Consumables and plastic

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problems/questions

 Problem list:

  • check volume of 20-100ml tubes
  • 0.1ml tubes for RT-PCR


Mol.biology // Next-generation sequencing

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Содержание


plasticproductsproperties
Polypropylene (PP)tips, tubes, plates, syringes, bottles
  • lowest density among plastics, ρ = 0.90g/ml
  • start to be soft at 140°C, Tm=175°C
  • autoclavable
  • high mechanical strength
  • swell after a contact with organic solvents (most distinguishable in laboratory: chloroform)
  • melt in aromatic hydrocarbons (benzol, toluene) at temperatures above 100°C
  • not so transparent as PS
  • low binding capacity to proteins and nucleic acids
Polystyrene (PS)Petri dishes, filter units, tissue culture flasks, serological pipets, microplates, immunological plates, beads, CD/DVD cases, foam plastic boxes, single-use dishes
  • ρ = 1.04-1.06g/ml
  • not autoclavable
  • transparent
  • more fragile, less mechanical strength if compare with PP
  • soluble in acetone, benzine, chloroform
  • high protein binding capacity
Polycarbonate (PC, Lexan)CD, DVD, PCR plates, drinking bottles, lenses and glasses, ultracentrifuge tubes
  • ρ = 1.20-1.22g/ml
  • Tm=267°C; temperature stable, can be weakened by repeated autoclaving
  • transparent
High density polyethylene (HDPE)bottles, caps, bags
  • ρ = 0.95g/ml
  • can be autoclaved at 120°C for 20 min
  • higher strength if compare with LDPE
  • higher chemical and thermal resistance if compare with polystyrene
Low density polyethylene (LDPE)bottles, caps, bags
  • ρ = 0.92g/ml
  • not autoclavable
  • usable untill 80°C
  • higher chemical and thermal resistance if compare with polystyren
Polytetrafluoroethylene (PTFE, Teflon)spacers, combs, filters
  • ρ = 1.7-2.2g/ml
  • keep elastic properties from -70 äî +270°C; Tm=327°C
  • very low coefficient of friction
  • autoclavable
  • very high chemical resistance
Poly(methyl methacrylate) (PMMA, Acrylic glass, Plexiglas, Acrylite)electrophoresis chambers, agarose plates
  • ρ = 1.19g/ml
  • not autoclavable; Tm=160°C
  • transparent
UV-Star resin ()UV-transparent plastic cuvettes 

Other types of plastic are used for ultracentrifuge tubes, filters, meshes.


[править] Chemical and thermal resistance of different types of plastic

factorPPPSHDPELDPEUV-StarPMMAPTFE
temperature [°C]-200/+120-20/+60-50/+120-50/+60-80/+40-80/+80-100/+250
compatible with all plasticsAmmonia acetate, DMSO, Formamide, Glucose, Glycerol, NaCl, NaOH, Urea
Acetic acid, 90%20°C20°C50°C20°C20°C20°C50°C
Acetone20°C20°C50°C20°C20°C20°C50°C
Ammonia, 25 %50°C20°C50°C50°C20°C20°C50°C
Chloroform, 100 %20°C20°C20°C20°C 20°C50°C
Diethyl ether20°C20°C20°C20°C 20°C50°C
Ethanol, 96 %50°C50°C20°C20°C20°C20°C50°C
Formaldehyde, 40 %20°C20°C20°C20°C  50°C
Heptane20°C20°C20°C20°C20°C20°C 
Hydrochloric acid, conc.50°C20°C50°C50°C20°C20°C50°C
Isobutanol50°C20°C50°C50°C   
Isopropanol50°C20°C50°C50°C20°C  
Liquid paraffin20°C50°C50°C20°C 20°C 
Methanol50°C20°C50°C50°C20°C20°C50°C
Phenol, 100 %50°C20°C20°C20°C 20°C50°C
Phosphoric acid, 85 %20°C50°C50°C50°C  50°C
Sodium acetate50°C20°C50°C50°C 20°C50°C
Sodium hypochloride20°C50°C20°C20°C20°C20°C50°C
Sulphuric acid, 60 %20°C20°C20°C20°C20°C 50°C
Sulphuric acid, conc.20°C20°C20°C20°C 20°C50°C
Toluene20°C20°C20°C20°C 20°C50°C
Trichloroacetic acid50°C20°C20°C20°C 20°C50°C
Xylene20°C20°C20°C20°C 20°C50°C


see also:




