Supporting Information. Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-protein Interactions by 19 F NMR Spectroscopy
|
|
- Natalie Anthony
- 6 years ago
- Views:
Transcription
1 Supporting Information Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-protein Interactions by 19 F NMR Spectroscopy Agata Olszewska, Radek Pohl and Michal Hocek # * Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, Prague 6, Czech Republic # Dept. of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Czech Republic Table of Contents 1. Additional results and figures SI 2. Copies of MALDI-TOF mass spectra SI 3. Copies of NMR spectra SI S1
2 1. Additional results and figures 1.1 Incorporation of dn TAP TP into DNA by PEX Table S1. List of oligonucleotides used or synthesized a Oligonucleotide Sequence prim A 5 -TCA AGA GAC ATG CCT-3 prim B 5 -CAT GGG CGG CAT GGG-3 prim C 5 -GGG TGG GTG GGT GGC TTT TGT-3 temp 19C 5 -C CCG CCC ATG CCG CCC ATG-3 temp 19A 5 -CCCTCCCATGCCGCCCATG-3 temp 19T 5 -CCCACCCATGCCGCCCATG-3 temp 19G 5 -AAACCCCATGCCGCCCATG-3 temp 30_1C 5 -ATA ATA AAC ATG TCT AGG CAT GTC TCT TGA-3 temp CTA GCA TGA GCT CAG TCC CAT GCC GCC CAT G CCC CTT TTT AAC AA A AGC CAC CCA CCC ACC C-3 temp 31_1U temp 30_2C temp 30_2A temp 30_2T temp 30_2G 5 -ATA ATA GAC ATG TCT AGG CAT GTC TCT TGA-3 5 -ACA ACA GAC AGT CTC AGG CAT GTC TCT TGA-3 5 -TTT TTA GGC ATG TCT AGG CAT GTC TCT TGA-3 5 -ATA ATA GAC ATG TCT AGG CAT GTC TCT TGA-3 19ON_1C TAP 5 -CAT GGG CGG CAT GGG CGG G-3 19ON_1A TAP 5 -CAT GGG CGG CAT GGG AGG G-3 19ON_1U TAP 5 -CAT GGG CGG CAT GGG UGG G-3 19ON_1G TAP 5 -CAT GGG CGG CAT GGG GTT T-3 30ON_1C TAP 5 -TCA AGA GAC ATG CCT AGA CAT GTT TAT TAT-3 30ON_2C TAP 5 -TCA AGA GAC ATG CCT AGA CAT GTC TAT TAT-3 31ON_1U TAP 5 -GGG TGG GTG GGT GGC TTT TGT UAA AAA GGG G-3 DNA_1U TAP 3 -GGG GAA AAA UTG TTT TCG GTG GGT GGG TGG G CCC CTT TTT AAC AA A AGC CAC CCA CCC ACC C-3 DNA_1C TAP 3 -AGT TCT CTG TAC GGA TCT GTA CAA ATA ATA-5 5 -TCA AGA GAC ATG CCT AGA CAT GTT TAT TAT-3 a primers are underline, p53 recognition sequences are red, nucleotides bearing modification are in bold. Table S2. List of oligonucleotides used in PCR study Oligonucleotide Sequence (5 3 ) Length prim FOR TAGGGGTTCCGCGCACATTTCCCCG 25-mer prim REV GGAGAGCGTTCACCGACAAACAACAG 26-mer prim FOR-L20 GACATCATGAGAGACATCGC 25-mer prim REV-LT25TH CAAGGACAAAATACCTGTATTCCTT 20-mer TAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGA 339-mer temp Pveg CGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAA TAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAATTCTATTT GACAAAAATGGGCTCGTGTTGTACAATAAATGTGTCTAAGC TTGGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAA CGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGA GAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTC AGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCG temp FVL-A GACATCATGAGAGACATCGCCTCTGGGCTAATAGGACTACT TCTAATCTGTAAGAGCAGATCCCTGGACAGGCAAGGAATAC AGGTATTTTGTCCTTG 98-mer S2
3 Scheme 1. Model reaction of TAP modified monophosphate (dc TAP TP) with N-acetylserine Experimental procedure: dc TAP MP (25 mg, 0.05 mmol) and N-acetylserine (0.36 mg, 2.5 mmol, 50 equiv) were dissolved in triethylammonium acetate (TEAA) buffer (0.3 M, ph 8.4, 2.5 ml) or in acetone/0.1 M NaOH (v/v, 2:1) and the mixture was stirred for 6 days at 25 C. The reaction was monitored by TLC using C3H7OH/H2O/NH4OH (v/v/v, 11/2/7) as a mobile phase. We didn t observe any difference in the mobility of the mixture in comparison to the starting dc TAP MP. Products were then submitted for NMR and mass spectroscopy measurement. We did not observe any formation of the desired cross-linked product. All prepared modified dn TAP TP (da TAP TP, dc TAP TP, du TAP TP and dg TAP TP) were successfully incorporated into short (temp 19_C, temp 19_T, temp 19_A and temp 19_G ) or long DNA (temp 31 ) by primer extension (PEX) using KOD XL, Vent (exo-) or PWO DNA polymerase. Only full length products were observed on denaturing PAGE (Figure S1 and S2). S3
