BIOMOLECULAR NMR PLATFORM

STAFF, SERVICES AND EQUIPMENT

POLICY

The Platform provides a service in NMR spectroscopy to the IRIC community at large and users external to the University where appropriate for minimum fee
As a platform at IRIC we will provide users with the following:

• Maintenance and running of the NMR spectrometers

• Advice and help on processing and interpretation of NMR spectra

• Access to and help in running software to analyse spectra and generate NMR structures via a local and super fast 20 CPU cluster. These include:

  • NMRPipe, NMRView, ARIA, XPLOR, CNS,CYANA

  • Access to in-house scripts to ease transfer of data to and from programmes

  • In-house NMRview scripts to aid analysis

• Help with using molecular visualisation programmes and other structure analysis programmes such as PYMOL, MOLMOL. 

In addition the platform may offer a service for complete structure determination and spectral analysis under exceptional circumstances. Please contact us for more information.

We will also be happy to lend our expertise in recombinant protein production techniques for enrichment of proteins with stable isotopes.

STAFF

In Decemeber 2005 we installed a coldprobe which substantially increases the sensitivity of the NMR spectrometer. We expect this probe to be used ~ 90% of the time

The spectrometers are supported by workstations and a range of peripherals and software.

RATES

Spectrometer:

The current fee sturcture is available upon request

Other services:

Fees for other services such as complete structure determination and spectral interpretation are available upon request

TRAINING

Training on the 600 may be arranged by a direct request to Mike Osborne. Formal training requires a minimum of 2 hours.

However, due to the expensive and fragile nature of NMR equipment - especially the coldprobe - training for users must first be OK'd by a committee.

Under no circumstances will a person operate the NMR spectrometer unless permission has first been granted by the NMR manager.

BOOKING PROCEDURES

Time requests for the NMR spectrometer and experiments will be made on-line. Time will be allocated subject to approval by a committee which will meet periodically. The NMR schedule can be viewed on-line.

AVAILABLE EXPERIMENTS

Most bimolecular experiments are available from the Biopack package distributed from Varian and are listed here.

However, a number of backbone assignment experiments such as HNCA, HN(CO)CA etc., have been coded to incorporate non-linear sampling, which decreases the time to acquire 3D NMR spectra by a factor of 5.

In combination with the cold-probe, these non-linear sampling experiments will greatly accelerate the tme required to assign biomolecules.

SAMPLES AND SAMPLE PREPARATION

Users are required to prepare their own samples, although we are always willing to provide advice and help, a brief guide can be found here. For more information on expressing in E. coli check out this powerpoint presentation. We will prepare samples for occasional users where no alternative arrangements can be made. All samples must be clearly labeled with the name of the user, the material, hazards (if any) and the solvent. 

Note sample tubes can affect the quality of NMR tubes. We recommend at least using wilmad 528-PP tubes, with Shigemi BMS-005V being the best.

EDUCATION

Prepared notes are available on various aspects of nuclear magnetic spectroscopy including the practical application of the techniques and problems that have been solved by us.
In addition some information is available by directly contacting us

SAFETY

NMR can be a dangerous business: for this reason only trained users are allowed in the NMR room unattended. Others must ask for permission.

RISK ASSESSMENT

The main risks come from the high magnetic fields, the handling of cryogens and high electrical voltages/RF sources. In general, the risks are minimised by limiting access to the NMR rooms to only the NMR staff and users of the instruments and by limiting any hardware modifications/maintenance to the
NMR staff (or exceptionally very experienced users) who have the requisite technical understanding and training.

Electrical/RF
Risks are similar to those encountered in the use/maintenance of other laboratory equipment and are minimised by restricting any modification/maintenance of the equipment to the NMR staff (or exceptionally very experienced users) in consultation with the manufacturer.


Only carbon dioxide fire extinguishers should be used to avoid equipment damage and exceptional care is needed to ensure that fire extinguishers are not used near the magnet cryostat. In case of serious flooding, or in other situations where there is risk of electrocution, the equipment circuit breakers should be turned off in the plant room. (No water supplies are actually used in the NMR rooms).

