Dataset Information

The rotation-coupled sliding of EcoRV.

ABSTRACT: It has been proposed that certain type II restriction enzymes (REs), such as EcoRV, track the helical pitch of DNA as they diffuse along DNA, a so-called rotation-coupled sliding. As of yet, there is no direct experimental observation of this phenomenon, but mounting indirect evidence gained from single-molecule imaging of RE-DNA complexes support the hypothesis. We address this issue by conjugating fluorescent labels of varying size (organic dyes, proteins and quantum dots) to EcoRV, and by fusing it to the engineered Rop protein scRM6. Single-molecule imaging of these modified EcoRVs sliding along DNA provides us with their linear diffusion constant (D(1)), revealing a significant size dependency. To account for the dependence of D(1) on the size of the EcoRV label, we have developed four theoretical models describing different types of motion along DNA and find that our experimental results are best described by rotation-coupled sliding of the protein. The similarity of EcoRV to other type II REs and DNA binding proteins suggests that this type of motion could be widely preserved in other biological contexts.

SUBMITTER: Dikic J

PROVIDER: S-EPMC3351190 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The rotation-coupled sliding of EcoRV.

Dikić Jasmina J Menges Carolin C Clarke Samuel S Kokkinidis Michael M Pingoud Alfred A Wende Wolfgang W Desbiolles Pierre P

Nucleic acids research 20120112 9

It has been proposed that certain type II restriction enzymes (REs), such as EcoRV, track the helical pitch of DNA as they diffuse along DNA, a so-called rotation-coupled sliding. As of yet, there is no direct experimental observation of this phenomenon, but mounting indirect evidence gained from single-molecule imaging of RE-DNA complexes support the hypothesis. We address this issue by conjugating fluorescent labels of varying size (organic dyes, proteins and quantum dots) to EcoRV, and by fus ...[more]

PMID: 22241781

Similar Datasets

Project description:BackgroundScapulothoracic upward rotation (UR) is an important shoulder complex motion allowing for a larger functional work space and improved glenohumeral muscle function. However, the kinematic mechanisms producing scapulothoracic UR remain unclear, limiting the understanding of normal and abnormal shoulder movements.ObjectiveThe objective of this study was to identify the coupling relationships through which sternoclavicular and acromioclavicular joint motions contribute to scapulothoracic UR.DesignThis was a cross-sectional observational study.MethodsSixty participants were enrolled in this study; 30 had current shoulder pain, and 30 had no history of shoulder symptoms. Shoulder complex kinematics were quantified using single-plane fluoroscopy and 2D/3D shape matching and were described as finite helical displacements for 30-degree phases of humerothoracic elevation (30 degrees-60 degrees, 60 degrees-90 degrees, and 90 degrees-120 degrees). A coupling function was derived to estimate scapulothoracic UR from its component motions of acromioclavicular UR, sternoclavicular posterior rotation, and sternoclavicular elevation as a function of acromioclavicular internal rotation. The proportional contributions of each of the component motions were also calculated and compared between phases of humerothoracic elevation and groups.ResultsScapulothoracic UR displacement could be effectively predicted using the derived coupling function. During the 30- to 60-degree humerothoracic elevation phase, acromioclavicular UR accounted for 84.2% of scapulothoracic UR, whereas sternoclavicular posterior rotation and elevation each accounted for < 10%. During later phases, acromioclavicular UR and sternoclavicular posterior rotation each accounted for 32% to 42%, whereas sternoclavicular elevation accounted for < 11%.LimitationsError due to the tracking of sternoclavicular posterior rotation may have resulted in an underprediction of its proportional contribution and an overprediction of the proportional contribution of acromioclavicular UR.ConclusionsAcromioclavicular UR and sternoclavicular posterior rotation are the predominant component motions of scapulothoracic UR. More research is needed to investigate how these coupling relationships are affected by muscle function and influenced by scapular dyskinesis.

Dataset Information

The rotation-coupled sliding of EcoRV.

Publications

The rotation-coupled sliding of EcoRV.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets