3. Nucleic Acids Electrophoresis. Agaroses Acrylamides Buffers & Reagents for DNA Electrophoresis DNA Ladders Horizontal Electrophoresis System

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1 3. Nucleic Acids Electrophoresis Agaroses Acrylamides Buffers & Reagents for DNA Electrophoresis DNA Ladders Horizontal Electrophoresis System

2 3 Nucleic Acids Electrophoresis Agaroses EuroClone offers a complete selection of high quality agaroses for standard and specific electrophoresis appications. GellyPhor LE GellyPhor LM GellyPhor ULTRA GellyPhor HR GellyPhor PFGE DNA separation 1-50 kb DNA/RNA separation 1 kb DNA/RNA separation 1 kb -. DNA separation bp Blotting - - DNA finger printing Nucleic Acid Recovery GellyPhor LE GellyPhor LE is ideal for general nucleic acids preparative and analytical gel electrophoresis as well as for blotting. This gel sharply resolves the different DNA fragments to be analyzed and provides consistent resolution from batch-to-batch. It forms high strength gels with low background upon ethidium bromide staining. Due to the low electroendosmosis value (EEO) of GellyPhor LE the DNA has a high electrophoretic mobility allowing shorter running time. Gelling Temperature (dynamic measurement in 1.5% solution) C Gel strength (1%) 1200 g/cm 2 Electroendosmosis (-m r ) 0.12 Sulphate 0.14% Moisture 8.5% Residue on ignition 0.60% none detected Format EMR GellyPhor LE 100 g EMR GellyPhor LE 500 g EMR GellyPhor LE 1 kg Five years at GellyPhor LM GellyPhor LM is a low melting temperature agarose. This molecular biology grade agarose produces gels with greater sieving properties and higher clarity than standard melting temperature agarose. The low melting temperature of GellyPhor LM makes it ideal for preparative nucleic acids electrophoresis, while its low geling temperature is perfect for cloning of tissue culture cells and viral plaque assays. Format EMR GellyPhor LM 100 g Five years at Gelling Temperature (dynamic measurement in 1.5% solution) C Gel strength (1,5%) 500 g/cm 2 Electroendosmosis (-m r ) 0.12 Sulphate 0.12% Moisture 7% Melting Temperature (1.5%) 65.5 C none detected 16

3 Nucleic Acids Electrophoresis 3 GellyPhor HR GellyPhor HR is a molecular biology grade standard melting temperature agarose, that yields strong gels for fine resolution of small nucleic acids fragments. Performance testing of GellyPhor HR ensures fine resolution of DNA fragments up to 1000 bp, though this agarose is capable of finely resolving DNA fragments ranging from 10 bp up to 1200 bp. GellyPhor HR is designed for analytical electrophoresis. Gelling Temperature (dynamic measurement in 3% solution) Gel strength 35.5 C Electroendosmosis (-mr) 0.12 Sulphate 0.11% Moisture 7% 600 g/cm 2 (for a 1.5% gel) 1500 g/cm 2 (for a 3% gel) Melting Temperature (3%) 80 C none detected Ranges of separation: 1.8% bp 3% bp 4.5% bp These ranges are approximate and have been calculated in TAE Buffer. To achieve the best resolution of GellyPhor HR gels, they should be stored at 4 C- 8 C for 30 minutes before use. Format EMR GellyPhor HR 100 g Five years at GellyPhor ULTRA GellyPhor ULTRA is an intermediate melting temperature agarose that provides twice the resolution capabilities of the finest sieving agarose products. You can resolve DNA fragments, PCR and RT-PCR products differing in size by 2%, in the range of 200 bp to 800 bp, by horizontal gel electrophoresis (for example, a 200 bp DNA fragment can be separated from a 204 bp fragment). Using fast run protocols, DNA fragments differing in size by 1% can be resolved in as little as 1.5 hours in a 20 cm long horizontal or vertical gel format. GellyPhor ULTRA agarose gels (2% to 4%) approximate the resolution of polyacrylamide gels (4% to 8%). Format EMR GellyPhor ULTRA 125 g Five years at Gelling Temperature (dynamic measurement in 3% solution) 36 C Gel strength (3%) 400 g/cm 2 Electroendosmosis (-m r ) Moisture 10% Melting Temperature (3%) 75 C none detected GellyPhor PFGE GellyPhor PFGE is a very high gel strength, low EEO, standard gelling temperature agarose. Due to its high gel strength, this agarose can be used for the preparation of low percentage gels for the analysis not only of high molecular weight nucleic acids (such as chromosomes), but also of largesized particles such as viruses and ribosomes. Gelling Temperature (dynamic measurement in 1.5% solution) Gel strength 36 ± 1.5 C Electroendosmosis (-m r ) 0.13 Moisture 7% 1600 g/cm 2 (for a 1% gel) 3000 g/cm 2 (for a 1.5% gel) Melting Temperature (1.5%) 1.5 C none detected Format EMR GellyPhor PFGE 100 g Five years at 17

4 3 Nucleic Acids Electrophoresis Acrylamides For the separation of oligonucleotides with a small number of bases, acrylamide gels with a small pore size are used. The pore size is determined by the total concentration of acrylamide and the ratio of Acrylamide/Bisacrylamide. For the sequencing of nucleic acids a ratio of Acrylamide/Bisacrylamide 19:1 is used. EuroClone offers a ready-to-use 40% Acrylamide/Bisacrylamide 19:1 mix. Format EMR Acrylamide/Bisacrylamide 19:1 (solution 40%) 500 ml EMR Acrylamide/Bisacrylamide 19:1 (solution 40%) 1 L Buffers and reagents for DNA electrophoresis EuroSafe Nucleic Acid Stain EuroSafe Nucleic Acid Staining Solution (20,000x) is a safe nucleic acid stain, an alternative to the traditional ethidium bromide (EtBr) stain for detecting nucleic acid in agarose gels. It emits green fluorescence when bound to DNA or RNA. This stain has two fluorescence excitation maxima when bound to nucleic acid, one centered at 309 nm and another at 419 nm. In addition, it has one visible excitation at 514 nm. The fluorescence emission of EuroSafe bound to DNA is centered at 537 nm. EuroSafe is as sensitive as EtBr. Compared to EtBr, known as a strong mutagen it causes much fewer mutations in the Ames test. In addition, EuroSafe Nucleic Acid Staining Solution (20,000x) has a negative result in mouse marrow chromophilous erythrocyte micronucleus test and mouse spermary spermatocyte chromosomal aberration test. Used for detecting DNA and RNA Alternative to the ethidium bromide staining As sensitive as EtBr or more sensitive than that Less mutagenic than EtBr Format EMR EuroSafe 1 ml Two years at For the complete list of EuroClone Biochemicals please refer to Chapter 7 or visit Format Format EMR Boric acid 1 kg EMR TBE Buffer, 10X - MBG 1 L EMR Boric acid 5 kg EMR TBE Buffer, 10X - MBG 500 ml EMR EDTA disodium salt dihydrate 1 kg EMR TBE Buffer, 10X - powder 1 L EMR EDTA disodium salt dihydrate 500 g EMR TE Buffer ph 8.0, 1X 1 L EMR EDTA - Solution ph 8.0 (0,5 M) 1 L EMR TE Buffer ph8.0, 100X 1 L EMR EDTA - Solution ph 8.0 (0,5 M) 500 ml EMR TE Buffer ph8.0, 100X 500 ml EMR Ethidium Bromide 0,07% 15 ml EMR Tris 1 kg EMR Ethidium Bromide 1% 25 ml EMR Tris 500 g EMR TAE Buffer 10X 1 L EMR Tris-HCl 1 kg EMR TAE Buffer 50X 1 L EMR Tris-HCl 500 g EMR TBE Buffer, 10X 5 L 18

5 Nucleic Acids Electrophoresis 3 DNA Ladders EuroClone has three different DNA Ladders for sizing and approximate quantification of double-stranded DNA fragments such us PCR products. The Ladders have extremely sharp bands and reference bands with higher DNA content for easy orientation. SHARPMASS 50 - DNA LADDER This 50 bp DNA-Ladder is composed of 13 chromatography-purified individual DNA ranging from 50 to 1000 bp. The 500 bp and 250 bp fragments have a higher DNA content and serve as size references. SHARPMASS DNA LADDER This Ladder includes many plasmids fully digested by restriction enzymes. This process leads to the creation of 10 bands suitable for use as molecular weight standards for agarose gel electrophoresis. The digested DNA includes fragments ranging from 100 to 1000 bp. The 500 bp fragment has enhanced brightness and can be used as reference point. Format EMR SHARPMASS μg EMR SHARPMASS μg EMR SHARPMASS μg EMR SHARPMASS μg EMR SHARPMASS 100 PLUS 100 lanes EMR SHARPMASS 1 50 μg EMR SHARPMASS μg SHARPMASS 100 PLUS - READY-TO- LOAD DNA LADDER This Ladder consists of 12 DNA fragments ranging from 100 bp to 3 kb. It is designed to show virtually uniform spacing over a wide fragment range. The Ladder allows sizing and concentration estimate of DNA fragments on agarose gels generated by PCR or restriction digest. The fragment mix is supplied in ready-to-use format containing orange and blue tracking dyes. SHARPMASS 1 - DNA LADDER This Ladder includes many plasmids fully digested by restriction enzymes. This process leads to the creation of 13 bands suitable for use as molecular weight standards for agarose gel electrophoresis. The digested DNA includes fragments ranging from 250 to bp. For an easier reference, the fragment of 1000 bp generates a three times brighter band and the bp generates a two times brighter band. One year at -20 C Blue Ice 19

