Papers by allen nicholson
Molecules
Cleavage of DNA at noncanonical recognition sequences by restriction endonucleases (star activity... more Cleavage of DNA at noncanonical recognition sequences by restriction endonucleases (star activity) in bulk solution can be promoted by global experimental parameters, including enzyme or substrate concentration, temperature, pH, or buffer composition. To study the effect of nanoscale confinement on the noncanonical behaviour of BamHI, which cleaves a single unique sequence of 6 bp, we used AFM nanografting to generate laterally confined DNA monolayers (LCDM) at different densities, either in the form of small patches, several microns in width, or complete monolayers of thiol-modified DNA on a gold surface. We focused on two 44-bp DNAs, each containing a noncanonical BamHI site differing by 2 bp from the cognate recognition sequence. Topographic AFM imaging was used to monitor end-point reactions by measuring the decrease in the LCDM height with respect to the surrounding reference surface. At low DNA densities, BamHI efficiently cleaves only its cognate sequence while at intermediat...
ABSTRACTWe used coarse-grained molecular dynamics simulations to characterize the global and loca... more ABSTRACTWe used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modu...
Biophysical Journal, 2019
Biophysical Journal, 2019
cytoplasmic ends of the transmembrane domains and of the nucleotidebinding domain interface, whic... more cytoplasmic ends of the transmembrane domains and of the nucleotidebinding domain interface, which would be needed for ATP hydrolysis. Chemical modification of specific compounds allows the SAR of inhibitory compounds to be studied and may provide a rational basis for the future design of ABCG2 inhibitors.
Nucleic Acids Research, 1988
To test the ability of an RNA processing enzyme to cleave chemicallymodified RNA substrates, RNA ... more To test the ability of an RNA processing enzyme to cleave chemicallymodified RNA substrates, RNA transcripts containing RNase III cleavage sites were enzymatically synthesized in vitro to contain specific phosphorothioate diester internucleotide linkages. One transcript (Rl.l RNA) was generated using phage T7 RNA polymerase and a cloned segment of phage T7 DNA containing the Rl.l RNase III processing site. The second transcript was the phage T7 polycistronic early mRNA precursor, which was synthesized using E. coli RNA polymerase and T7 genomic DNA. The RNA transcripts contained phosphorothioate diester groups at positions including the scissile bonds. The modified RNAs were stable to incubation in Mg2+-containing buffer, and were specifically cleaved by RNase III. RNA oligonucleotide sequence analysis showed that the modified Rl.l RNA processing site was the same as the canonical site and contained a phosphorothioate bond. Furthermore, RNase III cleaved the phosphorothioate internucleotide bond with 5' polarity. RNase III cleavage of phosphorothioate substituted T7 polycistronic early mRNA precursor produced the same gel electrophoretic pattern as that obtained with the control transcript. Thus, RNase III cleavage specificity is not altered by phosphorothioate internucleotide linkages.
Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1992
RNAi: A Guide to Gene Silencing. Cold Spring Harbor …, 2003
Nucleic Acids Research, 2010
Journal of cellular physiology, Jan 8, 2017
The study of the physiological action of microorganisms in artistic materials is one of the most ... more The study of the physiological action of microorganisms in artistic materials is one of the most interesting topics in biodeterioration nowadays. Pathologies and illnesses of organic and inorganic materials provoked by microorganisms can be treated by experts by a variety of preventive interventions. Artistic medicine encompasses the monitoring of the exhibition and storage of art, as well as proper environmental conditions and the regular cleaning of museums. Biodeterioration control is essential in order to prevent fungal and bacterial contamination in artwork. Biodeterioration of canvas paintings is a complex phenomenon, not well known at the moment. Canvas paintings are created by several artistic techniques on textile supports that are not always kept in the best conditions, and the best parameters of preventive conservation are often not applied. Therefore, we need to research the agents and the main causes that provoke canvas painting biodeterioration. By applying new methodo...
Journal of the American Chemical Society, 2011
It is controversial whether organic fluorine can form energetically important hydrogen bonds in a... more It is controversial whether organic fluorine can form energetically important hydrogen bonds in aqueous environments. We previously showed by NMR and molecular modeling that the unexpectedly high binding affinity of 2&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;F-ANA is largely due to a C-H···F-C pseudohydrogen bond at pyrimidine-purine steps. Comparisons of the melting of duplexes with identical sequence composition but a rearranged sequence confirm that energetically important fluorine-mediated pseudohydrogen bonding is in operation in these sequences. The effect is of particular importance when the H-bond donor (purine H8) is activated by the presence of fluorine at its own 2&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-position. These results provide a rational method to increase the binding affinity of antisense oligonucleotides by placement of 2&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;F-ANA modifications at pyrimidine-purine steps.
Progress in Nucleic Acid Research and Molecular Biology, Feb 1, 1996
Page 15. Structure, Reactivity, and Biology of Double-Stranded RNA1 Allen W. Nicholson Department... more Page 15. Structure, Reactivity, and Biology of Double-Stranded RNA1 Allen W. Nicholson Department of Biological Sciences Wayne State University Detroit, Michigan 48202 I. Biological Origins of dsRNA 2 II. Experimental Criteria for dsRNA 3 III. ...