4 Figure S1. Primer extension using KOD XL/Vent(exo-)/PWO polymerases and 19 mer templates (temp 19_1C, temp 19_1T, temp 19_1A, temp 19_1G ), temp 19_1C (lanes 2-4), temp 19_1T (lanes 5-7), temp 19_1A (lanes 8-10) or temp 19_1G (lanes 11-13) with primer prim B. Lane 1 (P): Primer; lanes 2, 5, 8, 11 (C+/T+/A+/G+): natural dntps; lanes 3, 6, 9, 12 (C-/T-/A-/G-): negative control without dctp, dttp, datp or dgtp; lane 4 (C TAP ): dc TAP TP, dttp, dgtp, datp; lane 7 (U TAP ): du TAP TP, datp, dgtp, dctp; lane 10 (A TAP ): da TAP TP, dttp, dgtp, dctp; lane 13 (dg TAP ): dg TAP TP, dttp, dctp, datp. Figure S2. Primer extension using KOD XL/Vent(exo-)/PWO polymerases and 31 mer templates (temp 31 ) with primer prim B. Lane 1, 11, 21 (P): Primer; lanes 2, 12, 22 (+): natural dntps; lanes 3, 5, 7 9, 13, 15, 17, 19, 23, 25, 27, 29 (C-/T-/A-/G-): negative control without dctp, dttp, datp or dgtp; lanes 4, 14, 24 (C TAP ): dc TAP TP, dttp, dgtp, datp; lanes 6, 16, 26, (U TAP ): du TAP TP, datp, dgtp, dctp; lane 8, 18, 28 (A TAP ): da TAP TP, dttp, dgtp, dctp; lanes 10, 20, 30 (dg TAP ): dg TAP TP, dttp, dctp, datp. S4
5 Figure S3. Primer extension using KOD XL polymerases and 31 mer templates (temp 31_1U ) with primer prim C. Lane 1 (P): Primer; lane 2 (+): natural dntps; lane 3(-): negative control without dttp; lane 4 (U TAP ): du TAP TP, dgtp, datp. Figure S4. Primer extension using KOD XL polymerases and 30 mer templates (temp 30_2C, temp 30_2A, temp 30_2T, temp 30_2G ), temp 30_2C (lanes 2-4), temp 30_2A (lanes 5-7), temp 30_2T (lanes 8-10) or temp 30_2G (lanes 11-13) with primer prim A. Lane 1 (P): Primer; lanes 2, 5, 8, 11 (C+/T+/A+/G+): natural dntps; lanes 3, 6, 9, 12 (C-/T-/A-/G-): negative control without dctp, dttp, datp or dgtp; lane 4 (C TAP ): dc TAP TP, dttp, dgtp, datp; lane 7 (A TAP ): da TAP TP, dttp, dgtp, dctp; lane 10 (U TAP ): du TAP TP, datp, dgtp, dctp; lane 13 (dg TAP ): dg TAP TP, dttp, dctp, datp. S5
6 Figure S5. Agarose gel analysis of PCR products amplified by Pwo, Vent(exo-) or KOD XL DNA polymerases, temp FVL-A ; Lane 1 (L): ladder; lanes 2, 5, 8 (+): natural dntps; lanes 3, 6, 9 (C-/A-/T-/G-): negative controls without dctp, dttp or datp; Lane 4 (C TAP ): dc TAP TP, dttp, dgtp, datp; lane 7 (A TAP ): da TAP TP, dctp, dgtp, dttp; lane 10 (U TAP ): du TAP TP, datp, dctp, dgtp; 1.3 % (2%) agarose gel for 339-mer (98-mer) stained with GelRed. Figure S6. Agarose gel analysis of PCR products amplified by Pwo, Vent(exo-) or KOD XL DNA polymerase, temp Pveg ; Lane 1 (L): ladder; lanes 2, 5, 8, 11 (+): natural dntps; lanes 3, 6, 9, 12 (C-/A-/T-/G-): negative controls without dctp, dttp, datp or dgtp; Lane 4 (C TAP ): ): dc TAP TP, dttp, dgtp, datp; lane 7 (A TAP ): da TAP TP, dctp, dgtp, dttp; lane 10 (U TAP ): du TAP TP, datp, dctp, dgtp; 1.3 % (2%) agarose gel for 339-mer (98-mer) stained with GelRed. S6
7 Figure S7. Agarose gel analysis of PCR products amplified by Pwo, Vent(exo-) or KOD XL DNA polymerase, temp FVL-A and temp Pveg ; Lane 1 (L): ladder; lanes 2, 5, 8, 11 (+): natural dntps; lanes 3, 6, 9, 12 (C-/A-/T-/G-): negative controls without dctp, dttp, datp or dgtp; Lane 4 (C TAP ): ): dc TAP TP, dttp, dgtp, datp; lane 7 (A TAP ): da TAP TP, dctp, dgtp, dttp; lane 10 (U TAP ): du TAP TP, datp, dctp, dgtp; 1.3 % (2%) agarose gel for 339-mer (98-mer). Incubation of modified DNA with tumour suppressor protein p53 Modified DNAs (DNA_2C TAP ) were prepared by PEX and incubated with different ratios of p53 mutants in order to test its binding activity. The ability of GSTp53_C275S or GSTp53_C277S mutants of p53 to recognize modified DNA was monitored by 5% EMSA (Figure S8A ) confirmed that the DNA modifications do not prevent binding of p53. Then SDS PAGE was performed to see if covalent cross-links have been formed. (Figure S8B) does not show formation of covalent conjugates represented by the bands with lower mobility. Figure S8. A) 5% EMSA analysis of formation of complex between DNA_1C TAP and GSTp53_C275S or GSTp53_C277S mutants of GSTp53 protein (with increasing number of equivalents of the protein, see below the gels); B) 12.5 % SDS PAGE analysis of the potential S7