6 3 Nucleic Acids Electrophoresis Horizontal Electrophoresis Systems Minigel Systems EuroClone minigel systems are ideal for use with low to medium sample numbers. Designed for a quick and reproducible separations, these minigel systems are perfectly suited for the daily needs of the research laboratory. System Components UV-Transmissible (UVT) Gel Tray with two Comb position Two Combs Convenient Handling Easy-to-use casting systems - gel directlly in the chamber by 90 degree rotation of the rubbers-seal-equipped gel tray Labeled Combs for easy identification of Comb type Venting slot prevents water condensation for clear gel viewing Gel tray and chamber lid are made of UV-Transmissible acrylic glass enabling the gel to be viewed under UV excitation Accessories A wide range of Combs, UV-transmissible gel trays featuring various Comb positions, multi casting rails for pouring several gels simultaneously, adjustable universal casting rail to accomodate gel trays of various sizes are available to complement this range. Mini S Gel Size 7 x 8 cm Footprint 12 x 9.5 x 16 cm Sample Flexibility max. 24 Buffer Volume 400 ml Gel Volume 30 ml EM The system Mini S includes: 2 Combs: 1.5 mm thickness (6,10 teeth) Descritpion Mini S Horizontal Accessories Descritpion EM C 10 tooth Comb, 1.0 mm thick, Sample volume: 18 µl EM D 10 tooth Comb, 1.2 mm thick, Sample volume: 26 µl EM C 12 tooth Comb, 1.0 mm thick, Sample volume: 14 µl EM D 12 tooth Comb, 1.5 mm thick, Sample volume: 21 µl EM C 5 tooth Combs, 1.0 mm thick, Sample volume: 42 µl EM D 5 tooth Combs, 1.5 mm thick, Sample volume: 64 µl EM C 6 tooth Comb, 1.0 mm thick, Sample volume: 34 µl EM D 6 tooth Comb, 1.5 mm thick, Sample volume: 51 µl EM C 8 tooth Comb, 1.0 mm thick, Sample volume: 24 µl EM D 8 tooth Comb, 1.5 mm thick, Sample volume: 36 µl EM PD 2 tooth, preparative Comb, 1.5 mm thick EM UVT RapidCast UVT Gel Tray 7 x 8 cm with two Comb slots & gasketed ends RapidCast Gel Caster 7 x 8 cm for use with RCGT EM CST Allows for three gels to be cast simultaneously. CASTER ONLY EM GK Gasket, RCGT, pk 2 20

