Introduction to Bioorganic Chemistry and Chemical Biology Answers to Chapter 3 (in-text & asterisked problems) Answer 3.1 OH -O P O O O O 5' O 3' O -O P O O NH N N O O N NH N dash/wedge drawing O -O P O O NH2 O O -O P O O 5' N The labor of drawing a simple tetranucleotide helps one to appreciate why we use a combination of one-letter code and atom-numbering to discuss DNA. N O N O 3' pTGCAp NH2 NH2 N N N O -O P O O Introduction to Bioorganic Chemistry and Chemical Biology | A3211 Van Vranken & Weiss | 978-0-8153-4214-4 Answer 3.2 design by www.blink.biz © www.garlandscience.com In the gas phase, the charge separation costs 83 kcal mol–1, which is much more costly than the maximum benefit of aromaticity (35 kcal mol–1). However, in water, where the dielectric constant is about 78, charge separation costs only 1.1 kcal mol–1, which is a small compared with the energetic benefits conferred by aromaticity. Energy = ke = q1 q2 4.0 Å ε distance 9.0 x 109 J•m C2 = 5.8 x 10-19 J (1.6 x 10 -19 C)(1.6 x 10 -19 C) 1 × × (4.0 Å) 1Å 10-10 m R N + gas phase water (25 ° C) 1 kJ 6.0 x 1023 1000 J mol O ε=1 ε = 78 = 35 kJ mol–1 or 83 kcal mol–1 (1 cal = 4.18 J) in gas phase ( ε = 1) Energy = 1.1 kcal mol–1 in water at 25 °C ( ε = 78) Introduction to Bioorganic Chemistry and Chemical Biology | A3212 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz It is important to recognize that the positive charge on nitrogen and negative charge on oxygen is a Lewis structure formalism. In fact, the nitrogen atom has a partial negative charge and most of the positive charge is distributed on the various hydrogen atoms. Surprisingly, ab initio calculations HF/STO-3G predict a dipole moment of 4.8 Debye units, not too different from the dipole moment predicted from a +1 charge and -1 charge separate by 4.0 Å (4.0 Debye units). 1 2 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 Answer 3.3 - .. :O: O amide N N+ N amidine most basic and most nucleophilic +N N .. N: most basic and most nucleophilic Introduction to Bioorganic Chemistry and Chemical Biology | A3213 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.4 O HO : OH2 N : AH O + H O HO NH2 N HO HO NH2 N H + N N N NH N HO O HO NH2 N + N OH HO .. H N NH2 :N + O HO N HO NH A H .. O HO N N + O HO NH2 N HO + NH H A .. N H N N : A- H N+ N NH2 N N NH2 HN N N Introduction to Bioorganic Chemistry and Chemical Biology | A3214 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.5 The major groove. major groove H N H N R N N R O H N N R N O Introduction to Bioorganic Chemistry and Chemical Biology | A3215 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.6 NH2 O NH NH2 NH2 N NH2 N N N H NH or N O O Introduction to Bioorganic Chemistry and Chemical Biology | A3216 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.7 Five possible 18-base probes (A–C) will have complete overlap with the 14-base sequence. Probes A–C will have the highest GC content and therefore the highest Tm. Probes D and E will have a slightly lower Tm. target probe probe probe probe probe 5'-CGGGGGTGGCGCAGTGAGGAGG-3' A 3'-GCCCCCACCGCGTCACTC -5' B 3'-CCCCCACCGCGTCACTCC-5' C 3'-CCCCACCGCGTCACTCCC -5' D 3'-CCCACCGCGTCACTCCCT -5' E 