Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds

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1 Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds February 27, 2009 Alexander Mastroianni, Shelley Claridge, A. Paul Alivisatos Department of Chemistry, University of California, Berkeley, California , and Division of Materials Science, Lawrence Berkeley National Laboratory, Berkeley, California Supplemental Information 1

2 Additional TEM Images a) b) 5 nm 100 nm c) 100 nm d) 100 nm Figure 1: a) Bare gold b) The contents of the band running ahead of the pyramid band c,d) Additional images of pyramids S2

3 Sequences G1 Each strand bears a hexyl-thiol linker at its 5 end. Strand 1 TTT GCC TGG AGA TAC ATG CAC ATT ACG GCT TTC CCT ATT AGA AGG TCT CAG GTG CGC GTT TCG GTA AGT AGA CGG GAC CAG TTC GCC Strand 2 TTT CGC GCA CCT GAG ACC TTC TAA TAG GGT TTG CGA CAG TCG TTC AAC TAG AAT GCC CTT TGG GCT GTT CCG GGT GTG GCT CGT CGG Strand 3 TTT GGC CGA GGA CTC CTG CTC CGC TGC GGT TTG GCG AAC TGG TCC CGT CTA CTT ACC GTT TCC GAC GAG CCA CAC CCG GAA CAG CCC Strand 4 TTT GCC GTA ATG TGC ATG TAT CTC CAG GCT TTC CGC AGC GGA GCA GGA GTC CTC GGC CTT TGG GCA TTC TAG TTG AAC GAC TGT CGC G2 Each strand is divided into two pieces (x.1, x.2). The first piece has the thiol linker Strand 1.1 TTT TTC CCT GTA CTG GCT AGG AAT TCA CGT TTT AAT CTG GGC TTT GGG TTA AGA AAC TCC CCG Strand 1.2 CGC TGG AGG CGC ATC ACC GTT TGC GTA TGT GTT CTG TGC GGC CTG CCG TCC CGT GTG GG Strand 2.1 TTT TTC GGT GAT GCG CCT CCA GCG CGG GGA GTT TCT TAA CCC TTT CCG ACT TAC AAG AGC CGG Strand 2.2 GCG AGA CTC AGG TGG TGC CTT TGG CAT TCG ACC AGG AGA TAT CGC GTT CAG CTA TGC CC Strand 3.1 TTT TTC CCA TGA GAA TAA TAC CGC CGA TTT ACG TCA GTC CGG TTT CCC ACA CGG GAC GGC AGG C Strand 3.2 CGC ACA GAA CAC ATA CGC TTT GGG CAT AGC TGA ACG CGA TAT CTC CTG GTC GAA TGC C Strand 4.1 S3

4 TTT TTG CCC AGA TTA AAA CGT GAA TTC CTA GCC AGT ACA GGG TTT CCG GAC TGA CGT AAA TCG G Strand 4.2 CGG TAT TAT TCT CAT GGG TTT GGC ACC ACC TGA GTC TCG CCC GGC TCT TGT AAG TCG G S4

5 SequenceDesign Program The following is the C + + code listing for designing pyramids. In this version, it will generate several sets of strands for pyramids with 26 bp sides. It can be modified slightly to produce larger pyramids by changing strandlength and modifying the makestrandx functions. /* Sequence Design Written by Alexander Mastroianni in 2007 This program is used to design sets of ssdna strands for constructing pyramids out of DNA. A sequence is constructed using functions which add a specific base, a guanine or cytosine only, or any random base. As each base is included it and the previous four bases define a snippet. The snippet and its complement are added to the 1-D array snippets. Upon addition of more bases snippets is searched and existing subsequences are avoided. A pyramid is defined as having vertices A, B, C, and D. Strand 1 traces ABC. Strand 2 traces CBD. Strand 3 traces DAC. Strand 4 traces BAD. The appropriate complementary relationships are accounted for in the program. In addition, GC clamps are added at the ends of the sides and thymine residues are added at the corners to relieve tension in the system. Sets of sequences with fewer than a chosen threshold of repeated snippets are output to the screen. */ //Standard libraries #include <iostream> #include <math.h> #include <time.h> S5