8 formation of covalently cross-linked product DNA_1C TAP + GSTp53_C275S or C277S ; (with increasing number of equivalents of the protein, see below the gels). Conditions: DNA (0.3 pmol), ph 7.6, 0 C/30 min (a) then 25 C/2 hours (b). Figure S9. A) 5% EMSA analysis of formation of complex between DNA_2X TAP and GSTp53_C277S mutant of GSTp53 protein; B) 12.5 % SDS PAGE analysis of the potential formation of covalently cross-linked product DNAC TAP + GSTp53_C277S. Lane 1: natural DNA; lanes 2, 4, 6, 8,11, 13, 15, 17: natural DNA with p53; lanes 3, 12: DNA_2C TAP + p53; Lanes 5, 14: DNA_2A TAP + p53; lane 7, 16 DNA_2U TAP + p53; lanes 9, 18: DNA_2G TAP + p53. Conditions: DNA_2X TAP (0.3 pmol), ph 7.6, 0 C/30 min (a) then 25 C/2 hours (b). Figure S10. 5% EMSA analysis of formation of complex between A) DNA_1C TAP and GSTp53CD B) DNA_1C TAP and BSA for 19 F NMR studies. lane 1: DNA_1C TAP, lane 2: DNA_1C TAP + GSTp53CD; lane 3: DNA_1C TAP ; lane 4: DNA_1C TAP + BSA. Conditions: DNA_1C TAP (0.7 nmol), GSTp53CD (1.19 nmol) BSA (1.19 nmol) ph 7.6, 0 C/30 min S8
9 Figure S11. 5% EMSA analysis of the formation of the complex between DNA_1C TAP and GSTp53CD for 19 F NMR studies A) DNA_1C TAP and GSTp53CD before 19 F NMR studies B) DNA_1C TAP and GSTp53CD after overnight 19 F NMR measurement C) DNA_1C TAP and GSTp53CD after protein denaturation. lane 1, 3, 5: DNA_1C TAP, lane 2, 4, 6: DNA_1C TAP + GSTp53CD. Conditions: DNA_1C TAP (0.7 nmol), GSTp53CD (1.75 nmol) ph 7.6, 0 C/30 min; for the denaturation 55 C/60 min. S9
10 Figure S F NMR spectra of DNA_1C TAP and GSTp53CD for 19 F NMR studies A) DNA_1C TAP B) DNA_1C TAP and GSTp53CD C) DNA_1C TAP and GSTp53CD after protein denaturation. Conditions: DNA_1C TAP (0.7 nmol), GSTp53CD (1.75 nmol) ph 7.6, 0 C/30 min; for the denaturation 55 C/60 min. Figure S13. Analysis of oligonucleotide annealing by electrophoresis in agarose gel; Lane 1 ssdna (31ON_1U TAP ); lane 2: dsdna. S10
11 2. Copies of MALDI-TOF mass spectra SI Figure S14. MALDI spectrum of 19ON_1C TAP. M (calcd) = Da, M (found) = Da [M+3H] -. S11
12 Figure S15. MALDI spectrum of 19ON_1G TAP. M (calcd) = Da, M (found) = Da [M+1H] -. Figure S16. MALDI spectrum of 19ON_1A TAP. M (calcd) = 6150 Da, M (found) = Da [M+H] -. S12
13 Figure S17. MALDI spectrum of 30ON_1C TAP. M (calcd) = Da, M (found) = Da [M+H] -. Figure S18. MALDI spectrum of 19ON_1U TAP. M (calcd) = Da, M (found) = Da [M+2H] -. S13
14 Figure S19. MALDI spectrum of 31ON_1U TAP. M (calcd) = Da, M (found) = 9958 Da [M+H] Copies of NMR spectra 1.dC TAP S14
15 S15
16 2.dC TAP MP S16
17 S17
18 3.dC TAP TP S18
19 S19
20 4. da TAP S20
21 S21
22 S22
23 5. da TAP MP S23
24 S24
25 6. da TAP TP S25
26 S26
27 7. du TAP S27
28 S28
29 S29
30 8. du TAP MP S30
31 S31
32 9. du TAP TP S32
33 S33
34 10. dg TAP S34
35 S35
36 S36
37 11. dg TAP MP S37
38 S38
39 12. dg TAP TP S39
40 S40
41 13. DNA_1C TAP A) Without C6F6 for external lock and reference signal (-163 ppm). B) With C6F6 in 1 mm coaxial capillary for external lock and reference signal (-163 ppm). S41
42 14. DNA_1C TAP + GSTp53CD A) Without C6F6 for external lock and reference signal (-163 ppm). DNA_1C TAP : GSTp53CD 1:1.7 B) With C6F6 in 1 mm coaxial capillary for external lock and reference signal (-163 ppm). DNA_1C TAP : GSTp53CD 1:2.5 S42
43 15. DNA_1C TAP after p53 denaturation With C6F6 in 1 mm coaxial capillary for external lock and reference signal (-163 ppm). 16. DNAC TAP + BSA S43
44 17. ssdna_u TAP 18. dsdna_u TAP S44
Electronic Supplementary Information
Electronic Supplementary Material (ESI) for Molecular BioSystems. This journal is The Royal Society of Chemistry 2017 Electronic Supplementary Information Dissecting binding of a β-barrel outer membrane
More informationLecture 10, 20/2/2002: The process of solution development - The CODEHOP strategy for automatic design of consensus-degenerate primers for PCR
Lecture 10, 20/2/2002: The process of solution development - The CODEHOP strategy for automatic design of consensus-degenerate primers for PCR 1 The problem We wish to clone a yet unknown gene from a known
More informationAdd 5µl of 3N NaOH to DNA sample (final concentration 0.3N NaOH).
