A CG CTTAA AATGC GAATT TTACG GC T CTTAACGCGCGAAATGC – 5’ GAATTGCGCGCT TTACG – 3’ A CG CTTAA AATGC GAATT TTACG GC T A CG CTTAA AATGC GAATT TTACG GC T A CG CTTAA AATGC GAATT TTACG GC T A CG CTTAA AATGC GAATT TTACG GC T A CG CTTAA AATGC GAATT TTACG GC T A CG CTTAA AATGC GAATT TTACG GC T cell division creates gap at telomere which disrupts DNA secondary structure 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

/* * 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; import java.util.ArrayList; import java.util.Iterator; public class ListEnd { 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) public ListEnd(int unitLength, String type) { this.unitLength = unitLength; this.type = type; } public static void main(String[] args) { ArrayList dnas = new ArrayList(); // to hold dna molecule objects // create original double-sttranded dna dnas.add(new ListEnd(startLength, "5'3'")); dnas.add(new ListEnd(startLength, "3'5'")); // simulate cell division for (int divisions = 1; divisions < 21; divisions++) { ArrayList dnasTemp = new ArrayList(); // holds newly created dnas Iterator itr = dnas.iterator(); 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'")); } else { dnasTemp.add(new ListEnd(0, "5'3'")); } } else { // if 5'to3', complementary copy will be same length if (obj.unitLength - 1 >= 0) { dnasTemp.add(new ListEnd(obj.unitLength, "3'5'")); } else { dnasTemp.add(new ListEnd(0, "3'5'")); } // add newly-created dnas to array dnas.addAll(dnasTemp); Iterator itr2 = dnas.iterator(); // iterate through sequences and record length frequencies while (itr2.hasNext()) { ListEnd obj2 = (ListEnd) itr2.next(); if (obj2.type.equals("5'3'")) { lengthArray[obj2.unitLength]++; } int cumSum = 0; // print length frequencies for (int i = 0; i < 12; i++) { System.out.printf("%8s", lengthArray[i] + " "); cumSum = cumSum + lengthArray[i]; } System.out.println(" " + cumSum); System.out.println(" "); } // end of for divisions loop }

9 off9 on9 rep do something (extracellular) strong inhibition weak inhibition (extracellular)

9 off9 on9 rep do something (extracellular) strong inhibition weak inhibition (extracellular) 9 off9 on9 rep do something (extracellular) strong inhibition weak inhibition (extracellular) 8 off8 on8 rep strong inhibition do something (extracellular)

strong inhibition weak inhibition 90 Thus when 9 hasn’t been eaten away, it dominates over 0 and lots of 9 is transcribed

strong indirect inhibition weak direct inhibition (extracellular) 90 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). (extracellular signal a mass function (do 9) intra-cellular signals

strong indirect inhibition weak direct inhibition 9 0 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. signal a mass function (extra-cellular signal)

strong indirect inhibition weak direct inhibition (extracellular) 9 on0 intra-cellular signals 9 off 9 on weak inhibition (extracellular) strong inhibition intra-cellular signals do something (possibly extracellular signal for greater coordination) 9 rep

9 off9 on weak inhibition (extracellular) strong inhibition intra-cellular signals do something (possibly extracellular signal for greater coordination) 9 rep 9 off9 on9 rep do something (extracellular) strong inhibition weak inhibition (extracellular)