6 //A snippet is a 5bp sequence. We re attempting not to repeat //snippets. This definition sets the size of a list used to hold //snippets being created. #define maxsnippets //The length of our DNA #define strandlength 87 //The number of times the program attempts to add a random base //while avoiding duplicating snippets. This is crude, but virtually //ensures that all bases get tried. #define randomattempts 100 //The four bases are represented as integers //G=0 //A=1 //C=2 //T=3 int snippets[maxsnippets]; //A list of all the snippets int snippetindex;//where we are in the snippet list //int maxrepeatlength; int overmax; //The number of repeated snippets in a sequence set int attempts; //The number of sets of sequences to generate //These 1-D arrays hold the sequences, with each base //represented as an integer int O1[strandlength]; int O2[strandlength]; int O3[strandlength]; int O4[strandlength]; //These functions set up and initialize the sequences. void get_parameters(); void initialize(); //makestrands() is function that actually generates the sequences, S6

7 //calling the four sub functions, makestrand1(), etc. void makestrands(); void makestrand1(); void makestrand2(); void makestrand3(); void makestrand4(); //These functions add any random base, a G or C only, //or a specific base, with the appropriate accounting of //the new snippet. int attemptaddany(int testsnippet); int attemptaddgc(int testsnippet); int attemptaddspecific(int testsnippet, int base); //A test to see if a particular snippet x is in the list already. bool snippetfound(int x); //This returns the complement of a given base. int complement(int x); //These functions return a random base, or GC only. //They simply return bases, but don t check for snippet repetition. //They are used internally by attemptaddany(), attemptaddgc(), //and attemptaddspecific(). int anybase(); int GorC(); //This function converts the numerical representation of a base //to a letter, for printing. char numtobase(int x); int main () { S7

8 int t; get_parameters(); initialize(); //attempts is set in get_parameters() for(t=0;t<attempts;t++) makestrands(); //main() void get_parameters(){ //This just sets the number of attempts to make //a set of strands. printf("enter the number of attempts: "); scanf("%d",&attempts); //get_parameters() void initialize(){ int x; //Initialize the random number generator. srand(time(null)); //Initialize the list of snippets. snippetindex=0; for(x=0;x<maxsnippets;x++) snippets[x]=0; //Initialize each strand. S8

9 // 5 represents a null base for(x=0;x<strandlength;x++){ O1[x]=5; O2[x]=5; O3[x]=5; O4[x]=5; //initialize() int attemptaddany(int testsnippet){ int x,test,temp; bool found; found = false; //Attempt to add a random base that doesn t complete //a snippet on the list for(x=0;x<randomattempts;x++){ if (found == false){ test=anybase(); if ( not snippetfound(testsnippet*10+test) ){ temp=test; found=true; //if found = false //for loop //If a snippet not on the list can t be found, give up and //return a random base. if (found==false){ overmax++; return anybase(); else S9

10 return temp; //attemptaddany() int attemptaddgc(int testsnippet){ int x,test,temp; bool found; found = false; //Attempt to add a Gor C base that doesn t complete //a snippet on the list. for(x=0;x<randomattempts;x++){ if (found == false){ test=gorc(); if ( not snippetfound(testsnippet*10+test) ){ temp=test; found=true; //if found = false //for loop //If a snippet not on the list can t be found, give up and //return a G or C base. if (found==false){ overmax++; return GorC(); else return temp; //attemptaddgc() S10

11 int attemptaddspecific(int testsnippet, int base){ //For adding a specific base the snippet is put on the //snippet list anyway. if (snippetfound(testsnippet*10+base)){ overmax++; return base; else return base; //attemptaddspecific() bool snippetfound(int x){ //Search the list of snippets for snippet x int y; bool temp; temp = false; for(y=0;y<maxsnippets;y++) if (snippets[y]==x) temp=true; return temp; //snippetfound() int complement(int x){ //Returns the complement of base x. S11

12 return (x+2)%4; //complement() int anybase(){ //Pick a random base int temp; temp=rand()%4; return temp; //anybase() int GorC(){ //Pick a G or C if((anybase() - 2) < 0) return 0; else return 2; //GorC() char numtobase(int x){ //Convert the numberical representation of a base to //the letter. Recall that 5 is the number used for //initialization and so x represents an untouched position S12