Cryogens
The cryogens used are liquid N2 and liquid He: Temperature: N2: -196 and He: -269 deg. C

Colour: none
Toxicity: very low

Fire hazard: non combustible
Volume Expansion (from normal boiling point to room temp.): ca. 700x 

The main risks are of burns when handling cryogens and of asphyxiation if a magnet quenches. These are minimized by only allowing very experienced technicians to fill the magnets with liquid nitrogen and (at present) by contracting out the filling with liquid helium to Oxford Instruments. The magnet cryostats are only filled using stainless steel transfer lines to reduce risk of rupture. At least two staff must be present during refilling and appropriate safety clothing must be worn (gloves and eye protection). Refills must be continously attended. It is particularly important that the person filling the magnet, once trained, should do so on a very regular basis so as to be very familar with the required routine.

Magnet quenches (the rapid release of gaseous cryogens from the cryostat into the room) should trigger the fire alarm and thus open the smoke vents thereby preventing any risk of asphyxiation due to the large volume expansion. In the event of a quench personnel should evacuate the area (a quench warranting evacuation would be obvious by the noise of the escaping gas and clouds of vapor). Access to the NMR rooms is strictly limited to the NMR staff during refills and any major maintenance. During other periods access is limited to a known set of users via combination locks. For the 800MHz NMR magnet system, which is standing in a pit, there is a potential danger of asphyxiation during N2 fills because the density of N2 is higher than of O2. Access to the pit is therefore prohibited during refilling of the magnet. The magnet cryostats continuously expel a small quantity of gaseous He and N2 into the air. This does not present a hazard since during everyday use the air is constantly changed in the NMR rooms by the air-conditioning system. Any drop in the oxygen content of the air can be detected by an oxygen monitoring system.

A site-specific operating procedure is available from the NMR staff for topping up of liquid cryogens.

High Magnetic Fields

Large attractive forces are exerted on magnetic materials or equipment bought in close proximity to the NMR magnet systems which are always at field. The force may become large enough to move tools or equipment uncontrollably towards the magnet system and the closer to the magnet system the larger the force. This is probably the main risk because it is one with which most people are unfamilar. Risks come from release of any steel items/tools or equipment which are bought near the magnets. Even belt buckles, steel tipped shoes etc. may be strongly attracted to a magnet. This might result in damage to the magnets/probes (possibly resulting in a quench) or serious injury or death to personnel working near or under a magnet. The latter is probably the most serious risk, as staff and users often need to work under the magnet during its normal operation. These risks are mimimised by preventing access to the NMR rooms by anyone other than the NMR staff and trained users. Anyone else needing to enter the NMR rooms can only do so in the presence of one of the NMR staff. Combination locks are reset regularly to prevent their codes becoming known by others.

It is necessary to use steel tools for maintenance and repair of the consoles, but such work should only be done by the NMR staff (or engineers from the manufacturers) and users are not allowed near the magnet during such work. Where possible non-magnetic tools are used on the magnets themselves.

Medical electronic implants such as e.g. cardiac pacemakers may be affected by static or changing magnetic fields (not all pacemakers respond the same way). Medical implants e.g. clips, protheses which may contain ferromagnetic materials would be subject to strong attractive forces near to the NMR magnet system. All people with such implants are excluded from the NMR rooms and appropriate warning signs are displayed.

Recent publications suggest that long term cumulative large exposures to oscillating magnetic fields (60 Hz) may be associated with increased incidence of brain cancer in power industry workers. The cumulative doses for an effect were large, and represent no hazard outside the 5 gauss safety line normally used. Reasonable caution in avoiding lengthy exposure to higher fields seems prudent, none the less.

Our current advice is that NMR staff and researchers should spend no longer than reasonably necessary within the 5 gauss line for sample changing and adjustments. No other equipment unrelated to the NMR system is placed within the 5 gauss line, which should be contained in the NMR rooms themselves.

see: David A. Savitz and Dana P. Loomis (1995). "Magnetic field exposure in relation to leukemia and brain cancer mortality among electric utility workers." Am. J. Epidemiology 141(1), 123-134.

Magnetic fields may permanently damage watches, calculators and certain types of credit cards. These items need to be kept well away from the magnets.

Video Display Terminals (VDTs) Extensive radiation measurements and health data do not indicate that these units present a health risk. Most of the symptoms related to the use of computer terminals are related to strain and discomfort that can be corrected by ergonomic measures. The potential for eye strain can be reduced by the use of non-glare screens, fitting a filter to the VDU, or by improving the lighting conditions. Users are strongly advised to consult the Universities Code of Practice for the safe use of VDUs (available from the NMR staff).

If the information on this website doesn't answer your questions, please contact

Dr Mike Osborne

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