3'-CCACCGCGTCACTCCCTC -5' Introduction to Bioorganic Chemistry and Chemical Biology | A3217 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Tm = Tm = Tm = Tm = Tm = 4x2 4x2 4x2 5x2 5x2 + + + + + 14x4 °C = 14x4 °C = 14x4 °C = 13x4 °C = 13x4 °C = 64 °C 64 °C 64 °C 62 °C 62 °C Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 3 Answer 3.8 415 = 1,073,741,824 416 = 4, 294,967,296 17 4 = 17,179,869,184 418 = 68,719,476,736 419 = 274,877,906,944 420 = 1,099,511,627,776 Introduction to Bioorganic Chemistry and Chemical Biology | A3218 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz There are 68 billion possible DNA sequences composed of 18 base pairs, over 20 times more than the number of bases in the human genome. At most, a human-size genome could contain only about 3 billion different 18 bp sequences. Thus, it is reasonably unlikely that an 18-base sequence would be present in the human genome as a result of random chance. Answer 3.9 This hairpin was selected from a library of oligonucleotides because it binds to the amino acid arginine. Only the first six and last six nucleotides form contiguous Watson–Crick base pairs. NMR studies of the hairpin•arginine complex (PDB 1DB6) revealed additional interactions not shown in the answer below, a Watson–Crick base pair between G9 and C16 as well as non-Watson–Crick interactions between other pairs of bases. CG T G T CG C 1 5'-CGACCA A 3'-GCTGGTC 22 Introduction to Bioorganic Chemistry and Chemical Biology | A3219 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.10 TT T G CAC T 3'-CCCGCTACC GTG A GG hairpin 5'-GGG GATGG Introduction to Bioorganic Chemistry and Chemical Biology | A3220 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.11 B .. R NH2 .. -O Ph H N O HO N H OH N + R N S 2C -O Me Me 2C R HO H N B H S good nuc O: Ph H N H N HO :N S HO2C Ph H H N R N HO H N good L.G. + S HO2C Me Me Me Me Introduction to Bioorganic Chemistry and Chemical Biology | A3221 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com Answer 3.12 design by www.blink.biz The guanidine moiety of arginine is protonated at pH 7, and these protonated arginine side chains confer a significant affinity for the phosphate backbone of DNA. The urea group of citrulline, which is not protonated at neutral pH, would have a lower affinity for an anionic phosphate diester. Deimination of histones would release the bound DNA, making it accessible to transcription factors. arginine H N H H N+ N H H O O - P O O stable salt bridge with DNA citrulline O N H N H O O - P O O H less stable interaction DNA Introduction to Bioorganic Chemistry and Chemical Biology | A3222 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz O: Me Me Ph O R N H HN HO2C H N HO S Me Me Ph 4 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 Answer 3.13 DNA polymerase can only add to the 3ʹ end of a growing strand. The primer will be identical to the 5ʹ end and complementary to the 3ʹ end. 5ʹ-CCATGCCTATGTTCATCGTGA-3ʹ 5ʹ-CCATGCCTATGTTCATCGTGAACACCAATGT……CTGGCCCCACTTACCTGCACCGCTGTTC-3ʹ 3ʹ-GTGAATGGACGTGGCGACAAG–5ʹ Answer 3.14 NHBz .. CH3NH2 B: N N R N R O Ph O H H N NHBz H3C + - N: H3C H N NHCH3 NH - N: N R O N N R O O