Conclusion and future directions

DNA computing has made huge strides since Adleman’s experiment in 1994. The field has made quite a lot of progress in theoretical aspects, ex-perimental computing with biomolecules, as well as practical aspects in deal-ing with nano-sized robots and microfluidics. With the current advancements, there is a great promise that DNA computing can have impact on diagnostic and therapeutic methods in the future. With all the ongoing work there are more research questions that answers. However, future directions can be along the following questions:

What are the potential experimental designs that can lead to discovery of gene regulation mechanisms? How can we use the various Web re-sources and available computational genomics tools to hypothesize dif-ferent experimental designs in order to discover essential computable elements for molecular computing outside and inside the cell?

Does the environment within the cell provide a mechanism that would enable computations that are (1) predictable, (2) safe, and (3) control-lable? When computations are performed in vitro, we have a highly controlled environment. When computations are done in vivo, the input can be any of the products of the signaling pathways of the cell. All these byproducts can interfere with the computable procedure that we want the cell to carry out, either in a positive or in a negative way.

How can we build up complete understanding of the elements that would perform molecular computations in a failsafe mode? What are all the mechanisms by which one can stop a DNA computing process at desir-able points in time?

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How can we extend any of the current imaging modalities for reading the results? Various types of fluorescent protein (green, red, yellow) are used today to show that a certain reaction has happened. In this manner, gene activity can be visualized and ‘seen’ under ordinary light microscope.

However, this approach is not practical for many tissues in the human body. Is there an equivalent of fluorescent protein that ‘lights up’ under a different imaging modality?

If certain genes can be expressed only under specific conditions (pres-ence/absence of repressor/promoter binding proteins), then, can we com-bine this knowledge with one of the diagnostic imaging modalities in order to get more specific readout from specific tissue cells which are in the ‘middle’ of their activities?

Can we use any of the imaging modalities to monitor the progress of the diagnostic and therapeutic computations?

Can any of the molecular imaging modalities be used for controlling the biomolecular computations in-vivo?

In the future, many of these research questions will open up a plethora of new engaging topics. Both DNA computing and synthetic biology are nascent areas and have much to answer and evolve from the current systems to true understanding of real dynamic systems.

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Chapter 3