Bisulfite Treatment of DNA Dilute DNA sample to 2µg DNA in 50µl ddh 2 O. Add 5µl of 3N NaOH to DNA sample (final concentration 0.3N NaOH). Incubate in a 37ºC water bath for 30 minutes. To 55µl samples
More informationSupporting Online Information
Supporting Online Information Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity Preeti Rathi, Sara Maurer, Grzegorz Kubik and Daniel Summerer* Department of Chemistry and Chemical
More informationPGRP negatively regulates NOD-mediated cytokine production in rainbow trout liver cells
Supplementary Information for: PGRP negatively regulates NOD-mediated cytokine production in rainbow trout liver cells Ju Hye Jang 1, Hyun Kim 2, Mi Jung Jang 2, Ju Hyun Cho 1,2,* 1 Research Institute
More informationArabidopsis actin depolymerizing factor AtADF4 mediates defense signal transduction triggered by the Pseudomonas syringae effector AvrPphB
Arabidopsis actin depolymerizing factor mediates defense signal transduction triggered by the Pseudomonas syringae effector AvrPphB Files in this Data Supplement: Supplemental Table S1 Supplemental Table
More informationY-chromosomal haplogroup typing Using SBE reaction
Schematic of multiplex PCR followed by SBE reaction Multiplex PCR Exo SAP purification SBE reaction 5 A 3 ddatp ddgtp 3 T 5 A G 3 T 5 3 5 G C 5 3 3 C 5 ddttp ddctp 5 T 3 T C 3 A 5 3 A 5 5 C 3 3 G 5 3 G
More informationSupplementary. Table 1: Oligonucleotides and Plasmids. complementary to positions from 77 of the SRα '- GCT CTA GAG AAC TTG AAG TAC AGA CTG C
Supplementary Table 1: Oligonucleotides and Plasmids 913954 5'- GCT CTA GAG AAC TTG AAG TAC AGA CTG C 913955 5'- CCC AAG CTT ACA GTG TGG CCA TTC TGC TG 223396 5'- CGA CGC GTA CAG TGT GGC CAT TCT GCT G
More informationstrain devoid of the aox1 gene [1]. Thus, the identification of AOX1 in the intracellular
Additional file 2 Identification of AOX1 in P. pastoris GS115 with a Mut s phenotype Results and Discussion The HBsAg producing strain was originally identified as a Mut s (methanol utilization slow) strain
More informationFigure S1. Characterization of the irx9l-1 mutant. (A) Diagram of the Arabidopsis IRX9L gene drawn based on information from TAIR (the Arabidopsis
1 2 3 4 5 6 7 8 9 10 11 12 Figure S1. Characterization of the irx9l-1 mutant. (A) Diagram of the Arabidopsis IRX9L gene drawn based on information from TAIR (the Arabidopsis Information Research). Exons
More informationSupporting information for Biochemistry, 1995, 34(34), , DOI: /bi00034a013
Supporting information for Biochemistry, 1995, 34(34), 10807 10815, DOI: 10.1021/bi00034a013 LESNIK 10807-1081 Terms & Conditions Electronic Supporting Information files are available without a subscription
More informationRPA-AB RPA-C Supplemental Figure S1: SDS-PAGE stained with Coomassie Blue after protein purification.
RPA-AB RPA-C (a) (b) (c) (d) (e) (f) Supplemental Figure S: SDS-PAGE stained with Coomassie Blue after protein purification. (a) RPA; (b) RPA-AB; (c) RPA-CDE; (d) RPA-CDE core; (e) RPA-DE; and (f) RPA-C
More informationHes6. PPARα. PPARγ HNF4 CD36
SUPPLEMENTARY INFORMATION Supplementary Table Positions and Sequences of ChIP primers -63 AGGTCACTGCCA -79 AGGTCTGCTGTG Hes6-0067 GGGCAaAGTTCA ACOT -395 GGGGCAgAGTTCA PPARα -309 GGCTCAaAGTTCAaGTTCA CPTa
More informationSupplementary Figure 1A A404 Cells +/- Retinoic Acid
Supplementary Figure 1A A44 Cells +/- Retinoic Acid 1 1 H3 Lys4 di-methylation SM-actin VEC cfos (-) RA (+) RA 14 1 1 8 6 4 H3 Lys79 di-methylation SM-actin VEC cfos (-) RA (+) RA Supplementary Figure
More informationSupporting Information
Supporting Information Table S1. Oligonucleotide sequences used in this work Oligo DNA A B C D CpG-A CpG-B CpG-C CpG-D Sequence 5 ACA TTC CTA AGT CTG AAA CAT TAC AGC TTG CTA CAC GAG AAG AGC CGC CAT AGT
More informationSupplemental Data Supplemental Figure 1.
Supplemental Data Supplemental Figure 1. Silique arrangement in the wild-type, jhs, and complemented lines. Wild-type (WT) (A), the jhs1 mutant (B,C), and the jhs1 mutant complemented with JHS1 (Com) (D)
More informationSupplementary Information
Supplementary Information A general solution for opening double-stranded DNA for isothermal amplification Gangyi Chen, Juan Dong, Yi Yuan, Na Li, Xin Huang, Xin Cui* and Zhuo Tang* Supplementary Materials
More informationLegends for supplementary figures 1-3
High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology Sidsel Nag 1,2 *, Marlene D. Dalgaard 3, Poul-Erik
More informationΔPDD1 x ΔPDD1. ΔPDD1 x wild type. 70 kd Pdd1. Pdd3
Supplemental Fig. S1 ΔPDD1 x wild type ΔPDD1 x ΔPDD1 70 kd Pdd1 50 kd 37 kd Pdd3 Supplemental Fig. S1. ΔPDD1 strains express no detectable Pdd1 protein. Western blot analysis of whole-protein extracts
More informationSupplemental material
Supplemental material Diversity of O-antigen repeat-unit structures can account for the substantial sequence variation of Wzx translocases Yaoqin Hong and Peter R. Reeves School of Molecular Bioscience,
More informationhcd1tg/hj1tg/ ApoE-/- hcd1tg/hj1tg/ ApoE+/+
ApoE+/+ ApoE-/- ApoE-/- H&E (1x) Supplementary Figure 1. No obvious pathology is observed in the colon of diseased ApoE-/me. Colon samples were fixed in 1% formalin and laid out in Swiss rolls for paraffin
More informationSupplement 1: Sequences of Capture Probes. Capture probes were /5AmMC6/CTG TAG GTG CGG GTG GAC GTA GTC
Supplementary Appendixes Supplement 1: Sequences of Capture Probes. Capture probes were /5AmMC6/CTG TAG GTG CGG GTG GAC GTA GTC ACG TAG CTC CGG CTG GA-3 for vimentin, /5AmMC6/TCC CTC GCG CGT GGC TTC CGC
More informationMaterials Protein synthesis kit. This kit consists of 24 amino acids, 24 transfer RNAs, four messenger RNAs and one ribosome (see below).
