Biomedical subjects

Kinneret Keren

Publications and source records attributed to Kinneret Keren.

5 recordsLinked to original sources

PubMed2006

Molecular shift register and its utilization as an autonomous DNA synthesizer.

A novel algorithmic approach to the synthesis of fairly long DNA molecules with nonrecurring sequences is demonstrated. The scheme exploits chemical embodiment of shift registers (SR) to execute algorithms similar to those used to generate pseudorandom numbers on a computer. Single stranded DNA molecules guide the synthesis of double stranded DNA according to the SR truth table. The SR logic facilitates an exponentially smaller synthesis effort compared with all other strategies. A redundancy based scheme, similar to those used in communication, is utilized to suppress synthesis errors.

Algorithms↗

PubMed2006

Fine-scale time-lapse analysis of the biphasic, dynamic behaviour of the two Vibrio cholerae chromosomes.

Using fluorescent repressor-operator systems in live cells, we investigated the dynamic behaviour of chromosomal origins in Vibrio cholerae, whose genome is divided between two chromosomes. We have developed a method of analysing fine-scale motion in the curved co-ordinate system of vibrioid bacteria. Using this method, we characterized two different modes of chromosome behaviour corresponding to periods between segregation events and periods of segregation. Between segregation events, the origin positions are not fixed but rather maintained within ellipsoidal caged domains, similar to eukaryotic interphase chromosome territories. These domains are approximately 0.4 microm wide and 0.6 microm long, reflecting greater restriction in the short axis of the cell. During segregation, movement is directionally biased, speed is comparable between origins, and cell growth can account for nearly 20% of the motion observed. Furthermore, the home domain of each origin is positioned by a different mechanism. Specifically, the oriC(I) domain is maintained at a constant actual distance from the pole regardless of cell length, while the oriC(II) domain is maintained at a constant relative position. Thus the actual position of oriC(II) varies with cell length. While the gross behaviours of the two origins are distinct, their fine-scale dynamics are remarkably similar, indicating that both experience similar microenvironments.

Cell Cycle↗

PubMed2005

Dynamic imaging of protease activity with fluorescently quenched activity-based probes.

Protease activity is tightly regulated in both normal and disease conditions. However, it is often difficult to monitor the dynamic nature of this regulation in the context of a live cell or whole organism. To address this limitation, we developed a series of quenched activity-based probes (qABPs) that become fluorescent upon activity-dependent covalent modification of a protease target. These reagents freely penetrate cells and allow direct imaging of protease activity in living cells. Targeted proteases are directly identified and monitored biochemically by virtue of the resulting covalent tag, thereby allowing unambiguous assignment of protease activities observed in imaging studies. We report here the design and synthesis of a selective, cell-permeable qABP for the study of papain-family cysteine proteases. This probe is used to monitor real-time protease activity in live human cells with fluorescence microscopy techniques as well as standard biochemical methods.

Animals↗

PubMed2003

DNA-templated carbon nanotube field-effect transistor.

The combination of their electronic properties and dimensions makes carbon nanotubes ideal building blocks for molecular electronics. However, the advancement of carbon nanotube-based electronics requires assembly strategies that allow their precise localization and interconnection. Using a scheme based on recognition between molecular building blocks, we report the realization of a self-assembled carbon nanotube field-effect transistor operating at room temperature. A DNA scaffold molecule provides the address for precise localization of a semiconducting single-wall carbon nanotube as well as the template for the extended metallic wires contacting it.

Bacteriophage lambda↗

PubMed2002

Sequence-specific molecular lithography on single DNA molecules.

Recent advances in the realization of individual molecular-scale electronic devices emphasize the need for novel tools and concepts capable of assembling such devices into large-scale functional circuits. We demonstrated sequence-specific molecular lithography on substrate DNA molecules by harnessing homologous recombination by RecA protein. In a sequence-specific manner, we patterned the coating of DNA with metal, localized labeled molecular objects and grew metal islands on specific sites along the DNA substrate, and generated molecularly accurate stable DNA junctions for patterning the DNA substrate connectivity. In our molecular lithography, the information encoded in the DNA molecules replaces the masks used in conventional microelectronics, and the RecA protein serves as the resist. The molecular lithography works with high resolution over a broad range of length scales from nanometers to many micrometers.

Antibodies↗