13 //in the strand. char temp; switch(x){ case 0: temp= G ; break; case 1: temp= A ; break; case 2: temp= C ; break; case 3: temp= T ; break; case 5: temp= x ; break; //switch statement return temp; //numtobase() void makestrands(){ //This function makes a set of strands. int x; //Initialize the number of strands with too many repeated S13

14 //snippets, and the list of snippets. overmax=0; snippetindex=0; for(x=0;x<maxsnippets;x++) snippets[x]=0; //Generate each strand makestrand1(); makestrand2(); makestrand3(); makestrand4(); //print strands //Here, for example, 10 snippet repeats is the threhold //for printing a strand. if(overmax<10){ //This is just a scale to identify bases the output. for(x=0;x<strandlength;x++) printf("%d",x%10); printf("\n"); //Each strand is now printed printf("strand 1:\n"); //An optional marker to lay out the positions of the sides. printf(" [ ]...AB...[ ] [ ]"); printf("...bc...[ ] [ ]...CA...[ ]\n"); for(x=0;x<strandlength;x++) printf("%c",numtobase(o1[x])); printf("\n"); printf("strand 2:\n"); printf(" [ ]...CB...[ ] [ ]"); printf("...bd...[ ] [ ]...DC...[ ]\n"); for(x=0;x<strandlength;x++) printf("%c",numtobase(o2[x])); printf("\n"); S14

15 printf("strand 3:\n"); printf(" [ ]...DA...[ ] [ ]"); printf("...ac...[ ] [ ]...CD...[ ]\n"); for(x=0;x<strandlength;x++) printf("%c",numtobase(o3[x])); printf("\n"); printf("strand 4:\n"); printf(" [ ]...BA...[ ] [ ]"); printf("...ad...[ ] [ ]...DB...[ ]\n"); for(x=0;x<strandlength;x++) printf("%c",numtobase(o4[x])); printf("\n"); //Report how many snippets were duplicated. printf("overmax = %d\n",overmax); //makestrands() //These functions make each strand. void makestrand1(){ int x,testsnippet; //The T spacer at the beginning of Strand 1 for(x=0;x<3;x++) O1[x]=3; //The start of the 5 GC clamp of AB for(x=3;x<5;x++) O1[x]=GorC(); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; S15

16 complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //The rest of the 5 GC clamp of AB x=5; testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddGC(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //the middle of AB for(x=6;x<26;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddany(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //the 3 GC clamp of AB for(x=26;x<29;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddGC(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; S16

17 complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //The T spacer between AB and BC for(x=29;x<32;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddspecific(testsnippet,3); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //the 5 GC clamp of BC for(x=32;x<35;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddGC(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //the middle of BC for(x=35;x<55;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddany(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 S17

18 +complement(o1[x-3])*10+complement(o1[x-4]); //the 3 GC clamp of AB for(x=55;x<58;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddGC(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //The T spacer between AB and BC for(x=58;x<61;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddspecific(testsnippet,3); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //the 5 GC clamp of CA for(x=61;x<64;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddGC(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 S18

19 +complement(o1[x-3])*10+complement(o1[x-4]); //the middle of CA for(x=64;x<84;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddany(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //the 3 GC clamp of CA for(x=84;x<87;x++){ testsnippet=o1[x-1]+o1[x-2]*10+o1[x-3]*100+o1[x-4]*1000; O1[x]=attemptaddGC(testsnippet); O1[x]+O1[x-1]*10+O1[x-2]*100+O1[x-3]*1000+O1[x-4]*10000; complement(o1[x])*10000+complement(o1[x-1])*1000+complement(o1[x-2])*100 +complement(o1[x-3])*10+complement(o1[x-4]); //makestrand1() void makestrand2(){ int x,testsnippet; //The tail of strand 2 S19

20 for(x=0;x<3;x++) O2[x]=3; //CB (complement of BC in strand 1) for(x=3;x<29;x++) O2[x]=complement(O1[60-x]); //Add snippets for TTT plus the beginning of CB for(x=4;x<7;x++){ O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The T spacer between CB and BD for(x=29;x<32;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddspecific(testsnippet,3); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The 5 GC clamp of BD for(x=32;x<35;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddGC(testsnippet); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; S20