Nucleic Acids Research, Mar 1, 1988
To test the ability of an RNA processing enzyme to cleave chemically-modified RNA substrates, RNA... more To test the ability of an RNA processing enzyme to cleave chemically-modified RNA substrates, RNA transcripts containing RNase III cleavage sites were enzymatically synthesized in vitro to contain specific phosphorothioate diester internucleotide linkages. One transcript (R1.1 RNA) was generated using phage T7 RNA polymerase and a cloned segment of phage T7 DNA containing the R1.1 RNase III processing site. The second transcript was the phage T7 polycistronic early mRNA precursor, which was synthesized using E. coli RNA polymerase and T7 genomic DNA. The RNA transcripts contained phosphorothioate diester groups at positions including the scissile bonds. The modified RNAs were stable to incubation in Mg2+-containing buffer, and were specifically cleaved by RNase III. RNA oligonucleotide sequence analysis showed that the modified R1.1 RNA processing site was the same as the canonical site and contained a phosphorothioate bond. Furthermore, RNase III cleaved the phosphorothioate internucleotide bond with 5&#39; polarity. RNase III cleavage of phosphorothioate substituted T7 polycistronic early mRNA precursor produced the same gel electrophoretic pattern as that obtained with the control transcript. Thus, RNase III cleavage specificity is not altered by phosphorothioate internucleotide linkages.
Nucleic Acids Research, Apr 25, 1991
Ribonuclease III of Escherichia coli is prominently involved in the endoribonucleolytic processin... more Ribonuclease III of Escherichia coli is prominently involved in the endoribonucleolytic processing of cell and viral-encoded RNAs. Towards the goal of defining the RNA sequence and structural elements that establish specific catalytic cleavage of RNase III processing signals, this report demonstrates that a 60 nucleotide RNA (R1.1 RNA) containing the bacteriophage T7 R1.1 RNase III processing signal, can be generated by in vitro enzymatic transcription of a synthetic deoxyoligonucleotide and accurately cleaved in vitro by RNase III. Several R1.1 RNA sequence variants were prepared to contain point mutations in the internal loop which, on the basis of a hypothetical &#39;dsRNA mimicry&#39; structural model of RNase III processing signals, would be predicted to inhibit cleavage by disrupting essential tertiary RNA-RNA interactions. These R1.1 sequence variants are accurately and efficiently cleaved in vitro by RNase III, indicating that the dsRNA mimicry structure, if it does exist, is not important for substrate reactivity. Also, we tested the functional importance of the strongly conserved CUU/GAA base-pair sequence by constructing R1.1 sequence variants containing base-pair changes within this element. These R1.1 variants are accurately cleaved at rates comparable to wild-type R1.1 RNA, indicating the nonessentiality of this conserved sequence element in establishing in vitro processing reactivity and selectivity.
Journal of the American Chemical Society, Jan 15, 2016
Over half of all antibiotics target the bacterial ribosome-Nature's complex, 2.5 MDa nanomach... more Over half of all antibiotics target the bacterial ribosome-Nature's complex, 2.5 MDa nanomachine responsible for decoding mRNA and synthesizing proteins. Macrolide antibiotics, exemplified by erythromycin, bind the 50S subunit with nM affinity and inhibit protein synthesis by blocking the passage of nascent oligopeptides. Solithromycin (1), a third-generation semi-synthetic macrolide discovered by combinatorial copper-catalyzed click chemistry, was synthesized in situ by incubating either E. coli 70S ribosomes or 50S subunits with macrolide-functionalized azide 2 and 3-ethynylaniline (3) precursors. The ribosome-templated in situ click method was expanded from a binary reaction (i.e., one azide and one alkyne) to a six-component reaction (i.e., azide 2 and five alkynes) and ultimately to a sixteen-component reaction (i.e., azide 2 and fifteen alkynes). The extent of triazole formation correlated with ribosome affinity for the anti (1,4)-regioisomers as revealed by measured Kd va...
The EMBO journal, Jan 15, 1996
Ethylation interference and hydroxyl radical footprinting were used to identify substrate ribose-... more Ethylation interference and hydroxyl radical footprinting were used to identify substrate ribose-phosphate backbone sites that interact with the Escherichia coli RNA processing enzyme, ribonuclease III. Two RNase III mutants were employed, which bind substrate in vitro similarly as wild-type enzyme, but lack detectable phosphodiesterase activity. Specifically, altering glutamic acid at position 117 to lysine or alanine uncouples substrate binding from cleavage. The two substrates examined are based on the bacteriophage T7 R1.1 RNase III processing signal. One substrate, R1.1 RNA, undergoes accurate single cleavage at the canonical site, while a close variant, R1.1[WC-L] RNA, undergoes coordinate double cleavage. The interference and footprinting patterns for each substrate (i) overlap, (ii) exhibit symmetry and (iii) extend approximately one helical turn in each direction from the RNase III cleavage sites. Divalent metal ions (Mg2+, Ca2+) significantly enhance substrate binding, and...
The Journal of biological chemistry, Jan 25, 1985
Previous work (Nicholson, A. W., Hall, C. C., Strycharz, W. A., and Cooperman, B. S. (1982) Bioch... more Previous work (Nicholson, A. W., Hall, C. C., Strycharz, W. A., and Cooperman, B. S. (1982) Biochemistry 21, 3797-3808) showed that [3H]p-azidopuromycin photoaffinity labeled 70 S Escherichia coli ribosomes and that photoincorporation into 50 S subunit proteins was in the order L23 greater than L18/22 greater than L15. In the present work we report on immunoelectron microscopic studies of the complexes formed by p-azidopuromycin-modified 50 S subunits with antibodies to the N6,N6-dimethyladenosine moiety of the antibiotic. The p-azidopuromycin-modified 50 S subunits appear to be identical to unmodified control subunits in electron micrographs. Complexes of modified subunits with antibodies to the N6,N6-dimethyladenosine moiety of p-azidopuromycin were visualized in micrographs. Individual subunits with a single bound antibody (monomeric complexes) and pairs of subunits cross-linked by a single antibody (dimeric complexes) were separately evaluated and showed similar results. Two reg...
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Papers by allen nicholson