Fast Kinetics of Reactions and Conformational Changes

Please acknowledge the SIP core facility ( RRID: SCR_018986) in publications, on posters, or in talks if you use any instruments in the SIP core facility. Please include SIP's RRID (RRID: SCR_018986) and the grant numbers for instruments funded through instrumentation grants in your acknowledgements. This is a requirement from the funding agencies and is crucial for future funding. Find example text on theÌýAcknowledgement PageÌýor the individual instrument pages.

Fast Kinetic Measurements in in Biochemistry, Biophysics and Structural Biology

Stopped-flow spectroscopy, including fluorescence, absorption, and circular dichroism (CD), is a powerful technique widely used in biochemistry and biophysics to study rapid molecular interactions and reaction kinetics. By rapidly mixing reactants and measuring spectroscopic changes in real-time, it enables researchers to capture fast biochemical events on the millisecond timescale. Stopped-flow spectroscopy is often employed to monitor conformational changes, binding events, or complex formation, offering detailed insights into the mechanisms of molecular interactions. This real-time monitoring capability makes stopped-flow fluorescence ideal for investigating processes such as enzyme kinetics, protein folding, ligand binding, and molecular association or dissociation. The versatility of stopped-flow spectroscopy allows it to be applied to various biological systems, including protein-protein, protein-DNA/RNA, and protein-ligand interactions. It can be performed under controlled conditions, such as specific temperatures, pH levels, and ionic strengths, facilitating a thorough characterisation of the factors that influence molecular processes.

Stopped-flow spectroscopy is particularly well-suited for studying single turnover reactions, where a single catalytic cycle of an enzyme or molecular process is observed. In these experiments, reactants are mixed, and changes in absorbance or fluorescence are tracked to capture the kinetics of individual turnover events. This is especially useful for studying enzymes with discrete catalytic steps, enabling researchers to follow the formation and decay of reaction intermediates. As enzyme concentrations are often limiting in single turnover reactions, stopped-flow spectroscopy provides precise kinetic data for each step of the reaction pathway, offering valuable insights into enzyme mechanisms and the timing of individual steps.

Complementing this technique, chemical quench flow allows for the study of rapid reactions by freezing them at specific time points. In quench flow experiments, reactants are mixed, and the reaction is halted at precise intervals by adding a chemical reagent, allowing for the analysis of intermediates or products through methods like chromatography or mass spectrometry. This is particularly valuable for studying reactions that can not be monitored spectroscopically or those requiring detailed stepwise analysis of multiple species. Together, stopped-flow spectroscopy and chemical quench flow provide powerful tools for dissecting complex, fast biochemical reactions.

Stopped-flow polarisation curve for the binding of DNA to Parp1

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Lysozyme refolding by ratio-mixing, stopped-flow CD

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Key Highlights of Stopped-Flow Spectroscopy and Chemical Quench Flow Experiments in Biology, Biochemistry, and Biophysics

  • Capture kinetic processes precisely from msec to minutes
  • Applicable to a wide range of reactions, including enzymatic, folding and unfolding, and ligand-binding processes
  • Suitable for a wide range of biomolecules and complexes including proteins, nucleic acids, lipids, and small molecule binding
  • Monitor real-time changes in absorbance, fluorescence (intensity, FP and FRET), or circular dichroism (stopped-flow)
  • Precisely capture and quench fast reactions at specific time points (quench flow)
  • Study both fast and slow phases of multiphase processes in one experiment
  • Investigate transient reaction kinetics, isolating and analysing reaction intermediates
  • Study enzyme mechanisms by isolating catalytic steps (quench flow), performing single turnover experiments and capturing pre-steady-state kinetics (stopped-flow)
  • Combine various analytical techniques (e.g. HPLC, mass spectrometry, UV-Vis, fluorescence) for detailed product identification
SX20 Stopped-Flow Spectrometer
Stopped Flow Unit
8 way reaction valve for chemical quench flow

Instrument and Accesories

Stopped-Flow Spectroscopy

SX20 Stopped Flow (Applied Photophysics)

  • Features:
  • Absorbance and Fluorescence (Intensity, Polarisation/Anisotropy, FRET)
  • Single mixing, ratio mixing, sequential mixing
  • Temperature control (water bath and jacket)
  • Dead time 1.3 ms (with 20 µl flow cell), 0.5 ms (with 5 µl flow cell)
  • Excitation monochromator, filter-based emission detection
  • Adapter flow cell for chemical quench flow operation (dead time: 15 ms)

Chirascan Plus CD with Stopped-Flow Module (Applied Photophysics)

Features:

  • Circular Dichroism, Absorbance and Fluorescence (Intensity, Polarisation/Anisotropy, FRET)
  • Single mixing, ratio mixing, sequential mixing
  • Temperature control (water bath and jacket)
  • Dead time 1.3 ms (with 20 µl flow cell),
  • Filter-based emission detection for fluorescence

Rapid-Mixing, Chemical Quench-Flow

Model RFQ-3 Quench-Flow (Kin Tek)

Features:

  • Kinetics Response Time:ÌýShortest reaction time 2.5 milliseconds.
  • Minimum Sample Volume:Ìý20 ul per reaction partner per shot.
  • Maximum Sample Volume:Ìý5 ml per sample per shot.
  • Syringe Volumes:Ìý5 ml standard. Syringes of 0.25, 0.5, 1.0, 2.0 and 10.0 ml volumes are also available.
  • Temperature Range:Ìý4 - 70°C range of temperature is maintained by circulating water bath.

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Essential Information for Using SIP's Stopped-Flow and Chemical Quench-Flow Instruments

Why?

Acknowledgements are essential for ensuring the continued success of the Shared Instruments Pool (SIP). They enable us to secure the necessary funding to sustain and expand the SIP, ensuring that our instruments are in optimal working condition and that the methods we offer are at the forefront of biochemical and biophysical research.

Please include SIP's RRID number (RRID: SCR_018986) in your acknowledgements. This allows funding organisations and potential grant reviewers to easily locate publications supported by SIP, helping to evaluate the impact of SIP on our research community.

If facility staff have provided substantial assistance, please consider acknowledging them. If they contributed significantly to the intellectual aspects or conducted important experiments, co-authorship may also be appropriate.

Example text:

We thank the Shared Instruments Pool (RRID: SCR_018986), Department of Biochemistry, University of Å·ÃÀ¿Ú±¬ÊÓƵ Boulder for the use of the Applied Photophysics Chirascan Plus CD spectrometer and Stopped-Flow Module. The CD was funded by NIH S10RR028036. We also thank [Name and title of the facility member providing significant help] for their invaluable assistance with data collection and evaluation.

We thank the Shared Instruments Pool (RRID: SCR_018986), Department of Biochemistry, University of Å·ÃÀ¿Ú±¬ÊÓƵ Boulder for the use of the Applied Photophysics SX20 Stopped-Flow spectrometer. We also thank [Name and title of the facility member providing significant help] for their invaluable assistance with data collection and evaluation.

Please contact Dr Erbse to obtain detailed protocols and arrange an initial project consultation and personalised training sessions. Protocols are available as PDF files on the instrument computer, with printed copies stored alongside the instruments.

Interested users can contact Dr Erbse to discuss planned experiments and arrange training sessions. These sessions will involve the use of actual user samples alongside standards, enabling users to collect preliminary data during the training and receive help from core staff right away if troubleshooting or optimisation is needed. Users are welcome to request additional training or support sessions at any time. We are always happy to provide a refresher if it has been a while.

After your training is completed, you will be invited to join the CD, Stopped-Flow Spectrometer, or the Quench-Flow Google calendar.

Sign Up Rules:Ìý
Up to Friday the week before the planned experiment users can sign up for a maximum of 2 days. In the week of the experiment users can sign up for additional time if available.

  • Initial consultation is free. SIP staff are happy to assist with a short pilot experiment if it can be accommodated within SIP's resources.
  • Regular user groups are expected to buy into SIP with a monthly flat fee according to their SIP usage level. For detailed information, please contact Dr Erbse.
  • Users are required to provide all consumables specific to their experiments. This includes the syringes needed for fast kinetic measurements.
  • Costs for necessary repairs, services, or replacement parts due to normal wear and tear will be shared among all user groups, based on the time used over the past two years. Please note that assuming the instrument is handled properly, such repairs or replacements are infrequent, and costs may arise after a user’s period of use has ended.
  • Users are responsible for covering the costs of repairs or replacement parts needed due to damage caused by carelessness or neglect.
  • Prospective Industry users should contact Dr Erbse for rates and requirements.Ìý

The Stopped-Flow and Quench-Flow instruments are located on the third floor of JSCBB in the D-Wing, room D381, on East Campus. Proxcard access is required at all times.