Protein Synthesis Instructions The purpose of today s lab is to: Understand how a cell manufactures proteins from amino acids, using information stored in the genetic code. Assemble models of four very
More informationSupplemental Data. mir156-regulated SPL Transcription. Factors Define an Endogenous Flowering. Pathway in Arabidopsis thaliana
Cell, Volume 138 Supplemental Data mir156-regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana Jia-Wei Wang, Benjamin Czech, and Detlef Weigel Table S1. Interaction
More informationGene synthesis by circular assembly amplification
Gene synthesis by circular assembly amplification Duhee Bang & George M Church Supplementary figures and text: Supplementary Figure 1. Dpo4 gene (1.05kb) construction by various methods. Supplementary
More informationSupporting Information. Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2006
Supporting Information Copyright Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, 2006 Copyright Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, 2006 Supporting Information for Expanding the Genetic
More informationAn engineered tryptophan zipper-type peptide as a molecular recognition scaffold
SUPPLEMENTARY MATERIAL An engineered tryptophan zipper-type peptide as a molecular recognition scaffold Zihao Cheng and Robert E. Campbell* Supplementary Methods Library construction for FRET-based screening
More informationSupplementary Materials for
www.sciencesignaling.org/cgi/content/full/10/494/eaan6284/dc1 Supplementary Materials for Activation of master virulence regulator PhoP in acidic ph requires the Salmonella-specific protein UgtL Jeongjoon
More informationPCR analysis was performed to show the presence and the integrity of the var1csa and var-
Supplementary information: Methods: Table S1: Primer Name Nucleotide sequence (5-3 ) DBL3-F tcc ccg cgg agt gaa aca tca tgt gac tg DBL3-R gac tag ttt ctt tca ata aat cac tcg c DBL5-F cgc cct agg tgc ttc
More informationSUPPORTING INFORMATION
SUPPORTING INFORMATION Investigation of the Biosynthesis of the Lasso Peptide Chaxapeptin Using an E. coli-based Production System Helena Martin-Gómez, Uwe Linne, Fernando Albericio, Judit Tulla-Puche,*
More informationPCR-based Markers and Cut Flower Longevity in Carnation
PCRbased Markers and Cut Flower Longevity in Carnation Laura De Benedetti, Luca Braglia, Simona Bruna, Gianluca Burchi *, Antonio Mercuri and Tito Schiva Istituto Sperimentale per la Floricoltura, Corso
More informationDisease and selection in the human genome 3
Disease and selection in the human genome 3 Ka/Ks revisited Please sit in row K or forward RBFD: human populations, adaptation and immunity Neandertal Museum, Mettman Germany Sequence genome Measure expression
More informationCat. # Product Size DS130 DynaExpress TA PCR Cloning Kit (ptakn-2) 20 reactions Box 1 (-20 ) ptakn-2 Vector, linearized 20 µl (50 ng/µl) 1
Product Name: Kit Component TA PCR Cloning Kit (ptakn-2) Cat. # Product Size DS130 TA PCR Cloning Kit (ptakn-2) 20 reactions Box 1 (-20 ) ptakn-2 Vector, linearized 20 µl (50 ng/µl) 1 2 Ligation Buffer
More informationORFs and genes. Please sit in row K or forward
ORFs and genes Please sit in row K or forward https://www.flickr.com/photos/teseum/3231682806/in/photostream/ Question: why do some strains of Vibrio cause cholera and others don t? Methods Mechanisms
More informationSupplementary Information. Construction of Lasso Peptide Fusion Proteins
Supplementary Information Construction of Lasso Peptide Fusion Proteins Chuhan Zong 1, Mikhail O. Maksimov 2, A. James Link 2,3 * Departments of 1 Chemistry, 2 Chemical and Biological Engineering, and
More informationQuantitative reverse-transcription PCR. Transcript levels of flgs, flgr, flia and flha were
1 Supplemental methods 2 3 4 5 6 7 8 9 1 11 12 13 14 15 16 17 18 19 21 22 23 Quantitative reverse-transcription PCR. Transcript levels of flgs, flgr, flia and flha were monitored by quantitative reverse-transcription
More informationSupporting Information
Supporting Information Barderas et al. 10.1073/pnas.0801221105 SI Text: Docking of gastrin to Constructed scfv Models Interactive predocking of the 4-WL-5 motif into the central pocket observed in the
More informationNAME:... MODEL ANSWER... STUDENT NUMBER:... Maximum marks: 50. Internal Examiner: Hugh Murrell, Computer Science, UKZN
COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 1 NAME:...... MODEL ANSWER... STUDENT NUMBER:...... Maximum marks: 50 Internal Examiner: Hugh Murrell, Computer
More informationTable S1. Bacterial strains (Related to Results and Experimental Procedures)
Table S1. Bacterial strains (Related to Results and Experimental Procedures) Strain number Relevant genotype Source or reference 1045 AB1157 Graham Walker (Donnelly and Walker, 1989) 2458 3084 (MG1655)
More informationSupplemental Data. Bennett et al. (2010). Plant Cell /tpc
BRN1 ---------MSSSNGGVPPGFRFHPTDEELLHYYLKKKISYEKFEMEVIKEVDLNKIEPWDLQDRCKIGSTPQNEWYFFSHKDRKYPTGS 81 BRN2 --------MGSSSNGGVPPGFRFHPTDEELLHYYLKKKISYQKFEMEVIREVDLNKLEPWDLQERCKIGSTPQNEWYFFSHKDRKYPTGS 82 SMB
More informationSupplemental Table 1. Mutant ADAMTS3 alleles detected in HEK293T clone 4C2. WT CCTGTCACTTTGGTTGATAGC MVLLSLWLIAAALVEVR
Supplemental Dataset Supplemental Table 1. Mutant ADAMTS3 alleles detected in HEK293T clone 4C2. DNA sequence Amino acid sequence WT CCTGTCACTTTGGTTGATAGC MVLLSLWLIAAALVEVR Allele 1 CCTGTC------------------GATAGC
More informationDierks Supplementary Fig. S1
Dierks Supplementary Fig. S1 ITK SYK PH TH K42R wt K42R (kinase deficient) R29C E42K Y323F R29C E42K Y323F (reduced phospholipid binding) (enhanced phospholipid binding) (reduced Cbl binding) E42K Y323F
More informationMacBlunt PCR Cloning Kit Manual
MacBlunt PCR Cloning Kit Manual Shipping and Storage MacBlunt PCR Cloning Kits are shipped on dry ice. Each kit contains a box with cloning reagents and an attached bag with Eco-Blue Competent Cells (optional).
