An overhang-based DNA block shuffling method for creating a customized random library

We have used a random library of 15-mer peptides expressed on phage to show that two monoclonal antibodies (mAbs) require only the first three amino acids of dystrophin (Leu-Trp-Trp) for binding. Since the mAbs recognize dystrophin in frozen muscle sections, the results suggest that this hydrophobic N-terminus of dystrophin is accessible to antibody in situ. Quantitative binding studies suggested minor differences in specificity between the two mAbs, so the Ig heavy-chain variable region (VH) sequences of the two hybridomas were determined by RT-PCR and cDNA sequencing. After elimination of PCR errors, the two cDNA sequences were found to be identical except for five somatic mutations which resulted in three amino acid changes in the second hypervariable region (CDR2). The results suggest that the two hybridomas originated from the same lymphocyte clone in a germinal centre of the spleen, but underwent different point mutations and subtype switches during clonal expansion to form blast cells.

Download Full-text

A CRYPTO SIGNATURE SCHEME FOR IMAGE AUTHENTICATION OVER WIRELESS CHANNEL

International Journal of Image and Graphics ◽

10.1142/s0219467805001690 ◽

2005 ◽

Vol 05 (01) ◽

pp. 135-148 ◽

Cited By ~ 18

Author(s):

QIBIN SUN ◽

SHUIMING YE ◽

CHING-YUNG LIN ◽

SHIH-FU CHANG

Keyword(s):

Packet Loss ◽

Digital Signature ◽

Digital Images ◽

Image Authentication ◽

Wireless Channel ◽

Experimental Results ◽

Signature Scheme ◽

Original Image ◽

Degraded Images ◽

Block Shuffling

With the ambient use of digital images and the increasing concern on their integrity and originality, consumers are facing an emergent need of authenticating degraded images despite lossy compression and packet loss. In this paper, we propose a scheme to meet this need by incorporating watermarking solution into traditional cryptographic signature scheme to make the digital signatures robust to these image degradations. Due to the unpredictable degradations, the pre-processing and block shuffling techniques are applied onto the image at the signing end to stabilize the feature extracted at the verification end. The proposed approach is compatible with traditional cryptographic signature scheme except that the original image needs to be watermarked in order to guarantee the robustness of its derived digital signature. We demonstrate the effectiveness of this proposed scheme through practical experimental results.

Download Full-text

Construction of a peptide library by way of YLBS(Y-ligation based block shuffling)

Seibutsu Butsuri ◽

10.2142/biophys.41.s49_1 ◽

2001 ◽

Vol 41 (supplement) ◽

pp. S49

Author(s):

S. Narazaki ◽

K. Kitamura ◽

Y. Kinoshita ◽

T. Kobayashi ◽

N. Nemoto ◽

...

Keyword(s):

Peptide Library ◽

Block Shuffling

Download Full-text

Aptamer-targeting of Aleutian mink disease virus (AMDV) can be an effective strategy to inhibit virus replication

Scientific Reports ◽

10.1038/s41598-021-84223-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Taofeng Lu ◽

Hui Zhang ◽

Jie Zhou ◽

Qin Ma ◽

Wenzhuo Yan ◽

...

Keyword(s):

Disease Virus ◽

Magnetic Beads ◽

Inhibitory Effect ◽

Three Dimensions ◽

Economic Losses ◽

Effective Vaccine ◽

Stem Loop ◽

Aleutian Mink Disease Virus ◽

Random Library

AbstractAleutian mink disease (AMD), which is caused by Aleutian mink disease virus (AMDV), is an important contagious disease for which no effective vaccine is yet available. AMD causes major economic losses for mink farmers globally and threatens some carnivores such as skunks, genets, foxes and raccoons. Aptamers have exciting potential for the diagnosis and/or treatment of infectious viral diseases, including AMD. Using a magnetic beads-based systemic evolution of ligands by exponential enrichment (SELEX) approach, we have developed aptamers with activity against AMDV after 10 rounds of selection. After incubation with the ADVa012 aptamer (4 μM) for 48 h, the concentration of AMDV in the supernatant of infected cells was 47% lower than in the supernatant of untreated cells, whereas a random library of aptamers has no effect. The half-life of ADVa012 was ~ 32 h, which is significantly longer than that of other aptamers. Sequences and three dimensions structural modeling of selected aptamers indicated that they fold into similar stem-loop structures, which may be a preferred structure for binding to the target protein. The ADVa012 aptamer was shown to have an effective and long-lasting inhibitory effect on viral production in vitro.

