An Improved Method for Identifying Specific DNA-Protein-Binding Sites In Vitro

2017 ◽  
Vol 59 (2-3) ◽  
pp. 59-65
Author(s):  
Liangyan Wang ◽  
Huizhi Lu ◽  
Yunguang Wang ◽  
Su Yang ◽  
Hong Xu ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Improved Method ◽  
Protein Binding Sites

EVALUATION OF TISSUE STEROID BINDING IN VITRO

1971 ◽  
Vol 68 (1_Suppl) ◽  
pp. S223-S246 ◽  
Author(s):  
C. R. Wira ◽  
H. Rochefort ◽  
E. E. Baulieu
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Experimental System ◽  
Specific Protein ◽  
Coupling Mechanism ◽  
Target Tissue ◽  
Protein Binding Sites ◽  
Definition Of ◽  
Hormone Specificity

ABSTRACT The definition of a RECEPTOR* in terms of a receptive site, an executive site and a coupling mechanism, is followed by a general consideration of four binding criteria, which include hormone specificity, tissue specificity, high affinity and saturation, essential for distinguishing between specific and nonspecific binding. Experimental approaches are proposed for choosing an experimental system (either organized or soluble) and detecting the presence of protein binding sites. Techniques are then presented for evaluating the specific protein binding sites (receptors) in terms of the four criteria. This is followed by a brief consideration of how receptors may be located in cells and characterized when extracted. Finally various examples of oestrogen, androgen, progestagen, glucocorticoid and mineralocorticoid binding to their respective target tissues are presented, to illustrate how researchers have identified specific corticoid and mineralocorticoid binding in their respective target tissue receptors.

scholarly journals Transcription signals and protein binding sites for sericin gene transcription in vitro

1989 ◽  
Vol 264 (31) ◽  
pp. 18707-18713 ◽  
Author(s):  
K Matsuno ◽  
C C Hui ◽  
S Takiya ◽  
T Suzuki ◽  
K Ueno ◽  
...  
Keyword(s):  
Protein Binding ◽  
Gene Transcription ◽  
Binding Sites ◽  
Protein Binding Sites ◽  
Transcription In Vitro ◽  
Transcription Signals

Characterization of a single strong tissue-specific enhancer downstream from the three human genes encoding placental lactogen

1994 ◽  
Vol 14 (1) ◽  
pp. 93-103
Author(s):  
P Jacquemin ◽  
C Oury ◽  
B Peers ◽  
A Morin ◽  
A Belayew ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Chromosome 17 ◽  
Placental Lactogen ◽  
Cell Nuclei ◽  
Enhancer Activity ◽  
Protein Binding Sites ◽  
Human Genes ◽  
Genes Encoding

The human genes coding for growth hormone (hGH) and placental lactogen (choriosomatomammotropic hormone [hCS]) are clustered on chromosome 17 in the following order: 5' hGH-N hCS-L hCS-A hGH-V hCS-B 3'. So far, a single placenta-specific enhancer has been identified in the locus, 2 kb downstream from the hCS-B gene, and shown to comprise one in vitro binding site for a nuclear protein. We here provide evidence that the hCS-B enhancer is more complex: (i) protection against DNase I digestion in the 3' flanking region of the hCS-B gene reveals four binding sites (DF-1, DF-2, DF-3, and DF-4) for nuclear proteins from either placental or HeLa cells, and (ii) placenta-specific enhancer activity can be fully exerted in transient expression experiments by a 126-bp fragment comprising the DF-3 and DF-4 protein-binding sites. By dissecting this region, we show that enhancer activity is mediated by a synergy between DF-3 and DF-4. Competitions with various oligonucleotides in footprinting and gel retardation experiments indicate that the same protein or set of proteins, different in HeLa and placenta cell nuclei, interacts with sites DF-2, DF-3, and DF-4. We also studied the regions of the hCS-L and hCS-A genes which are highly similar to the hCS-B enhancer. Although they each present the same four protein-binding sites, they exhibit only minor enhancer activity.

scholarly journals Conserved Structure Modules within the lncRNA SChLAP1 Mediate Protein Recognition Implicated in Aggressive Prostate Cancer

2021 ◽  
Author(s):  
Emily J McFadden ◽  
James P Falese ◽  
Amanda E Hargrove
Keyword(s):  
Prostate Cancer ◽  
Secondary Structure ◽  
Protein Binding ◽  
Binding Sites ◽  
Cancer Metastasis ◽  
Magnesium Concentration ◽  
Purification Method ◽  
Aggressive Prostate Cancer ◽  
Protein Binding Sites

