A study of specific interaction of the transcription factor and the DNA element by atomic force microscopy

2004 ◽  
Vol 49 (13) ◽  
pp. 1376 ◽  
Author(s):  
Feng QIN
Keyword(s):  
Atomic Force Microscopy ◽  
Transcription Factor ◽  
Specific Interaction ◽  
Force Microscopy ◽  
Atomic Force

The Specific Binding between Galactose Group and Ricinus Communis Agglutinin (RCA) Investigated with Microcantilever

2012 ◽  
Vol 531-532 ◽  
pp. 600-604
Author(s):  
Hui Yong Zhang ◽  
Ji Hu ◽  
Hui Min Liu
Keyword(s):  
Atomic Force Microscopy ◽  
Self Assembly ◽  
Control Experiment ◽  
Ricinus Communis ◽  
Specific Binding ◽  
Specific Interaction ◽  
Protein Layer ◽  
Force Microscopy ◽  
Atomic Force ◽  
Ricinus Communis Agglutinin

The specific recognization between galactose group and Ricinus Communis Agglutinin (RCA) was investigated by microcantilever. The gold side of the microcantilever was covalently bound with N-galactose, RCA and asialofetuin (ASF) via mixed self assembly monolayer of 11-mercaptoundecanoic acid and 6-mercaptohexanol, respectively. After adding RCA into the flowing cell, the deflection could be observed on the N-galactose or ASF modified microcantilever. Meanwhile, the deflection could also be observed after ASF bound to the RCA modified microcantilever. In order to prove that the deflection is caused by the specific interaction between the galactose group and RCA, bovine serum albumin (BSA) was introduced into the flowing cell as control experiment and no obvious deflection was observed. The specific interaction was also confirmed by the evidence that the bound protein layer can be mechanically removed with atomic force microscopy nanolithography technology.

Fuzzy logic algorithm to extract specific interaction forces from atomic force microscopy data

2000 ◽  
Vol 71 (5) ◽  
pp. 2082-2086 ◽  
Author(s):  
Sandor Kasas ◽  
Beat M. Riederer ◽  
Stefan Catsicas ◽  
Brunero Cappella ◽  
Giovanni Dietler
Keyword(s):  
Atomic Force Microscopy ◽  
Fuzzy Logic ◽  
Specific Interaction ◽  
Atomic Force Microscopy Data ◽  
Interaction Forces ◽  
Fuzzy Logic Algorithm ◽  
Force Microscopy ◽  
Atomic Force ◽  
Microscopy Data

Study on the specific interaction between angiogenin and aptamer by atomic force microscopy (AFM)

2008 ◽  
Vol 53 (2) ◽  
pp. 198-203 ◽  
Author(s):  
XiaoXiao He ◽  
Rong Jin ◽  
Liu Yang ◽  
KeMin Wang ◽  
Wei Li ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Specific Interaction ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Low-affinity binding incisto P2Y2R mediates force-dependent integrin activation during hantavirus infection

2017 ◽  
Vol 28 (21) ◽  
pp. 2887-2903 ◽  
Author(s):  
Virginie Bondu ◽  
Chenyu Wu ◽  
Wenpeng Cao ◽  
Peter C. Simons ◽  
Jennifer Gillette ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Tensile Force ◽  
Specific Interaction ◽  
Hantavirus Infection ◽  
Integrin Activation ◽  
Force Microscopy ◽  
Rgd Sequence ◽  
Atomic Force ◽  
Cis Interaction

Pathogenic hantaviruses bind to the plexin-semaphorin-integrin (PSI) domain of inactive, β3integrins. Previous studies have implicated a cognate cis interaction between the bent conformation β5/β3integrins and an arginine-glycine-aspartic acid (RGD) sequence in the first extracellular loop of P2Y2R. With single-molecule atomic force microscopy, we show a specific interaction between an atomic force microscopy tip decorated with recombinant αIIbβ3integrins and (RGD)P2Y2R expressed on cell membranes. Mutation of the RGD sequence to RGE in the P2Y2R removes this interaction. Binding of inactivated and fluorescently labeled Sin Nombre virus (SNV) to the integrin PSI domain stimulates higher affinity for (RGD)P2Y2R on cells, as measured by an increase in the unbinding force. In CHO cells, stably expressing αIIbβ3integrins, virus engagement at the integrin PSI domain, recapitulates physiologic activation of the integrin as indicated by staining with the activation-specific mAB PAC1. The data also show that blocking of the Gα13protein from binding to the cytoplasmic domain of the β3integrin prevents outside-in signaling and infection. We propose that the cis interaction with P2Y2R provides allosteric resistance to the membrane-normal motion associated with the switchblade model of integrin activation, where the development of tensile force yields physiological integrin activation.