More informationSupplementary Figures
Supplementary Figures Supplementary Fig. 1 Characterization of GSCs. a. Immunostaining of primary GSC spheres from GSC lines. Nestin (neural progenitor marker, red), TLX (green). Merged images of nestin,
More informationSequencing of DNA lesions facilitated by site-specific excision via base. excision repair DNA glycosylases yielding ligatable gaps
Supporting information Sequencing of DNA lesions facilitated by site-specific excision via base excision repair DNA glycosylases yielding ligatable gaps Jan Riedl, Aaron M. Fleming, and Cynthia J. Burrows*
More informationProject 07/111 Final Report October 31, Project Title: Cloning and expression of porcine complement C3d for enhanced vaccines
Project 07/111 Final Report October 31, 2007. Project Title: Cloning and expression of porcine complement C3d for enhanced vaccines Project Leader: Dr Douglas C. Hodgins (519-824-4120 Ex 54758, fax 519-824-5930)
More informationComplexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions
Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions Vered Israeli-Ruimy 1,*, Pedro Bule 2,*, Sadanari Jindou 3, Bareket Dassa
More informationOverexpression Normal expression Overexpression Normal expression. 26 (21.1%) N (%) P-value a N (%)
SUPPLEMENTARY TABLES Table S1. Alteration of ZNF322A protein expression levels in relation to clinicopathological parameters in 123 Asian and 74 Caucasian lung cancer patients. Asian patients Caucasian
More informationSupporting Information
Supporting Information Wiley-VCH 2007 69451 Weinheim, Germany Site-Specific Control of Distances between Gold Nanoparticles using Phosphorothioate Anchors on DNA and a Short Bifunctional Molecular Fastener
More informationConverting rabbit hybridoma into recombinant antibodies with effective transient production in an optimized human expression system
Converting rabbit hybridoma into recombinant antibodies with effective transient production in an optimized human expression system Dr. Tim Welsink Molecular Biology Transient Gene Expression OUTLINE Short
More informationSUPPLEMENTARY INFORMATION
doi: 10.1038/nature07182 SUPPLEMENTAL FIGURES AND TABLES Fig. S1. myf5-expressing cells give rise to brown fat depots and skeletal muscle (a) Perirenal BAT from control (cre negative) and myf5-cre:r26r3-yfp
More informationMultiplexing Genome-scale Engineering
Multiplexing Genome-scale Engineering Harris Wang, Ph.D. Department of Systems Biology Department of Pathology & Cell Biology http://wanglab.c2b2.columbia.edu Rise of Genomics An Expanding Toolbox Esvelt
More informationII 0.95 DM2 (RPP1) DM3 (At3g61540) b
Table S2. F 2 Segregation Ratios at 16 C, Related to Figure 2 Cross n c Phenotype Model e 2 Locus A Locus B Normal F 1 -like Enhanced d Uk-1/Uk-3 149 64 36 49 DM2 (RPP1) DM1 (SSI4) a Bla-1/Hh-0 F 3 111
More informationSupporting Information
Supporting Information Transfection of DNA Cages into Mammalian Cells Email: a.turberfield@physics.ox.ac.uk Table of Contents Supporting Figure 1 DNA tetrahedra used in transfection experiments 2 Supporting
More informationSupplemental Information. Human Senataxin Resolves RNA/DNA Hybrids. Formed at Transcriptional Pause Sites. to Promote Xrn2-Dependent Termination
Supplemental Information Molecular Cell, Volume 42 Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination Konstantina Skourti-Stathaki, Nicholas
More informationDet matematisk-naturvitenskapelige fakultet
UNIVERSITETET I OSLO Det matematisk-naturvitenskapelige fakultet Exam in: MBV4010 Arbeidsmetoder i molekylærbiologi og biokjemi I MBV4010 Methods in molecular biology and biochemistry I Day of exam: Friday
More informationElectronic Supplementary Information. Transcription Monitoring Using Fused RNA with a Dye-Binding Light-Up Aptamer as a Tag: A Blue Fluorescent RNA
Electronic Supplementary Information for Transcription Monitoring Using Fused RNA with a Dye-Binding Light-Up Aptamer as a Tag: A Blue Fluorescent RNA Shinsuke Sando,* Atsushi Narita, Masayoshi Hayami,
More informationLecture 11: Gene Prediction
Lecture 11: Gene Prediction Study Chapter 6.11-6.14 1 Gene: A sequence of nucleotides coding for protein Gene Prediction Problem: Determine the beginning and end positions of genes in a genome Where are
More informationPrimer Design Workshop. École d'été en géné-que des champignons 2012 Dr. Will Hintz University of Victoria
Primer Design Workshop École d'été en géné-que des champignons 2012 Dr. Will Hintz University of Victoria Scenario You have discovered the presence of a novel endophy5c organism living inside the cells
More informationProtein Structure Analysis
BINF 731 Protein Structure Analysis http://binf.gmu.edu/vaisman/binf731/ Iosif Vaisman COMPUTATIONAL BIOLOGY COMPUTATIONAL STRUCTURAL BIOLOGY COMPUTATIONAL MOLECULAR BIOLOGY BIOINFORMATICS STRUCTURAL BIOINFORMATICS
More information2
1 2 3 4 5 6 7 Supplemental Table 1. Magnaporthe oryzae strains generated in this study. Strain background Genotype Strain name Description Guy-11 H1:RFP H1:RFP Strain expressing Histone H1- encoding gene
More informationSupplementary Figure 1. Localization of MST1 in RPE cells. Proliferating or ciliated HA- MST1 expressing RPE cells (see Fig. 5b for establishment of