7 Nucleic Acids Electrophoresis 3 Mini M Gel Size 9 x 11 cm Footprint 15 x 9.5 x 22 cm Sample Flexibility max. 36 Buffer Volume 600 ml Gel Volume 50 ml EM Combs: 1.5 mm thick (10, 14 teeth) Mini M Horizontal Accessories EM C 10 tooth Comb, 1.0 mm thick, Sample volume: 25 µl EM D 10 tooth Comb, 1.5 mm thick, Sample volume: 38 µl EM C 12 tooth Comb, 1.0 mm thick, Sample volume: 20 µl EM D 12 tooth Comb, 1.5 mm thick, Sample volume: 30 µl EM C 14 tooth Comb, 1.0 mm thick, Sample volume: 16 µl EM D 14 tooth Comb, 1.5 mm thick, Sample volume: 25 µl EM C 5 tooth Comb, 1.0 mm thick, Sample volume: 58 µl EM D 5 tooth Comb, 1.5 mm thick, Sample volume: 86 µl EM C 8 tooth Comb, 1.0 mm thick, Sample volume: 34 µl EM D 8 tooth Comb, 1.5 mm thick, Sample volume: 51 µl EM C 18 tooth Comb, 2 x (8+1), 2 x microtiter format, 1.0 mm thick, Sample volume: 11 µl EM D 18 tooth Comb, 2 x (8+1), 2 x microtiter format, 1.5 mm thick, Sample volume: 16 µl EM C 9 tooth Comb, (8+1), 1 x microtiter format, 1.0 mm thick EM D 9 tooth Comb, (8+1), 1 x microtiter format, 1.5 mm thick EM PD 2 tooth, preparative Comb, 1.5 mm thick EM UVT RapidCast UVT Gel Tray with two Comb slots RapidCast Gel Caster, 9 x 11 cm for use with EM CST RCGT Allows casting of three gels simultaneously. CASTER ONLY EM GK Gasket, for RapidCast Gel Tray RCGT, pk 2 Mini L Gel Size 12 x 14 cm Footprint 17 x 9.5 x 25 cm Sample Flexibility max. 50 Buffer Volume 800 ml Gel Volume 85 ml EM Combs: 1.5 mm thick (12, 20 teeth) Mini L Horizontal Accessories EM C 16 tooth Comb, 1.0 mm thick, Sample volume: 20 µl EM D 16 tooth Comb, 1.5 mm thick, Sample volume: 30 µl EM C 20 tooth Comb, 1.0 mm thick, Sample volume: 15 µl EM D 20 tooth Comb, 1.5 mm thick, Sample volume: 22 µl EM C 24 tooth Comb, 1.0 mm thick, Sample volume: 11 µl EM D 24 tooth Comb, 1.5 mm thick, Sample volume: 17 µl EM C 8 tooth Comb, 1.0 mm thick, Sample volume: 47 µl EM D 8 tooth Comb, 1.5 mm thick, Sample volume: 70 µl EM C 12 tooth Comb, 1 x microtiter format, 1.0 mm thick, Sample volume: 27 µl EM D 12 tooth Comb, 1 x microtiter format, 1.5 mm thick, Sample volume: 35 µl EM C 25 tooth (12x2)+1), 2x microtiter format, 1.5 mm thick, Sample volume: 11 µl EM D 25 tooth (12x2)+1), 2x microtiter format, 1.0 mm thick, Sample volume: 16 µl EM C 8+1 tooth Comb, 1 x microtiter format, 1.0 mm thick, Sample volume: 27 µl EM D 8+1 tooth Comb, 1 x microtiter format, 1.5 mm thick, Sample volume: 40 µl EM PD 2 well, Preparative Comb, 1.5 mm thick, Sample volume: 596/28 µl EM WC Wall Comb, 1.5 mm thick EM GK Gasket, for RapidCast UVT Tray RCGT, pk. 2 EM UVT12 RapidCast UVT Gel Tray, 12 x 14 for with twelve Comb slots EM UVT4 RapidCast UVT Gel Tray, 12 x 14 for with four Comb slots RapidCast Gel Caster 12 x 14 cm for use with 80- EM CST 1214-RCGT Allows for three gels to be cast simultaneously. CASTER ONLY 21

8 3 Nucleic Acids Electrophoresis Mini ExM Gel Size 14.4 x 10.2 cm Footprint 19 x 9.5 x 20 cm Sample Flexibility max. 80 Buffer Volume 600 ml Gel Volume 70 ml EM Mini ExM Horizontal Accessories: A wide range of Combs (compatible with multichannel pipettors) are available. Please contact EuroClone for the complete list of accessories. Casting Chamber 4 Combs: 1.5 mm thickness (2 x 30, 2 x 40 teeth) Mini ExW Gel Size 23 x 14 cm Footprint 30 x 10.5 x 24 cm Sample Flexibility max. 200 Buffer Volume 800 ml Gel Volume 160 ml EM Mini ExW Horizontal Accessories: A wide range of Combs (compatible with multichannel pipettors) are available. Please contact EuroClone for the complete list of accessories. Maxi L system allows 40 cm long runs). SuperSafe with Attached Leads, Casting Chamber 4 Combs: 1.5 mm thickness (50 teeth microtiter format) Maxigel Systems Maxi Gel Systems are very high quality electrophoresis systems designed for medium to high sample throughput (up to 600 samples can be run simultaneously) and for high-resolution nucleic acid separations requiring long migration paths (the Maxi L system allows 40 cm long runs). Maxi S Gel Size 13 x 25 cm Footprint 10 x 21.5 x 37.5 cm Sample Flexibility max. 112 Buffer Volume 1600 ml Gel Volume 160 ml EM Maxi S Horizontal UV-Transmissible (UVT) Gel Tray with Endgates Three Point Leveling Base 3 Combs: 1.5 mm thickness (12, 16, 20 teeth) Accessories: A wide range of Combs (compatible with multichannel pipettors) are available. Please contact EuroClone for the complete list of accessories. 22

