scholarly journals Efficient Delivery of Cyclic Peptides into Mammalian Cells with Short Sequence Motifs

2012 ◽  
Vol 8 (2) ◽  
pp. 423-431 ◽  
Author(s):  
Ziqing Qian ◽  
Tao Liu ◽  
Yu-Yu Liu ◽  
Roger Briesewitz ◽  
Amy M. Barrios ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Cyclic Peptides ◽  
Sequence Motifs ◽  
Short Sequence ◽  
Efficient Delivery

scholarly journals Protein Transduction Domain of HIV-1 Tat Protein Promotes Efficient Delivery of DNA into Mammalian Cells

2001 ◽  
Vol 276 (28) ◽  
pp. 26204-26210 ◽  
Author(s):  
Akiko Eguchi ◽  
Teruo Akuta ◽  
Hajime Okuyama ◽  
Takao Senda ◽  
Haruhiko Yokoi ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Protein Transduction ◽  
Protein Transduction Domain ◽  
Tat Protein ◽  
Efficient Delivery ◽  
Hiv 1

Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction

1986 ◽  
Vol 6 (12) ◽  
pp. 4295-4304
Author(s):  
D B Roth ◽  
J H Wilson
Keyword(s):  
Mammalian Cells ◽  
Simian Virus 40 ◽  
Restriction Enzymes ◽  
Simian Virus ◽  
T Antigen ◽  
Short Sequence ◽  
End Joining ◽  
Nonhomologous Recombination ◽  
Sequence Homologies ◽  
Linear Molecules

Although DNA breakage and reunion in nonhomologous recombination are poorly understood, previous work suggests that short sequence homologies may play a role in the end-joining step in mammalian cells. To study the mechanism of end joining in more detail, we inserted a polylinker into the simian virus 40 T-antigen intron, cleaved the polylinker with different pairs of restriction enzymes, and transfected the resulting linear molecules into monkey cells. Analysis of 199 independent junctional sequences from seven constructs with different mismatched ends indicates that single-stranded extensions are relatively stable in monkey cells and that the terminal few nucleotides are critical for cell-mediated end joining. Furthermore, these studies define three mechanisms for end joining: single-strand, template-directed, and postrepair ligations. The latter two mechanisms depend on homologous pairing of one to six complementary bases to position the junction. All three mechanisms operate with similar overall efficiencies. The relevance of this work to targeted integration in mammalian cells is discussed.

scholarly journals Epitope Mapping of Antibodies against Prostate-specific Antigen with Use of Peptide Libraries

2002 ◽  
Vol 48 (12) ◽  
pp. 2208-2216 ◽  
Author(s):  
Jari Leinonen ◽  
Ping Wu ◽  
Ulf-Håkan Stenman
Keyword(s):  
Prostate Specific Antigen ◽  
Cyclic Peptides ◽  
Epitope Mapping ◽  
Specific Antigen ◽  
Peptide Libraries ◽  
Sequence Motifs ◽  
Large Panel ◽  
Distinct Sequence ◽  
Binding Peptides ◽  
Important Marker

Abstract Background: Prostate-specific antigen (PSA) is the most important marker for prostate cancer, but PSA concentrations determined by various assays can differ significantly because of differences in specificity of the antibodies used. To identify epitopes recognized by various monoclonal antibodies (MAbs) to PSA, we have isolated peptides that react with the paratopes of these. Methods: Six anti-PSA MAbs representing three major epitope groups were screened with five cyclic phage display peptide libraries. After selection, the peptide sequences were determined by sequencing of the relevant part of viral DNA. Binding of the phage peptides to the MAbs was monitored by immunoassay. Results: For each MAb, several paratope-binding peptides with distinct sequence motifs were identified, but only ∼10% showed similarity with the PSA sequence. Some of these correctly predicted the location of the epitopes. By sequential panning of the library with two closely related MAbs, we identified peptides reacting equally with both MAbs. When analyzed against a large panel of PSA MAbs, the peptides generally showed restricted specificity toward the MAb used for selection, but some peptides bound to several related MAbs. Conclusions: Most of the cyclic peptides selected with PSA MAbs are specific for the MAb used for selection and do not resemble any sequence on the antigen. Peptides reactive with two MAbs recognizing the same epitope can be obtained by sequential panning. This method can be used to predict the location of some epitopes, but additional methods are needed to confirm the result.

scholarly journals Histidine-rich amphipathic peptide antibiotics promote efficient delivery of DNA into mammalian cells

2003 ◽  
Vol 100 (4) ◽  
pp. 1564-1568 ◽  
Author(s):  
A. Kichler ◽  
C. Leborgne ◽  
J. Marz ◽  
O. Danos ◽  
B. Bechinger
Keyword(s):  
Mammalian Cells ◽  
Peptide Antibiotics ◽  
Amphipathic Peptide ◽  
Efficient Delivery

scholarly journals Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells

2010 ◽  
Vol 107 (5) ◽  
pp. 1870-1875 ◽  
Author(s):  
Alex K. Shalek ◽  
Jacob T. Robinson ◽  
Ethan S. Karp ◽  
Jin Seok Lee ◽  
Dae-Ro Ahn ◽  
...  
Keyword(s):  
Small Molecules ◽  
High Throughput ◽  
Silicon Nanowires ◽  
Mammalian Cells ◽  
Living Cells ◽  
Diverse Range ◽  
Viral Packaging ◽  
Neuronal Progenitor ◽  
Efficient Delivery ◽  
Surface Modified

A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cell’s membrane and subsequently release surface-bound molecules directly into the cell’s cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technology’s potential as a robust, monolithic platform for high-throughput, miniaturized bioassays.

scholarly journals Short-Sequence DNA Repeats in Prokaryotic Genomes

1998 ◽  
Vol 62 (2) ◽  
pp. 275-293 ◽  
Author(s):  
Alex van Belkum ◽  
Stewart Scherer ◽  
Loek van Alphen ◽  
Henri Verbrugh
Keyword(s):  
Pathogenic Bacteria ◽  
Gene Expression Regulation ◽  
Epidemiological Studies ◽  
Phenotypic Flexibility ◽  
Dna Repeats ◽  
Sequence Motifs ◽  
Short Sequence ◽  
Bacterial Cell Division ◽  
Dna Repeat ◽  
Prokaryotic Genomes

SUMMARY Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10−4 per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.

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