Introduction to Bioorganic Chemistry and Chemical Biology | A3224 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com Answer 3.15 design by www.blink.biz OR i-Pr H P N H A O i-Pr N N N N NC N N H i-Pr2N : OR + i-Pr H P N H O i-Pr N N N N NC OR H + P i-Pr N O i-Pr .. N N - NC .. OR P i-Pr .. N O i-Pr H N N N N NC OR H P O + N N N N NC OR P N O N N N NC Introduction to Bioorganic Chemistry and Chemical Biology | A3225 Van Vranken & Weiss | 978-0-8153-4214-4 Answer 3.16 design by www.blink.biz © www.garlandscience.com B: H O :O OH OH OH O Gal Gal O Gal O O O OSO3Na OSO3Na O O Introduction to Bioorganic Chemistry and Chemical Biology | A3226 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.17 The amount of inhibitor drug is increasing from lane 1 to lane 6. At the highest concentration of drug, most of the plasmid DNA remains in the fully supercoiled state. (Figure adapted from I. Larosche et al., J. Pharmacol. Exp. Ther. 321: 526–535, 2007.) least inhibitor sample 1 most inhibitor 2 3 4 5 6 relaxed partially supercoiled supercoiled actual [inhibitor] (µM) ~0 5 10 Introduction to Bioorganic Chemistry and Chemical Biology | A3227 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz 20 50 100 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 Answer 3.18 A 5'- AACTGAATTTCAGGGGGATCCGCATGGCGT -3' AACTGAATTTCAGGGGGATCCGCATGGCGT 5'-5'-3'-3' AACTGAATTTCAGGGGGATCCGCATGGCGT 3'-TTGACTTAAAGTCCCCCTAGGCGTACCGCA -5' 3'-3'-5'-5' TTGACTTAAAGTCCCCCTAGGCGTACCGCA TTGACTTAAAGTCCCCCTAGGCGTACCGCA B Design and synthesize two oligonucleotides with BamHI overhangs on the ends. These will hybridize to any site cut with BamHI. 5'- AACTGAATTTCAGGGGGATCCGCATGGCGT -3' AACTGAATTTCAGGGGGATCCGCATGGCGT 5'-5'-3'-3' AACTGAATTTCAGGGGGATCCGCATGGCGT 3'-TTGACTTAAAGTCCCCCTAGGCGTACCGCA -5' 3'-3'-5'-5' TTGACTTAAAGTCCCCCTAGGCGTACCGCA TTGACTTAAAGTCCCCCTAGGCGTACCGCA BamH1 BamH1 BamH1 GATCCGCATGGCGT -3' GATCCGCATGGCGT GATCCGCATGGCGT -3'-3' GCGTACCGCA -5' GCGTACCGCA design and GCGTACCGCA -5'-5' design design and and 5'- AACTGAATTTCAGGGG AACTGAATTTCAGGGG 5'-5'AACTGAATTTCAGGGG synthesizesynthesize synthesize 3'TTGACTTAAAGTCCCCCTAG 3'-3'TTGACTTAAAGTCCCCCTAG TTGACTTAAAGTCCCCCTAG kinase kinase kinase pGATCCGCATGGGTTTCAAATCG pGATCCGCATGGGTTTCAAATCG pGATCCGCATGGGTTTCAAATCG GCGTACCCTTTGTTTAGCCTAGp GCGTACCCTTTGTTTAGCCTAGp GCGTACCCTTTGTTTAGCCTAGp 5'- AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG GATCCGCATGGCGT -3' AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG 5'-5'GATCCGCATGGCGT AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG GATCCGCATGGCGT -3'-3' 3'-TTGACTTAAAGTCCCCCTAG GCGTACCGCA -5' GCGTACCCTTTGTTTAGCCTAG GCGTACCGCA GCGTACCCTTTGTTTAGCCTAG 3'-3'TTGACTTAAAGTCCCCCTAG GCGTACCGCA -5'-5' GCGTACCCTTTGTTTAGCCTAG TTGACTTAAAGTCCCCCTAG T4 DNA ligase Mg•ATP DNA ligase T4T4 DNA ligase Mg•ATP Mg•ATP 5'- AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG -3' GATCCGCATGGCGT AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG 5'-5'GATCCGCATGGCGT AACTGAATTTCAGGGG GATCCGCATGGGTTTCAAATCG -3'-3' GATCCGCATGGCGT 3'-TTGACTTAAAGTCCCCCTAG GCGTACCGCA GCGTACCCTTTGTTTAGCCTAG -5' GCGTACCGCA GCGTACCCTTTGTTTAGCCTAG 3'-3'TTGACTTAAAGTCCCCCTAG GCGTACCGCA GCGTACCCTTTGTTTAGCCTAG -5'-5' TTGACTTAAAGTCCCCCTAG C The sequence contains two BamHI sites. Any new overhangs on the ends could hybridize within the oligonucleotide or between oligonucleotides. GATCCTTTCATAAGTGGTGGGATCCCCATTCAATTG GATCCTTTCATAAGTGGTGGGATCCCCATTCAATTG GATCCTTTCATAAGTGGTGGGATCCCCATTCAATTG GAAAGTATTCACCACCCTAGGGGTAAGTTAACCTAG GAAAGTATTCACCACCCTAGGGGTAAGTTAACCTAG GAAAGTATTCACCACCCTAGGGGTAAGTTAACCTAG Introduction to Bioorganic Chemistry and Chemical Biology | A3228 Introduction to Bioorganic Chemistry Chemical Biology | A3228 Introduction to Bioorganic Chemistry andand Chemical Biology | A3228 Vranken & Weiss | 978-0-8153-4214-4 Vranken &Van Weiss | 978-0-8153-4214-4 VanVan Vranken & Weiss | 978-0-8153-4214-4 design by www.blink.biz © www.garlandscience.com design by www.blink.biz © www.garlandscience.com design by www.blink.biz © www.garlandscience.com Answer 3.19 O O CF 3 HN O S- .. N R O O F2 .. C - F HN N R H2.. N O Enz O CF 2 HN S Enz N R HN S Enz HN .. CF 2 - N R O Enz S O HN N R O Enz Enz Introduction to Bioorganic Chemistry and Chemical Biology | A3229 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.20 O N O: - O N H A O .. H N H A .. -A .. Gua N N .. OH Gua H N N H A Gua O O N N R NH N N + N N R N NH HN N N R O O N N H2N .. N H N :O - N HN N R Introduction to Bioorganic Chemistry and Chemical Biology | A3230 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz N N R O .. N Gua N H + N + OH2 - H A O + Gua N N O HN NH + N N N H N 2 + N .. AH N OH Gua + N H H O N Gua + N OH2+ .. .. .. Gua .. + NH2 N O .. O+ N .. :O N N R Enz HN CF 2 5 6 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 Answer 3.21 ..N C6H13 C6H13 N + C6H13 N .. Nu S C N fascicularin O N+ aziridinium ion NH N DNA N NH2 Introduction to Bioorganic Chemistry and Chemical Biology | A3231 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Answer 3.22 abstraction of the two H atoms is not concerted H H • • • H H • H H abstract H atom H abstract H atom H + H H H H Answer 3.23 H uncialamycin O HN reducing intracellular environment R O OH O HO OH OH H2O R = CH(OH)CH 3 OH H R HN HO HO OH reduced in the cell Bergman rearrangement HO HN R OH HO HN HO HO O R OH OH S N1 OH HO Introduction to Bioorganic Chemistry and Chemical Biology | A3232 Van Vranken &to Weiss | 978-0-8153-4214-4 Introduction Bioorganic Chemistry and Chemical Biology | A3233 www.garlandscience.com design by www.blink.biz Van Vranken & Weiss | 978-0-8153-4214-4 © © www.garlandscience.com design by www.blink.biz OH Answer 3.24 H H H H • H H H H H H H H H H H H • H H H H H • H H H H H H H • H H H H H H H H H H H H H Introduction to Bioorganic Chemistry and Chemical Biology | A3234 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz H H H H + H H H Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 7 *Answer 3.26 A OH -O P O O The conformational depiction below and the dash/wedge depiction to the right are equally acceptable B O O HO O Thy -O O -O P O O Gua O O P O O -O O d( GACA) Ade "d" prefix means 2-deoxy OH -O O O P O O -O P O O Thy O -O O O P O O -O O pTATA Ade O P O O presence of Thy suggests that this is DNA C O HO Thy -O O O P O Ade HO O O -O P O O Thy O Ade HO Gua O -O P O O OH O O -O