J E Bennett

Two isoenzymes of maltase (EC 3.2.1.20) were purified to homogeneity from Candida albicans. Isoenzymes I and II were found to have apparent molecular masses of 63 and 66 kDa on SDS/PAGE with isoelectric points of 5.0 and 4.6 respectively. Both isoenzymes resembled each other in similar N-terminal sequence, specificity for the alpha(1-−>4) glycosidic linkage and immune cross-reactivity on Western blots using a maltase II antigen-purified rabbit antibody. Maltase was induced by growth on sucrose whereas beta-fructofuranosidase activity could not be detected under similar conditions. Maltase I and II were shown to be unglycosylated enzymes by neutral sugar assay, and more than 90% of alpha-glucosidase activity was recoverable from spheroplasts. These data, in combination with other results from this laboratory [Geber, Williamson, Rex, Sweeney and Bennett (1992) J. Bacteriol. 174, 6992-6996] showing lack of a plausible leader sequence in genomic or mRNA transcripts, suggest an intracellular localization of the enzyme. To establish further the mechanism of sucrose assimilation by maltase, the existence of a sucrose-inducible H+/sucrose syn-transporter was demonstrated by (1) the kinetics of sucrose-induced [14C]sucrose uptake, (2) recovery of intact [14C]sucrose from ground cells by t.l.c. and (3) transport of 0.83 mol of H+/mol of [14C]sucrose. In total, the above is consistent with a mechanism whereby sucrose is transported into C. albicans to be hydrolysed by an intracellular maltase.


2021 ◽  
Author(s):  
Sebastian Ponath ◽  
Chetan Joshi ◽  
Amy T. Merrill ◽  
Volker Schmidts ◽  
Kim Greis ◽  
...  

A comprehensive analysis of the organocatalytic α‐chlorination of aldehydes with N‐chloroimides and differ‐ ent catalysts is presented. For this reaction, alternate mechanisms were proposed that differ in the role of resting state intermediates and the rationalization of the observed enantioselectivity. This manuscript aims at resolving these funda‐ mental questions on the basis of rigorous structural characterization of intermediates (configuration and conformation), NMR studies, ion mobility‐mass spectrometry, concentration profiles, isotope studies, and DFT calculations. <br>


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