Supplementary Figure 1. Localization of MST1 in RPE cells. Proliferating or ciliated HA- MST1 expressing RPE cells (see Fig. 5b for establishment of the cell line) were immunostained for HA, acetylated
More information11th Meeting of the Science Working Group. Lima, Peru, October 2012 SWG-11-JM-11
11th Meeting of the Science Working Group Lima, Peru, 15-19 October 2012 Russian population genetics studies of jack mackerel in the South Pacific P.K.Afanasiev M.A.Rabchun A.I.Glubokov Introduction. In
More informationS4B fluorescence (AU)
A S4B fluorescence (AU) S4B fluorescence (AU) dsbb csgba csgd dsbb csgba bcsa 5000 * NS NS 4000 * 3000 2000 1000 0 ΔcsgBAΔbcsA ΔcsgDΔdsbBΔbcsA ΔcsgBA ΔdsbBΔcsgBA ΔcsgDΔdsbB B -1000 4000 * * NS 3500 * 3000
More informationTable S1. Sequences of mutagenesis primers used to create altered rdpa- and sdpa genes
Supplementary Table and Figures for Structural Basis for the Enantiospecificities of R- and S-Specific Phenoxypropionate/α-Ketoglutarate Dioxygenases by Tina A. Müller, Maria I. Zavodszky, Michael Feig,
More informationSAY IT WITH DNA: Protein Synthesis Activity by Larry Flammer
TEACHER S GUIDE SAY IT WITH DNA: Protein Synthesis Activity by Larry Flammer SYNOPSIS This activity uses the metaphor of decoding a secret message for the Protein Synthesis process. Students teach themselves
More informationAnti-Pim-1 (Cat#3247), anti-met (Cat#3127), anti-ron (Cat#2654), Anti-EGFR
Supplementary Methods Antibodies Anti-Pim-1 (Cat#3247), anti-met (Cat#3127), anti-ron (Cat#2654), Anti-EGFR (Cat#2646), anti-igf1r (Cat#3018), anti-insr (Cat#3020), anti-akt (pan, Cat#4691), anti-phospho-akt
More informationCodon Bias with PRISM. 2IM24/25, Fall 2007
Codon Bias with PRISM 2IM24/25, Fall 2007 from RNA to protein mrna vs. trna aminoacid trna anticodon mrna codon codon-anticodon matching Watson-Crick base pairing A U and C G binding first two nucleotide
More informationSearch for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice (Oryza sativa, Oryza rufipogon) and Establishment of SNP Markers
DNA Research 9, 163 171 (2002) Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice (Oryza sativa, Oryza rufipogon) and Establishment of SNP Markers Shinobu Nasu, Junko Suzuki, Rieko
More informationSupplemental Table 1. Primers used for PCR.
Supplemental Table 1. Primers used for PCR. Gene Type Primer Sequence Genotyping and semi-quantitative RT-PCR F 5 -TTG CCC GAT CAC CAT CTG TA-3 rwa1-1 R 5 -TGT AGC GAT CAA GGC CTG ATC TAA-3 LB 5 -TAG CAT
More informationSUPPORTING INFORMATION FILE
Intrinsic and extrinsic connections of Tet3 dioxygenase with CXXC zinc finger modules Nan Liu, Mengxi Wang, Wen Deng, Christine S. Schmidt, Weihua Qin, Heinrich Leonhardt and Fabio Spada Department of
More informationPhosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP- Driven Ribonuclease
Supplemental Information Molecular Cell, Volume 42 hosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an AT- Driven Ribonuclease Elif Sarinay Cenik, Ryuya Fukunaga, Gang Lu, Robert Dutcher,
More information-15 diopter negative lenses in wild-type and homozygous CHRM2-deleted mice, and
Supplementary Materials Supplementary Figure 1: Myopia induction was performed using uniocular -10 and -15 diopter negative lenses in wild-type and homozygous CHRM2-deleted mice, and results at 2, 4 and
More informationLecture 19A. DNA computing
Lecture 19A. DNA computing What exactly is DNA (deoxyribonucleic acid)? DNA is the material that contains codes for the many physical characteristics of every living creature. Your cells use different
More informationCreation of A Caspese-3 Sensing System Using A Combination of Split- GFP and Split-Intein
Supplementary Information Creation of A Caspese-3 Sensing System Using A Combination of Split- GFP and Split-Intein Seiji Sakamoto,* Mika Terauchi, Anna Hugo, Tanner Kim, Yasuyuki Araki and Takehiko Wada*
More informationA green method of staining DNA in polyacrylamide gel electrophoresis based on fluorescent copper nanoclusters synthesized in situ
Electronic Supplementary Material A green method of staining DNA in polyacrylamide gel electrophoresis based on fluorescent copper nanoclusters synthesized in situ Xiaoli Zhu 1, Hai Shi 1, Yalan Shen 1,
More informationA netlike rolling circle nucleic acid amplification technique
Electronic Supplementary Material (ESI) for Analyst. This journal is The Royal Society of Chemistry 2014 Supplementary Information A netlike rolling circle nucleic acid amplification technique Xiaoli Zhu,
More informationGlutathione (GSH)-Decorated Magnetic Nanoparticles for Binding Glutathione-S-transferase (GST) Fusion Protein and Manipulating Live Cells
Glutathione (GSH)-Decorated Magnetic Nanoparticles for Binding Glutathione-S-transferase (GST) Fusion Protein and Manipulating Live Cells Yue Pan, Marcus J. C. Long, Xinming Li, Junfeng Shi, Lizbeth Hedstrom,
More informationA high efficient electrochemiluminescence resonance energy. transfer system in one nanostructure: its application for
Supporting Information for A high efficient electrochemiluminescence resonance energy transfer system in one nanostructure: its application for ultrasensitive detection of microrna in cancer cells Zhaoyang
More informationG+C content. 1 Introduction. 2 Chromosomes Topology & Counts. 3 Genome size. 4 Replichores and gene orientation. 5 Chirochores.