O GUCU Ura P O OH O O -O presence of Ura suggests that this is RNA Cyt O P O OH O HO Ura OH Introduction to Bioorganic Chemistry and Chemical Biology | A3236 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.27 H N H N dR N N N N CH3 H N N N O dR Introduction to Bioorganic Chemistry and Chemical Biology | A3237 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.30 A In PDB 1AIO, cisplatin forms a crosslink between the N7 atoms of guanine bases (rendered in yellow). B Van Vranken & Weiss | 978-0-8153-4214-4 The platinum atom sits in the major groove. © www.garlandscience.com design by www.blink.biz C The crosslink is intrastrand, between adjacent guanine bases. Introduction to Bioorganic Chemistry and Chemical Biology | A3238 Ade O O P O Cyt O -O O P O O HO Ade 8 Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 Answer 3.32 *A 3ʹ-AGCTTACGTAATAAGCA-5ʹ or 5ʹ-ACGAATAATGCATTCGA-3ʹ *Answer 3.33 A The following secondary structures are expected for each oligonucleotide or pair of oligonucleotides. The sites of oxidation are shown with arrows. arrows highlight sites of oxidation ssDNA 5'-CATGCGTTCCCGTG -3' duplex formation 5'-CATGCGTTCCCGTG -3' 3'-GTGCGCAAGGGCAC -5' hairpin or duplex with mismatch bulge 5'- AGTCTA 3'- TCAGAT G duplex with mismatch bulge 5'-ACGTCAG 3'-TGCAGTC hairpin or duplex with mismatch bulge 5'- AGTCTAT G 3'- TCAGATT G strand not analyzed G 5'- AGTCTA 3'- TCAGAT TAGACT -3' ATCTGA -5' G or G TGGCAT -3' ACCCGTA -5' G strand not analyzed TGGGT TAGACT -3' ATCTGA -5' TGGGT 5'-AGTCTA 3'-TCAGAT or Introduction to Bioorganic Chemistry and Chemical Biology | A3239 Van Vranken & Weiss | 978-0-8153-4214-4 B On the basis ofbythe structures, the susceptible bases seem to be guanidines that design www.blink.biz © www.garlandscience.com are not protected by both base-pairing and π stacking. Therefore, Gs at the ends of duplexes or in bulges or loops are susceptible. *Answer 3.37 MeO MeO N O O HO O hv O O O OH -O * MeO hv R 2N O or... HO N CO2- 2C MeO ON OH R' MeO N MeO N N Ca O O HO O Introduction to Bioorganic Chemistry and Chemical Biology | A3242 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.38 A O N O: - O N H A O .. H N H A .. -A N N .. OH N H A Ph O .. N Ph N + OH2 H + N N - H A O + Ph N N .. Ph Ph H N OH2+ .. H H O N Ph + N .. AH N OH Ph + N .. .. Ph .. + NH2 N O .. O+ N .. :O OH .. O R 2N R' O R' CO2- MeO + ON O H MeO NH 2C -O OH N MeO N O MeO Ca2+ H2O N Ca MeO MeO NO2 O O O OH N O: - N H A N H A N .. OH2+ .. -A H O .. H to Bioorganic Chemistry H H H Introduction - H Aand Chemical Biology: Answers to Chapter 3 + O O N N N O Ph + N Ph N Ph N .. .. .. Ph .. + NH2 N O .. B Ph N N .. OH H A Ph .. N N + OH2 + Ph N N .. AH N OH Ph + N as in part A. NH2 N N DNA O .. N DNA + OH2 :N- N DNA O C N H2O N O guanine N N DNA N NH2 H2O N DNA O H O + NH N DNA O A- O NH N DNA O O O N N DNA NH N O NaNO 2 HCl NH H A N N DNA NaNO 2 HCl N N DNA OH OH + N O NH2 adenine H A .. N 2 .. +N OH2+ .. N2+ N N DNA NH N H O Introduction to Bioorganic Chemistry and Chemical Biology | A3243 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.41 A : B N O 2N N H H : :B :N O N O 2N N CH3 N H O N N CH3 O 2N N C NH O: N H B N CH3 O 2N N C