9 Nucleic Acids Electrophoresis 3 Maxi M Gel Size 20 x 25 cm Footprint 29 x 10 x 37 cm Sample Flexibility max. 168 Buffer Volume max ml Gel Volume 250 ml EM Maxi M Horizontal UV-Transmissible (UVT) Gel Tray with Endgates Three Point Leveling Base 3 Combs: 1.5 mm thickness (16, 24, 36 teeth) Accessories: EM BP Long Horizontal Gel Box, 20 x 25 cm with integral leveling platform & Buffer Exchange Ports; ExpressCast Gel Tray with six Comb slots and three Combs EM EG End gates for ExpressCast UVT Gel Tray EXGT, pk 2 includes gaskets EM GK Gasket, for ExpressCast UVT Gel Tray EXGT, pk 2 EM UVT ExpressCast UVT Gel Tray 20 x 25 cm with gasketed end gates and six Comb slots that allows for 1, 2, 3 or 4 gels of equal length to be run in the tray EM C 12 tooth Comb 1.0 mm thick, Sample volume: 54 µl EM D 12 tooth Comb 1.5 mm thick, Sample volume: 82 µl EM C 16 tooth Comb 1.0 mm thick, Sample volume: 39 µl EM D 16 tooth Comb 1.5 mm thick, Sample volume: 59 µl EM C 20 tooth Comb, 1.0 mm thick, Sample volume: 30 µl EM D 20 tooth Comb, 1.5 mm thick, Sample volume: 45 µl EM C 24 tooth Comb, 1.0 mm thick, Sample volume: 24 µl EM D 24 tooth Comb, 1.5 mm thick, Sample volume: 37 µl EM C 28 tooth Comb, 1.0 mm thick, Sample volume: 19 µl EM D 28 tooth Comb, 1.5 mm thick, Sample volume: 28 µl EM C 32 tooth Comb, 1.0 mm thick, Sample volume: 15 µl EM D 32 tooth Comb, 1.5 mm thick, Sample volume: 22 µl EM C 36 tooth Comb, 1.0 mm thick, Sample volume: 13 µl EM D 36 tooth Comb, 1.5 mm thick, Sample volume: 20 µl EM C 8 tooth Comb, 1.0 mm thick, Sample volume: 85 µl EM D 8 tooth Comb, 1.5 mm thick, Sample volume: 127 µl EM C 18 tooth (16 sample lanes & 2 marker lanes) 1 x microtiter Comb, 1.0 mm thick, Sample volume: 27 µl EM D 18 tooth (16 sample lanes & 2 marker lanes) 1 x microtiter Comb 1.5 mm thick, Sample volume: 40 µl EM MTC 21 tooth 1 x microtiter Comb, 1.0 mm thick, Sample volume: 27 µl EM MTD 21 tooth 1 x microtiter Comb, 1.5 mm thick, Sample volume: 40 µl EM MT2C 42 tooth 2 x microtiter Comb, 1.0 mm thick, Sample volume: 11 µl EM MT2D 42 tooth 2 x microtiter Comb, 1.5 mm thick, Sample volume: 16 µl EM PD Preparative Comb, 1.5 mm thick, Sample volume: 1052/28 µl EM WC Wall Comb, 1.5 mm thick Maxi L Gel Size 23 x 40 cm Footprint 32 x 10 x 53 cm Sample Flexibility max. 600 Buffer Volume 4500 ml Gel Volumne 460 ml EM Maxi ExW Maxi L Horizontal Gel Size 23 x 25 cm Footprint (W x H x L) 30 x 11 x 37 cm Sample Flexibility max. 500 Buffer Capacity max ml Gel Volume 160 ml EM Maxi ExW Horizontal SuperSafe with Attached Leads UV-Transmissible (UVT) Gel Tray with Endgates Three Point Leveling Base 4 Combs: 1.5 mm thickness (2 x 25, 2 x 50 teeth) Accessories* Buffer Chamber UV-Transmissible (UVT) Gel Tray with Endgates Three Point Leveling Base 4 Combs: 1.5 mm thickness (2 x 25, 2 x 50 teeth) Accessories* *A wide range of Combs (compatible with multichannel pipettors) are available. Please contact EuroClone for the complete list of accessories. 23

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