The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and driver of aggressive prostate cancer. Recent work suggests that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of apo SChLAP1 or the SChLAP1:SWI/SNF complex. Herein, we report the first secondary structure model of SChLAP1 utilizing SHAPE-MaP both in vitro and in cellulo. Comparison of the in vitro and in cellulo data via ΔSHAPE identified putative protein binding sites within SChLAP1, specifically to evolutionarily conserved exons of the transcript. We also demonstrate that global SChLAP1 secondary structure is sensitive to both purification method and magnesium concentration. Further, we identified a 3'-fragment of SChLAP1 (SChLAP1Frag) that harbors multiple potential protein binding sites and presents a robustly folded secondary structure, supporting a functional role for this region. This work lays the foundation for future efforts in selective targeting and disruption of the SChLAP1:protein interface and the development of new therapeutic avenues in prostate cancer treatment.

scholarly journals Characterization of a single strong tissue-specific enhancer downstream from the three human genes encoding placental lactogen.

1994 ◽  
Vol 14 (1) ◽  
pp. 93-103 ◽  
Author(s):  
P Jacquemin ◽  
C Oury ◽  
B Peers ◽  
A Morin ◽  
A Belayew ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Chromosome 17 ◽  
Placental Lactogen ◽  
Cell Nuclei ◽  
Enhancer Activity ◽  
Protein Binding Sites ◽  
Human Genes ◽  
Genes Encoding

The human genes coding for growth hormone (hGH) and placental lactogen (choriosomatomammotropic hormone [hCS]) are clustered on chromosome 17 in the following order: 5' hGH-N hCS-L hCS-A hGH-V hCS-B 3'. So far, a single placenta-specific enhancer has been identified in the locus, 2 kb downstream from the hCS-B gene, and shown to comprise one in vitro binding site for a nuclear protein. We here provide evidence that the hCS-B enhancer is more complex: (i) protection against DNase I digestion in the 3' flanking region of the hCS-B gene reveals four binding sites (DF-1, DF-2, DF-3, and DF-4) for nuclear proteins from either placental or HeLa cells, and (ii) placenta-specific enhancer activity can be fully exerted in transient expression experiments by a 126-bp fragment comprising the DF-3 and DF-4 protein-binding sites. By dissecting this region, we show that enhancer activity is mediated by a synergy between DF-3 and DF-4. Competitions with various oligonucleotides in footprinting and gel retardation experiments indicate that the same protein or set of proteins, different in HeLa and placenta cell nuclei, interacts with sites DF-2, DF-3, and DF-4. We also studied the regions of the hCS-L and hCS-A genes which are highly similar to the hCS-B enhancer. Although they each present the same four protein-binding sites, they exhibit only minor enhancer activity.

AN IMPROVED METHOD FOR THE ASSAY OF PROGESTERONE BY COMPETITIVE PROTEIN BINDING

1970 ◽  
Vol 63 (2) ◽  
pp. 225-241 ◽  
Author(s):  
B. D. Reeves ◽  
M. L. A. de Souza ◽  
I. E. Thompson ◽  
E. Diczfalusy
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Entire Range ◽  
Improved Method ◽  
Plasma Progesterone ◽  
Extraction And Purification ◽  
Corticosteroid Binding Globulin ◽  
Competitive Protein Binding ◽  
The Individual ◽  
Range Of Values

ABSTRACT An improved method for the assay of plasma progesterone by competitive protein binding is described. The improvement is based upon rigorous control of the variables, the compensation for and standardisation of interfering factors inherent in the method and the use of a human corticosteroid binding globulin, that meets the requirements for sensitivity at levels of 1.0 ng of progesterone and below. The assessment of the reliability of the individual steps in the method as well as that of the complete method is presented. The sensitivity of the method is around 0.2 ng progesterone per ml plasma. Accuracy was measured by adding progesterone in amounts ranging from 0.0 to 1.0 ng to 1.0 ml plasma. There was a linear relationship between the progesterone added and recovered throughout the entire range of values, with a coefficient of correlation (r) of 0.94. Of 52 related steroids tested, none was found which would remain associated with progesterone following extraction and purification and which would also compete with progesterone for binding sites.

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