NH :N + H OH N C H H Introduction to Bioorganic Chemistry and Chemical Biology | A3246 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.42 AWith a calculator: 430 = 1,152,921,504,606,847,000 = 1.2 × 1018 Even better, work this without a calculator using the approximation 410 ≈ 106: [410]3 = [106]3 = 1018 B 5'-GGGAGAATTCCCAGACC-3' 5'-GGGAGAATTCCCAGACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGAGGGAAATTCTCCC-3' 3'-GACTCCCTTTAAGAGGG-5' 5'-GGGAGAATTTCCCTCAG-3' C AC GT 5'-GGGATCGAA A G 3'-CCCTAGCTT CC GC Arg D H + N H N NH2 H + N N NH2 Arg H + N H N NH2 B: N N+ C H H H NN+ C H H 9 5'-GGGAGAATTTCCCTCAG-3' C AC GT 5'-GGGATCGAA A Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 10 Introduction to G 3'-CCCTAGCTT CC GC Arg D H H N H + N N NH2 H H N H or O H + N H N N NH2 H N H O N or H N N O dC *Answer 3.44 Me OH Me HO DNA: Me Me HO .. SR OH OH OH SR OH OH DNA Me Me Me +H O 2 OH SR OH H A Me OH Me + OH Me OH : SR - O Me OH Me Me OH Me SR OH *Answer 3.48 Introduction Chemistry and Chemical Biology | A3251 Hto Bioorganic H N | 978-0-8153-4214-4 Van Vranken & Weiss © www.garlandscience.com design by www.blink.biz N N DNA N H O + N DNA N R O HN HO Introduction to Bioorganic Chemistry and Chemical Biology | A3255 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.51 A B N N N .. HN H N dC Introduction to Bioorganic Chemistry and Chemical Biology | A3248 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz Me NH2 H H N dC Arg H N H + N Arg H N N + H N N O N H O O Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 *Answer 3.54 O Introduction to Bioorganic Chemistry and Chemical Biology | A3258 OMe NHCO2Me Van Vranken & Weiss | 978-0-8153-4214-4 HO NHEt Sby www.blink.biz design © www.garlandscience.com O O OH N O aromatic by-product O can intercalate between base pairs Me S Me O HN OH Introduction to Bioorganic Chemistry and Chemical Biology | A3261 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz *Answer 3.57 5ʹ-TCCTNNAGGA-3ʹ head (H) A The oligosaccharide is asymmetric with a head (H), a tail (T), a left-hand side and a OH right-hand side.Me MeO head (H) O HO OH MeO O MeO Me I O HO MeO lefthand side HN HO HN O HO Me EtHN O tail (T) hand side O O O O Me Me O OMe Me right- HO O I side left- MeMeO hand O S side HO O O S O Me rightMeOhand O O O EtHN OMe B tail (T) Because the minor groove is also asymmetric, the 3ʹ end is different from the 5ʹ end. Therefore the oligosaccharide will bind in a preferred orientation. 5' | 3' | T A 3' H 5'| | C G C GT H A G T T AC | | C G 3' 5' T T A | 3' | 5' 11 12 C G T T A | | Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 3 3' C 5' If you link the oligosaccharide tail to tail, each half still wants to bind with the original orientation. 5' 3' | | T C C T N N A G G A| A G G T A N O N T T C C H T | H 3' 5' *Answer 3.58 Chemistry and Chemical Biology | A3264 Introduction to Bioorganic Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz - Cl : NC para-benzyne intermediate + - .. O HO NC - Cl : O OH OH O enediyne precursor - .. + O HO NC O OH OH O Introduction to Bioorganic Chemistry and Chemical Biology | A3265 Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz O O OH HO OH O