Direct Observation of Specific Interaction between Enzyme-substrate Complexes Using Colloidal Probe Atomic Force Microscopy

2004 ◽  
Vol 33 (5) ◽  
pp. 536-537 ◽  
Author(s):  
Takehiro Suzuki ◽  
Yuan-Wei Zhang ◽  
Tanetoshi Koyama ◽  
Darryl Y. Sasaki ◽  
Kazue Kurihara
Keyword(s):  
Atomic Force Microscopy ◽  
Direct Observation ◽  
Specific Interaction ◽  
Colloidal Probe ◽  
Force Microscopy ◽  
Enzyme Substrate ◽  
Atomic Force

Identification of Transcription Factor AP-1 Bound to Untranslated 5′ Regulatory Region DNA of mdr1 Gene with Atomic Force Microscopy.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4195-4195
Author(s):  
Bao-An Chen ◽  
Jie Xiong ◽  
Long Ba ◽  
Feng Gao ◽  
Chong Gao ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Transcription Factor ◽  
Regulatory Region ◽  
Mdr1 Gene ◽  
Dna Complexes ◽  
Force Microscopy ◽  
Atomic Force ◽  
Spin Column ◽  
Target Dna ◽  
Afm Image

Abstract Multidrug resistance(MDR) phenotype of cancer cells is a major obstacle for cancer chemotherapy, this phenotype is main due to the overexprssion of the mdr1 gene. Transcription factor AP-1, which is one of important regulate proteins in the promoter region of mdr1 gene. To date, no direct data of AP-1-DNA regulating complexes on mdr1 gene. A novel method for identifying DNA-binding proteins from image analysis using atomic force microscopy(AFM) was developed. This study is to image and map the structure of Untranslated 5′ regulatory region DNA of mdr1gene, identificate and analysis of transcription factor AP-1 bound to Untranslated 5′ regulatory region DNA of mdr1 gene complex with atomic force microscopy, to find out the molecule mechanism of multidrug resistance. Human leukemia adriamycin resistant strain K562/A02 was used as a target cells, transcription factor AP-1 was used as a target protein. Cultivate and PCR technique was used to amplify K562/A02 cells with the 769bp 5′regulatory region DNA of mdr1 gene, which fragment from −755 to +14. The amplified DNA products were purified by the PCR product purification kit, AP-1 of hela nuclear extract were purified by Sephadex spin-column filled with a bed of Sephadex G-100. The target DNA fragments were incubated with the target protein AP-1 at a 1:2 molar ratio in binding buffer and then immobilized the the AP-1-DNA complexes on a freshly cleaved mica surface which treated by MgCl2. AFM was used to idificate image of the structure of target DNA and the AP-1-DNA complexes. We show here the applicability of AFM in the quantitative analysis of the molecular mechanisms of DNA-protein interaction: The optimum DNA concentration to yield well-absorbed DNA molecular on the mica surface was found to be 10ng/ul. the contour of target DNA AFM image :the length of the DNA fragment measured by AFM image was 260.13± 2.29nm, the width was 11.88 ± 0.92nm, the mean height was 1.2nm(mean±SD, N = 50). Sephadex spin-column (Ultrafree- MC 0.22) can be used to purificate DNA and protein-DNA complex, the contour data of AP-1 protein AFM image:: the width of proteinlarge was 30±3.2nm, protein small was 19±2.8nm; the height of proteinlarge was 3.8±1.4nm, proteinsmall was 3.2±1.8nm (mean±SD, N = 30). we got the contour data of pro- tein-DNA complexes: the width of protein large was 28±2.7nm, the height was 3.4± 0.94nm (mean±SD, N = 8), the width of proteinsmall was 18±1.7nm, the height was 3.1±2.2nm (mean±SD, N = 22), and deduced the possible AP-1 site on mdr1DNA located between bases −126 and −115bp, this result is in close agreement with the expected −121 and −115 bp values. the overall connection efficiency of protein was about 10%. The AFM method to visualize individual biomolecules allows us to investigate the conformation of protein-DNA complexes.

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