Download Full-text

Enhancing a De Novo Enzyme Activity by Computationally-Focused, Ultra-Low-Throughput Sequence Screening

10.26434/chemrxiv.11749854.v2 ◽

2020 ◽

Author(s):

Valeria A. Risso ◽

Adrian Romero-Rivera ◽

Luis I. Gutierrez-Rus ◽

Mariano Ortega-Muñoz ◽

Francisco Santoyo-Gonzalez ◽

...

Keyword(s):

Directed Evolution ◽

Active Site ◽

De Novo ◽

Enzymatic Reaction ◽

Valence Bond ◽

Computational Procedure ◽

Enzyme Design ◽

Computational Enzyme Design ◽

Stability Ranking ◽

Random Library

<div> <div> <div> <p>Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains a sluggish process, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib (funclib-weizmann.ac.il) is a novel automated computational procedure which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of a stability metric. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this a particularly challenging system to optimize. Yet, experimental screening of a very small number of active-site, multi-point variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers (~2·104 M-1 s-1 and ~102 s-1) that compare well with modern natural enzymes, and that approach the catalysis levels for the best Kemp eliminases derived from extensive screening. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within ~2 kcal·mol-1 and indicate that the improvements in activity are linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stability-guidance of FuncLib by EVB-based computational predictions of catalytic activity, as a generalized approach for computational enzyme design. </p> </div> </div> </div>

Download Full-text

Block Cipher Enhancement Using Pseudo-random Block Shuffling

2009 Fourth International Conference on Computer Sciences and Convergence Information Technology ◽

10.1109/iccit.2009.9 ◽

2009 ◽

Author(s):

Jiun-Hau Liew ◽

Hee-Yuan Tan ◽

Hoon-Jae Lee ◽

Hyotaek Lim ◽

Sanggon Lee

Keyword(s):

Block Cipher ◽

Random Block ◽

Block Shuffling

Download Full-text

In vitro selection of GTP-binding proteins by block shuffling of estrogen-receptor fragments

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2009.10.029 ◽

2009 ◽

Vol 390 (3) ◽

pp. 689-693 ◽

Cited By ~ 8

Author(s):

Toru Tsuji ◽

Michiko Onimaru ◽

Nobuhide Doi ◽

Etsuko Miyamoto-Sato ◽

Hideaki Takashima ◽

...

Keyword(s):

Estrogen Receptor ◽

Binding Proteins ◽

In Vitro Selection ◽

Gtp Binding Proteins ◽

Gtp Binding ◽

Receptor Fragments ◽

Block Shuffling ◽

Selection Of

Download Full-text

Efficient image encryption with block shuffling and chaotic map

Multimedia Tools and Applications ◽

10.1007/s11042-014-1861-1 ◽

2014 ◽

Vol 74 (15) ◽

pp. 5429-5448 ◽

Cited By ~ 41

Author(s):

Zhenjun Tang ◽

Xianquan Zhang ◽

Weiwei Lan

Keyword(s):

Image Encryption ◽

Chaotic Map ◽

Block Shuffling

Download Full-text

Characterizing Cannabinoid CB2 Receptor Ligands Using DiscoveRx PathHunter™ β-Arrestin Assay

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057108327329 ◽

2008 ◽

Vol 14 (1) ◽

pp. 49-58 ◽

Cited By ~ 45

Author(s):

Debra Mcguinness ◽

Asra Malikzay ◽

Richard Visconti ◽

Karen Lin ◽

Marvin Bayne ◽

...

Keyword(s):

Cb2 Receptor ◽

Receptor Ligands ◽

Camp Assay ◽

Cryopreserved Cell ◽

Random Library ◽

A Cell ◽

Multiple Cell ◽

Screening Platform ◽

Protein Complementation ◽

Camp Levels

The authors have characterized a set of cannabinoid CB2 receptor ligands, including triaryl bis sulfone inverse agonists, in a cell-based receptor/β-arrestin interaction assay (DiscoveRx PathHunter™). The results were compared with results using a competitive ligand binding assay, and with effects on forskolin-stimulated cAMP levels (PerkinElmer LANCE™). The authors show good correlation between the 3 assay systems tested, with the β-arrestin protein complementation assay exhibiting a more robust signal than the cAMP assay for cannabinoid CB2 agonists. Further assay validation shows that DiscoveRx PathHunter™ HEK293 CB2 β-arrestin assay can be carried out from cryopreserved cell suspensions, eliminating variations caused by the need for multiple cell pools during live cell screening campaigns. These results, and the authors' results evaluating a test set of random library compounds, validate the use of ligand-induced interaction between the human cannabinoid CB2 receptor and β-arrestin as an appropriate and valuable screening platform for compounds specific for the cannabinoid CB2 receptor. ( Journal of Biomolecular Screening 2009:49-58)

Download Full-text