Need help summarizing this section of a research paper. The key is to summarize

Question

Need help summarizing this section of a research paper. The key is to summarize what they did to get their results, I just don't understand what they are saying to even start summarizing what they did. Please someone explain and summarize their step by step process
DNA curvature prediction and electrophoretic mobility shift assays: The upaC promoter region was analyzed in silico using bend.it, a program that enables the prediction of a curvature propensity plot calcu- lated with DNase I-based parameters . The curvature is calculated as a vector sum of dinucleotide geome- tries (roll, tilt, and twist angles) and expressed as degrees per helical turn (10.5°/helical turn 1°/bp). Experimentally tested curved motifs produce curvature values of 5 to 25°/helical turn, whereas straight motifs give val- ues below 5°/helical turn. The upaC 250-bp promoter region was ampli-fied using primers upaC.pro.ext-5 250 and upaC.pro.ext-3-1ATG, and its intrinsic curvature was assessed by comparing its electrophoretic mo- bility with that of an unbent marker fragment (Promega; 100-bp DNA ladder) on a 0.5% Tris-borate-EDTA (TBE), 7.5% PAGE gel at 4°C for retarded gel electrophoretic mobility. Gel shift assays were performed essentially as previously described (3). A DNA mixture comprising an equimolar ratio of the PCR-amplified upaC promoter region and TaqI-SspI-digested pBR322 was incubated at room temperature for 15 min with increasing amounts of native purified H-NS protein (a gift from S. Rimsky) in 30 l of reaction mixture con- taining 40 mM HEPES (pH 8), 60 mM potassium glutamate, 8 mM mag- nesium aspartate, 5 mM dithiothreitol, 10% glycerol, 0.1% octylphenoxy- polyethoxyethanol, 0.1 mg/ml BSA (H-NS binding buffer). DNA fragments and DNA-protein complexes were resolved by gel electropho- resis (0.5% TBE, 3% MS agarose gel run at 50 V at 4°C) and visualized after staining with ethidium bromide. Need help summarizing this section of a research paper. The key is to summarize what they did to get their results, I just don't understand what they are saying to even start summarizing what they did. Please someone explain and summarize their step by step process
DNA curvature prediction and electrophoretic mobility shift assays: The upaC promoter region was analyzed in silico using bend.it, a program that enables the prediction of a curvature propensity plot calcu- lated with DNase I-based parameters . The curvature is calculated as a vector sum of dinucleotide geome- tries (roll, tilt, and twist angles) and expressed as degrees per helical turn (10.5°/helical turn 1°/bp). Experimentally tested curved motifs produce curvature values of 5 to 25°/helical turn, whereas straight motifs give val- ues below 5°/helical turn. The upaC 250-bp promoter region was ampli-fied using primers upaC.pro.ext-5 250 and upaC.pro.ext-3-1ATG, and its intrinsic curvature was assessed by comparing its electrophoretic mo- bility with that of an unbent marker fragment (Promega; 100-bp DNA ladder) on a 0.5% Tris-borate-EDTA (TBE), 7.5% PAGE gel at 4°C for retarded gel electrophoretic mobility. Gel shift assays were performed essentially as previously described (3). A DNA mixture comprising an equimolar ratio of the PCR-amplified upaC promoter region and TaqI-SspI-digested pBR322 was incubated at room temperature for 15 min with increasing amounts of native purified H-NS protein (a gift from S. Rimsky) in 30 l of reaction mixture con- taining 40 mM HEPES (pH 8), 60 mM potassium glutamate, 8 mM mag- nesium aspartate, 5 mM dithiothreitol, 10% glycerol, 0.1% octylphenoxy- polyethoxyethanol, 0.1 mg/ml BSA (H-NS binding buffer). DNA fragments and DNA-protein complexes were resolved by gel electropho- resis (0.5% TBE, 3% MS agarose gel run at 50 V at 4°C) and visualized after staining with ethidium bromide. Need help summarizing this section of a research paper. The key is to summarize what they did to get their results, I just don't understand what they are saying to even start summarizing what they did. Please someone explain and summarize their step by step process
DNA curvature prediction and electrophoretic mobility shift assays: The upaC promoter region was analyzed in silico using bend.it, a program that enables the prediction of a curvature propensity plot calcu- lated with DNase I-based parameters . The curvature is calculated as a vector sum of dinucleotide geome- tries (roll, tilt, and twist angles) and expressed as degrees per helical turn (10.5°/helical turn 1°/bp). Experimentally tested curved motifs produce curvature values of 5 to 25°/helical turn, whereas straight motifs give val- ues below 5°/helical turn. The upaC 250-bp promoter region was ampli-fied using primers upaC.pro.ext-5 250 and upaC.pro.ext-3-1ATG, and its intrinsic curvature was assessed by comparing its electrophoretic mo- bility with that of an unbent marker fragment (Promega; 100-bp DNA ladder) on a 0.5% Tris-borate-EDTA (TBE), 7.5% PAGE gel at 4°C for retarded gel electrophoretic mobility. Gel shift assays were performed essentially as previously described (3). A DNA mixture comprising an equimolar ratio of the PCR-amplified upaC promoter region and TaqI-SspI-digested pBR322 was incubated at room temperature for 15 min with increasing amounts of native purified H-NS protein (a gift from S. Rimsky) in 30 l of reaction mixture con- taining 40 mM HEPES (pH 8), 60 mM potassium glutamate, 8 mM mag- nesium aspartate, 5 mM dithiothreitol, 10% glycerol, 0.1% octylphenoxy- polyethoxyethanol, 0.1 mg/ml BSA (H-NS binding buffer). DNA fragments and DNA-protein complexes were resolved by gel electropho- resis (0.5% TBE, 3% MS agarose gel run at 50 V at 4°C) and visualized after staining with ethidium bromide.

Explanation / Answer

answers:

DNA Curvature Prediction: It prediction of a curvature propensity plot calculated with DNase-I-based parameters.

The curvature is calculated as a vector sum of dinucleotide geometries and expressed as degrees per helical turn.

Intrinsic curvature was assessed by comparing its electrophoretic mobility with that of an unbent marker fragment.

Gel shift assays :

PCR- amplified upaC promoter region and Increasing of native purified H-NS protein

DNA fragments and DNA-protein complexes were resolved by gel electrophoresis and visualized after staining with ethidium bromide

Related Questions

Navigate

• Browse (All)
• Browse N
• Subjects

---

---

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.