[править] Tips

itemprice per onenotes
Combitip, sterile1€
  • dispensing of ePCR
  • practically useless for aliquoting in our group
  • normally, we do not need sterility, but sterile combitips are individually wrapped, so also more clean in PCR sense
Combitip, non-sterile56¢
Positive-displacement tip28¢viscous solutions
Tip with filter~5¢tips with aerosol filters should be used for work with "PCR-contamination sensitive" and "important" material:
  • preparation of aliquotes of enzymes, oligos, buffers
  • library construction and setting up of PCR and RT-PCR reactions (and handling of library- and PCR-related reagents: oligos, buffers, polymerases, etc.)
  • handling of amplified material (to prevent pipette contamination)
Tip, 5ml3-7¢cheap alternative of plastic pipettes
Tip, blue; bulk / rack0.7 / 2-4¢
  • analytical:
» titrations
» concentration measurements (spectrophotometer, nanodrop)
» preparation of samples for analytical gel-loading
  • handling of molecular weight markers
  • plasmid purifications
Tip, yellow; bulk / rack0.22 / 1-3¢


We use "MAXYMum Recovery" Filter Tips, Axygen. They have two advantages:

  • filters
  • very nice low liquid-binding surface.

In principle, MAXYMum Recovery tips w/o filters are also available. They have nice surface, but only 20-30% cheaper. For our group it is unpractical to organise separate stocks of tips and special application list because of such price difference. More practical to have only two options:

  • nice filtered tips
  • cheap tips w/o filters for analytical purposes



[править] Tubes

typeprice per tubevolume [ml]notes
0.2ml strips55-110¢ (7-14 per tube)0.3ml
  • strips are more expensive, than individual tubes
  • thin walls accelerate heat transfer, which is good for PCR
  • caps are not suited for numerous opening/closing, so do not use these tubes for storage
  • not good for water bath, high-speed centrifugation, rotation, vortexing
0.2ml tubes5-10¢
0.5mlLoBind7.6¢0.62ml
  • the best size for storage of enzymes, oligos, libraries, etc.: larger tubes are too deep for 2µl tips, pipette may touch the wall of a tube
  • use 2ml tube w/o cap as adaptor for -20°C box and centrifuge
  • cheap 0.5ml tubes are best for analytical measurements, titrations, test experiments, etc.
optical, Qubit3.9¢
expensive: Eppendorf
cheap: Sarstedt
1.4 (0.2-0.5)¢
1.5mlLoBind4.1¢1.6ml
  • Ethanol precipitation
  • phenol/chloroform extraction
normal3.4 (0.7-1)¢
2mlnormal2.15ml
  • round-bottom modification of 1.5ml tubes; if compare with conical tubes: mixing is better, pellet is less stable
  • the same applications as for 1.5ml but for a bit larger volume
  • w/o caps: collection tubes for spin-columns. Instead of discarding flow-through it is more convenient to transfer purification column to a new tube before each loading
w/o caps & volume marks1.6¢
5mlsterile12¢7.6mlscrew-cap storage tube; convenient intermediate volume between 2ml and 50ml
non-sterile
15ml80 (25-50)¢15.8mlvery inconvenient tube, it is difficult to pipette close to the bottom without touching internal surface by a pipette
20ml9.5¢ screw-cap, round bottom tube; used for preparation of ePCR water phase in SOLiD protocol
50ml70 (30-40)¢ general use tubes:
  • storage
  • extraction and precipitation
100ml12¢ screw-cap, round bottom vessel


LoBind tubes should be used for "important" and "surface-sensitive" applications:

  • all operations with paramagnetic and polystyrene beads
  • storage of very diluted NA (<10ng/µl for genomic DNA or <10pmol/µl for oligonucleotide solution) or protein solutions
  • storage of expensive or sensitive enzymes
  • NGS libraries preparation


Do not use colored tubes. Pellet is less visible. They also may inhibit some chemical reactions (Maxam-Gilbert sequencing).

Soft polyethylene tubes are not suitable for centrifugation, they might crack!

[править] Autoclaved tips & tubes

The only one advantage of autoclaved consumables if compared to non-autoclaved is that they are sterile. However, in all other respects they are worse:

  • most of our applications do not need sterility
  • plastic was dispensed for autoclaving in boxes of questionable purity
  • plastic was heated up to significant temperature. Autoclave steam has condensed and then dried out on walls of tubes and tips.


Autoclaved tubes and tips should be used for:

  • molecular cloning and microbiology (because they are sterile)
  • (if they are cost-free for the group) for handling of not important non-amplifiable material




Личные инструменты


Инструменты




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