1 Introduction 2 Chromosomes Topology & Counts 3 Genome size 4 Replichores and gene orientation 5 Chirochores 6 7 Codon usage 121 marc.bailly-bechet@univ-lyon1.fr Bacterial genome structures Introduction
More informationNESTED Sequence-based Typing (SBT) protocol for epidemiological typing of Legionella pneumophila directly from clinical samples
NESTED Sequence-based Typing (SBT) protocol for epidemiological typing of Legionella pneumophila directly from clinical samples VERSION 2.0 SUMMARY This procedure describes the use of nested Sequence-Based
More informationSupplemental Information. Target-Mediated Protection of Endogenous. MicroRNAs in C. elegans. Inventory of Supplementary Information
Developmental Cell, Volume 20 Supplemental Information Target-Mediated Protection of Endogenous MicroRNAs in C. elegans Saibal Chatterjee, Monika Fasler, Ingo Büssing, and Helge Großhans Inventory of Supplementary
More informationHomework. A bit about the nature of the atoms of interest. Project. The role of electronega<vity
Homework Why cited articles are especially useful. citeulike science citation index When cutting and pasting less is more. Project Your protein: I will mail these out this weekend If you haven t gotten
More informationNongenetic Reprogramming of the Ligand Specificity. of Growth Factor Receptors by Bispecific DNA Aptamers
Supporting Information For Nongenetic Reprogramming of the Ligand Specificity of Growth Factor Receptors by Bispecific DNA Aptamers Ryosuke Ueki,* Saki Atsuta, Ayaka Ueki and Shinsuke Sando* Department
More informationWet Lab Tutorial: Genelet Circuits
Wet Lab Tutorial: Genelet Circuits DNA 17 This tutorial will introduce the in vitro transcriptional circuits toolkit. The tutorial will focus on the design, synthesis, and experimental testing of a synthetic
More informationSupplementary Figure 1. Analysis of replication rates by Pol. Nature Structural & Molecular Biology: doi: /nsmb.3207
Supplementary Figure 1 Analysis of replication rates by Pol (a) Electrophoretic Mobility Shift Assay (EMSA) of Pol -DV binding to template-primer DNA (Fried, M. & Crothers, D.M. Equilibria and kinetics
More informationSupporting Information
Supporting Information CLOSTRIDIOLYSIN S: A POST-TRANSLATIONALLY MODIFIED BIOTOXIN FROM CLOSTRIDIUM BOTULINUM David J. Gonzalez 1, Shaun W. Lee 9, Mary E. Hensler 6, Andrew L. Markley 1, Samira Dahesh
More informationSUPPLEMENTAL TABLE S1. Additional descriptions of plasmid constructions and the oligonucleotides used Plasmid or Oligonucleotide
SUPPLEMENTAL TABLE S1. Additional descriptions of plasmid constructions and the oligonucleotides used Plasmid or Oligonucleotide former/ working Description a designation Plasmids pes213a b pes213-tn5
More informationElectronic Supplementary Information
Electronic Supplementary Information Ultrasensitive and Selective DNA Detection Based on Nicking Endonuclease Assisted Signal Amplification and Its Application in Cancer Cells Detection Sai Bi, Jilei Zhang,
More informationSUPPLEMENTAL MATERIAL GENOTYPING WITH MULTIPLEXING TARGETED RESEQUENCING
SUPPLEMENTAL MATERIAL GENOTYPING WITH MULTIPLEXING TARGETED RESEQUENCING All of the patients and control subjects were sequenced and genotyped in the same way. Shotgun libraries of approximately 250 bp
More informationSUPPLEMENTARY INFORMATION
1. RNA/DNA sequences used in this study 2. Height and stiffness measurements on hybridized molecules 3. Stiffness maps at varying concentrations of target DNA 4. Stiffness measurements on RNA/DNA hybrids.
More informationThe B1 Protein Guides the Biosynthesis of a Lasso Peptide
The B1 Protein Guides the Biosynthesis of a Lasso Peptide Shaozhou Zhu 1,2, Christopher D. Fage 1, Julian D. Hegemann 1, Andreas Mielcarek 1, Dushan Yan 1, Uwe Linne 1 & Mohamed A. Marahiel*,1 1 Department
More informationChapter 13 Chromatin Structure and its Effects on Transcription
Chapter 13 Chromatin Structure and its Effects on Transcription Students must be positive that they understand standard PCR. There is a resource on the web for this purpose. Warn them before this class.
More informationfor Programmed Chemo-enzymatic Synthesis of Antigenic Oligosaccharides
Supporting Information Design of α-transglucosidases of Controlled Specificity for Programmed Chemo-enzymatic Synthesis of Antigenic Oligosaccharides Elise Champion ±,,,, Isabelle André ±,,, Claire Moulis
More informationEngineering Escherichia coli for production of functionalized terpenoids using plant P450s
Supplementary Information for Engineering Escherichia coli for production of functionalized terpenoids using plant P450s Michelle C. Y. Chang, Rachel A. Eachus, William Trieu, Dae-Kyun Ro, and Jay D. Keasling*
More informationSupplementary Methods Quantitative RT-PCR. For mrna, total RNA was prepared using TRIzol reagent (Invitrogen) and genomic DNA was eliminated with TURB
Supplementary Methods Quantitative RT-PCR. For mrna, total RNA was prepared using TRIzol reagent (Invitrogen) and genomic DNA was eliminated with TURBO DNA-free Kit (Ambion). One µg of total RNA was reverse
More informationYeast BioBrick Assembly (YBA)
Yeast BioBrick Assembly (YBA) Standardized method for vector assembly of BioBrick devices via homologous recombination in Saccharomyces cerevisiae Martin Schneider, Leonard Fresenborg, Virginia Schadeweg
More informationSupplementary information
Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2017 Supplementary information Structural insights into the EthR-DNA interaction from native mass spectrometry
More informationElectronic Supplementary Information
Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2014 Electronic Supplementary Information Multiplexed Detection of Lung Cancer Cells at the Single-Molecule
More informationEngineering D66N mutant using quick change site directed mutagenesis. Harkewal Singh 09/01/2010
Engineering D66N mutant using quick change site directed mutagenesis Harkewal Singh 09/01/2010 1 1- What is quick change site directed mutagenesis? 2- An overview of the kit contents. 3- A brief information
More information