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A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
cell division creates gap at telomere which
disrupts DNA secondary structure
A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
A
CG
CG
CG
CTTAA AATGC
GAATT TTACG
GC
GC
GC
T
CTTAACGCGCGAAATGC – 5’
GAATTGCGCGCT TTACG – 3’
exonuclease removes everything from end up to
resistant DNA secondary structure (including
whole genes and part of immortal template
strand)
Requirements
• A DNA plasmid molecule that regulates gene
expression after a time delay
• Determines sequential gene expression and
dictates how long each stages lasts
• Linear DNA molecule will be destroyed after
its use – i) by wasting away or ii) by
destroying the cell (kill switch)
• Functionality is (preferably) induced
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/*
* Program which simulates the shortening of one end of a DNA molecule of
* starting length 10 units. The DNA has a functional telomere repair
* mechanism for one end of the DNA, but not the other. This repair mechanism
* is present on the 5' end of the 5' to 3' strand. Thus when copying
* a 5' to 3' strand, the resulting 3' to 5' strand is always the same length
* as the template strand. However, when replicating a 3' to 5' strand,
* the resulting 5' to 3' strand is one unit shorter than the template. The
* missing unit is removed from the 3' end of this resulting strand.
*
* It is assumed genes are only encoded meaningfully on the 3' to 5' stand.
* Therefore although the 5' to 3' strand will be eaten away, the loss will
* consist of complementary base sequences which do not meaningfully encode
* genes. Therefore, all we are interested in is the 3' to 5' stand being eaten
* away from its 5' end. When this shorter molecule is copied, it will
* indirectly result in a shorter 5' to 3' strand.
*/
package lineardna;
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import java.util.ArrayList;
import java.util.Iterator;
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public class ListEnd {
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int unitLength; // current length of dna sequence in units
String type; // whether the dna molecule is 5'3' or 3'5'
static int startLength = 11; // length of dna sequence before shortening
static int[] lengthArray = new int[12]; // array of dna length frequencies (one more than startLength and same as last for loop)
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public ListEnd(int unitLength, String type) {
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}
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public static void main(String[] args) {
this.unitLength = unitLength;
this.type = type;
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ArrayList dnas = new ArrayList(); // to hold dna molecule objects
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// create original double-sttranded dna
dnas.add(new ListEnd(startLength, "5'3'"));
dnas.add(new ListEnd(startLength, "3'5'"));
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// simulate cell division
for (int divisions = 1; divisions < 21; divisions++) {
ArrayList dnasTemp = new ArrayList(); // holds newly created dnas
Iterator itr = dnas.iterator();
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while (itr.hasNext()) {
ListEnd obj = (ListEnd) itr.next();
if (obj.type.equals("3'5'")) { // if 3' to 5'
// create a copy 5' to 3' copy that is one unit shorter
if (obj.unitLength - 1 >= 0) {
dnasTemp.add(new ListEnd(obj.unitLength - 1, "5'3'"));
do something (extracellular)
9 rep
9 on
9 off
weak inhibition (extracellular)
strong inhibition
do something (extracellular)
9 rep
9 on
9 off
weak inhibition (extracellular)
strong inhibition
do something (extracellular)
strong inhibition
9 rep 8 rep
8 on
8 off
9 on
9 off
weak inhibition (extracellular)
strong inhibition
do something (extracellular)
0
9
weak inhibition
strong inhibition
Thus when 9 hasn’t been eaten away, it dominates over 0 and lots of 9 is
transcribed
strong indirect inhibition
intra-cellular signals
0
9
weak direct inhibition (extracellular)
(extracellular signal a
mass function (do 9)
Thus when 9 hasn’t been eaten away, it dominates over 0 and lots of 9 is
transcribed. 9 inhibits 0 indirectly by activating an inhibitor protein (left).
9, as an activator, also activates another gene, which can be any cellular
function (variable part).
strong indirect inhibition
0
9
weak direct inhibition
signal a mass function
(extra-cellular signal)
When 9 has been eaten away, it cant dominate over 0 because the signal
between 9 and 0 is intracellular. However, since 0 is no longer repressed,
its extracellular signal can shut down any “immortal 9’s” in other cells
through an extracellular message! Could also involve direct binding to
existing product of 9’s as well as transcriptional inhibition.
strong indirect inhibition
intra-cellular signals
0
9 on
weak direct inhibition (extracellular)
do something (possibly extracellular signal
for greater coordination)
intra-cellular signals
9 rep
9 on
9 off
weak inhibition (extracellular)
strong inhibition
9 off
do something (possibly extracellular signal
for greater coordination)
intra-cellular signals
9 rep
9 on
9 off
weak inhibition (extracellular)
strong inhibition
do something (extracellular)
9 rep
9 on
9 off
weak inhibition (extracellular)
strong inhibition