Editing DNA computing (section)

===Enzymes===
Enzyme-based DNA computers are usually of the form of a simple [[Turing machine]]; there is analogous hardware, in the form of an enzyme, and software, in the form of DNA.<ref>{{cite journal  | last = Shapiro
  | first = Ehud  | author-link = Ehud Shapiro  | title = A Mechanical Turing Machine: Blueprint for a Biomolecular Computer  | journal = Interface Focus | publisher = [[Weizmann Institute of Science]]  | date = 1999-12-07
  | volume = 2 | issue = 4 | pages = 497–503 | url = http://www.wisdom.weizmann.ac.il/~udi/DNA5/scripps_short/index.htm  | doi =  10.1098/rsfs.2011.0118| pmid = 22649583 | pmc = 3363030 | archive-url=https://web.archive.org/web/20090103224150/http://www.wisdom.weizmann.ac.il/~udi/DNA5/scripps_short/index.htm  |archive-date=2009-01-03 | access-date = 2009-08-13 }}</ref>
    
Benenson, Shapiro and colleagues have demonstrated a DNA computer using the [[FokI]] enzyme<ref name="shapiro">{{Cite journal |last1=Benenson |first1=Y. |last2=Paz-Elizur |first2=T. |last3=Adar |first3=R. |last4=Keinan |first4=E. |last5=Livneh |first5=Z. |last6=Shapiro |first6=E. |year=2001 |title=Programmable and autonomous computing machine made of biomolecules |journal=Nature |volume=414 |issue=6862 |pages=430–434 |bibcode=2001Natur.414..430B |doi=10.1038/35106533 |pmc=3838952 |pmid=11719800}}. Also available here: [http://www.technion.ac.il/~keinanj/pub/110.pdf] {{Webarchive|url=https://web.archive.org/web/20120510194658/http://www.technion.ac.il/~keinanj/pub/110.pdf|date=2012-05-10}}</ref> and expanded on their work by going on to show automata that diagnose and react to [[prostate cancer]]: under expression of the genes [[PPAP2B]] and [[GSTP1]] and an over expression of [[PIM1]] and [[HPN (gene)|HPN]].<ref name="shapiro_cancer">{{Cite journal|last1=Benenson|first1=Y.|last2=Gil|first2=B.|last3=Ben-Dor|first3=U.|last4=Adar|first4=R.|last5=Shapiro|first5=E.|year=2004|title=An autonomous molecular computer for logical control of gene expression|journal=Nature|volume=429|issue=6990|pages=423–429|bibcode=2004Natur.429..423B|doi=10.1038/nature02551|pmc=3838955|pmid=15116117}}. Also available here: [https://web.archive.org/web/20131023055858/http://www.wisdom.weizmann.ac.il/~udi/papers/automoleculcomp_nat04.pdf An autonomous molecular computer for logical control of gene expression]</ref> Their automata evaluated the expression of each gene, one gene at a time, and on positive diagnosis then released a single strand DNA molecule (ssDNA) that is an antisense for [[MDM2]]. MDM2 is a repressor of [[p53|protein 53]], which itself is a tumor suppressor.<ref>
{{Cite journal | last1 = Bond | first1 = G. L. | last2 = Hu | first2 = W. | last3 = Levine | first3 = A. J. | doi = 10.2174/1568009053332627 | title = MDM2 is a Central Node in the p53 Pathway: 12 Years and Counting | journal = [[Current Cancer Drug Targets]] | volume = 5 | issue = 1 | pages = 3–8 | year = 2005 | pmid =  15720184}}
</ref> On negative diagnosis it was decided to release a suppressor of the positive diagnosis drug instead of doing nothing. A limitation of this implementation is that two separate automata are required, one to administer each drug. The entire process of evaluation until drug release took around an hour to complete. This method also requires transition molecules as well as the FokI enzyme to be present. The requirement for the FokI enzyme limits application ''in vivo'', at least for use in "cells of higher organisms".<ref name="kahan08">
{{Cite journal |last1=Kahan |first1=M. |last2=Gil |first2=B. |last3=Adar |first3=R. |last4=Shapiro |first4=E. |year=2008 |title=Towards molecular computers that operate in a biological environment |journal=Physica D: Nonlinear Phenomena |volume=237 |issue=9 |pages=1165–1172 |bibcode=2008PhyD..237.1165K |doi=10.1016/j.physd.2008.01.027}}. Also available here: [http://www.ece.gatech.edu/research/labs/bwn/nanos/papers/Towards_molecular_computers_that_operate_in_a_biological_environment.pdf]
</ref> It should also be pointed out that the 'software' molecules can be reused in this case.