21 complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The middle of BD for(x=35;x<55;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddany(testsnippet); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The 3 GC clamp of BD for(x=55;x<58;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddGC(testsnippet); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The T spacer between BD and DC for(x=58;x<61;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddspecific(testsnippet,3); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; S21

22 complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The 5 GC clamp of DC for(x=61;x<64;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddGC(testsnippet); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The middle of DC for(x=64;x<84;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddany(testsnippet); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 +complement(o2[x-3])*10+complement(o2[x-4]); //The 3 GC clamp of DC for(x=84;x<87;x++){ testsnippet=o2[x-1]+o2[x-2]*10+o2[x-3]*100+o2[x-4]*1000; O2[x]=attemptaddGC(testsnippet); O2[x]+O2[x-1]*10+O2[x-2]*100+O2[x-3]*1000+O2[x-4]*10000; complement(o2[x])*10000+complement(o2[x-1])*1000+complement(o2[x-2])*100 S22

23 +complement(o2[x-3])*10+complement(o2[x-4]); //makestrand2() void makestrand3(){ int x, testsnippet; //The T spacer at the beginning of Strand 3 for(x=0;x<3;x++) O3[x]=3; //The start of the 5 GC clamp of DA for(x=3;x<5;x++) O3[x]=GorC(); O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); //The rest of the 5 GC clamp of DA x=5; testsnippet=o3[x-1]+o3[x-2]*10+o3[x-3]*100+o3[x-4]*1000; O3[x]=attemptaddGC(testsnippet); O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); S23

24 //the middle of DA for(x=6;x<26;x++){ testsnippet=o3[x-1]+o3[x-2]*10+o3[x-3]*100+o3[x-4]*1000; O3[x]=attemptaddany(testsnippet); O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); //the 3 GC clamp of DA for(x=26;x<29;x++){ testsnippet=o3[x-1]+o3[x-2]*10+o3[x-3]*100+o3[x-4]*1000; O3[x]=attemptaddGC(testsnippet); O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); //The T spacer between DA and AC for(x=29;x<32;x++){ testsnippet=o3[x-1]+o3[x-2]*10+o3[x-3]*100+o3[x-4]*1000; O3[x]=attemptaddspecific(testsnippet,3); O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); //AC (complement of CA in strand 1) S24

25 for(x=32;x<58;x++) O3[x]=complement(O1[118-x]); //Add snippets for TTT plus the beginning of AC for(x=32;x<35;x++){ O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); //The T spacer between AC and CD for(x=58;x<61;x++){ testsnippet=o3[x-1]+o3[x-2]*10+o3[x-3]*100+o3[x-4]*1000; O3[x]=attemptaddspecific(testsnippet,3); O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); //CD (complement of DC in strand 2) for(x=61;x<87;x++) O3[x]=complement(O2[147-x]); //Add snippets for TTT plus the beginning of CD for(x=61;x<64;x++){ O3[x]+O3[x-1]*10+O3[x-2]*100+O3[x-3]*1000+O3[x-4]*10000; complement(o3[x])*10000+complement(o3[x-1])*1000+complement(o3[x-2])*100 +complement(o3[x-3])*10+complement(o3[x-4]); S25

26 //makestrand3() void makestrand4(){ int x; //The 5 tail of strand 4 for(x=0;x<3;x++) O4[x]=3; //BA (complement of AB in strand 1) for(x=3;x<29;x++) O4[x]=complement(O1[31-x]); //The spacer between BA and AD for(x=29;x<32;x++) O4[x]=3; //AD (complement of DA in strand 3) for(x=32;x<58;x++) O4[x]=complement(O3[60-x]); //The spacer between AD and DB for(x=58;x<61;x++) O4[x]=3; //DB (complement of BD in strand 2) for(x=61;x<87;x++) O4[x]=complement(O2[118-x]); //makestrand4() S26

Genome Reconstruction: A Puzzle with a Billion Pieces Phillip E. C. Compeau and Pavel A. Pevzner

Genome Reconstruction: A Puzzle with a Billion Pieces Phillip E. C. Compeau and Pavel A. Pevzner Outline I. Problem II. Two Historical Detours III.Example IV.The Mathematics of DNA Sequencing V.Complications