CHEMISTRY G25.1815

MACROMOLECULAR CHEMISTRY

Spring 1998

MAIN 1003

14:50-16:05, Tuesdays and Thursdays

Nadrian C. Seeman
1066 Waverly

Ned.Seeman@NYU.edu

INSTRUCTIONS FOR PRESENTATIONS:

[1] EVERYBODY WILL HAVE A TOTAL OF 35 MINUTES. PLEASE COME TO CLASS AS EARLY AS POSSIBLE, BECAUSE IF EVERYONE IS THERE WE CAN START. WE WILL START WHEN EVERYONE IS THERE, OR 2:50, WHICHEVER COMES FIRST.

[2]PLAN TO SPEND NO MORE THAN 27 MINUTES ON YOUR TALK. THE REST OF THE TIME IS FOR DISCUSSION. I WILL CUT YOU OFF AFTER 27 MINUTES

[3]YOU SHOULD USE OVERHEADS TO ILLUSTRATE THE IMPORTANT FIGURES AND POINTS IN THE PAPER. THESE SHOULD BE DERIVED FROM THE ORIGINAL PUBLICATION, NOT FROM THE REDUCED B&W XEROX IN THE LIBRARY. START LOOKING FOR YOUR ARTICLES NOW. IF THEY ARE HARD TO FIND, TELL ME. IF YOU START MAKING YOUR OVERHEADS THE NIGHT BEFORE YOUR TALK, YOU MAY HAVE ONLY GARBAGE TO SHOW.

[4] EVERYBODY IS RESPONSIBLE FOR EVERY PAPER. THAT IS WHY WE HAVE 8 MINUTES OF DISCUSSION SCHEDULED. YOU WILL BE GRADED ON YOUR DISCUSSION PARTICIPATION. EVERYBODY STARTS WITH A DISCUSSION GRADE OF 'C', A FAILING GRADE FOR A GRADUATE STUDENT. HOWEVER, IF YOU ASK A DUMB QUESTION, INDICATING THAT YOU HAVE NOT READ THE ARTICLE, YOU WILL GET A GRADE BELOW 'C'. GOOD QUESTIONS DO NOT REPEAT WHAT THE SPEAKER JUST SAID, BUT INVOLVE CLARIFICATION OF POINTS RAISED. IF I AM UNSATISFIED WITH THE QUALITY OF DISCUSSION, I WILL GIVE A FINAL EXAM ON THE CONTENT OF THE PAPERS. OTHERWISE I WON'T.

[5] PRACTICE YOUR TALK AT LEAST 30 TIMES!!!

PRESENTATION TOPICS:

(1) RECOMBINATION SYSTEMS
Thursday, April 16--Qian Ruan

1. Guo F, Gopaul DN, Van Duyne GD (1997) Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse, Nature 389 40-46.

2. Hickman AB, Waninger S, Scocca JJ, Dyda F (1997) Molecular organization in site-specific recombination: The catalytic domain of bacteriophage HP1 integrase at 2.7 A resolution, Cell 89, 227-237.

3. Miick SM, Fee RS, Millar DP, Chazin WJ (1997) Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions, Proc. Nat. Acad. Sci. (USA) 94, 9080-9084.

(2) TOPOISOMERASES
Thursday, April 16--Katie Charlston

1. Redinbo MR, Steward L, Kuhn P., Champoux JJ, Hol, WGJ (1998), Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA, Science 279, 1505-1513.

2. Stewart L, Redinbo MR, Qiu X, Hol WGJ, Champoux JJ (1998) A model for the mechanism of human topoisomerase I, Science 279, 1534-1541.

3. Cabral JHM, Jackson AP, Smith CV, Shikotra N, Maxwell A, Liddington RC (1997) Crystal structure of the breakage-reunion domain of DNA gyrase, Nature 388, 903-906.

(3) RIBOZYMES AND DEOXYRIBOZYMES
Tuesday, April 21--Kev Adjemian

1. Hertel KJ, Peracchi A, Uhlenbeck OC, Herschlag D (1997) Use of intrinsic binding energy for catalysis by an RNA enzyme, Proc. Nat. Acad. Sci. (USA) 94, 8497-8502.

2. Zhang B and Cech TR (1997) Peptide bond formation by in vitro selected ribozymes, Nature 390, 96-100.

3. Carmi N, Balkhi SR, Breaker RR (1998) Cleaving DNA with DNA, Proc. Nat. Acad. Sci. (USA) 95, 2233-2237.

(4) UNUSUAL DNA COMPONENTS
Tuesday, April 21--Zhengshuang Shi

1. Moran S, Ren RX-F, Kool ET (1997) A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity, Proc. Nat. Acad. Sci. (USA) 94, 10506-10511.

2. Good L, Nielsen PE (1998) Inhibition of translation and bacterial growth by peptide nucleic acid targeted to ribosomal RNA, Proc. Nat. Acad. Sci. (USA) 95, 2073-2076.

3. Tereshko V, Gryazmov S, Egli M (1998) Consequences of replacing the DNA 3' oxygen by an amino group: High-resolution crystal structure of a fully modified N3'-->P5' phosphoramidate DNA dodecamer duplex, J. Am. Chem. Soc. 120, 269-283.

(5) PROTEIN ENGINEERING
Thursday, April 23--Kan Zhou

1. Hill RB, DeGrado WF (1998) Solution structure of a2D, a native-like de novo designed protein, J. Am. Chem. Soc. 120, 1138-1145.

2. Liu DR, Magliery TJ, Pasternak M, Schultz PG (1997) Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo, Proc. Nat. Acad. Sci. (USA) 94, 10092-10097.

3. Kim Y-G, Kim PS, Herbert A, Rich A (1997) Construction of a Z-DNA-specific restriction endonuclease, Proc. Nat. Acad. Sci. (USA) 94, 12875-12879.

(6) ENGINEERING THE RECOGNITION OF DNA
Thursday, April 23--Eileen Dimalanta

1. Liu Q, Segal DJ, Ghara JB, Barbas III, CF (1997), Design of polydactyl zinc-finger proteins for unique addressing within complex genomes, Proc. Nat. Acad. Sci. (USA) 94, 5525-5530.

2. Kopka ML, Goodsell DS, Han GW, Chiu TK, Lown JW, Dickerson RE (1997) Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G, Structure 5, 1033-1046.

3. White S, Szewczyk JW, Turner JM, Baird EE, Dervan, PB (1998) Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands, Nature 391, 468-471.

(7) APPLYING FORCE TO DNA
Tuesday, April 28--Sang Lim

1. Noy, A, Vezenov DV, Kayyem JF, Meade TJ, Lieber CM (1997) Stretching and breaking duplex DNA by chemical force microscopy, Chem. & Biol. 4, 519-527.

2. Baumann CG, Smith SB, Bloomfield VA, Bustamante C (1997) Ionic effects on the elasticity of single DNA molecules, Proc. Nat. Acad. Sci. (USA) 94, 6185-6190.

3. Essavaz-Roulet B, Bockelmann U, Heslot F (1997) Mechanical separation of the complementary strands of DNA, Proc. Nat. Acad. Sci. (USA) 94, 11935-11940.

(8) NUCLEIC ACIDS IN NON-BIOLOGICAL SYSTEMS
Tuesday, April 28--Guiping Xu

1. Elghanian R, Storhoff JJ, Mucic RC, Letsinger RL, Mirkin CA (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles, Science 277, 1078-1079.

2. Braun E, Eichen Y, Sivan U, Ben-Yoseph G (1998) DNA-templated assembly and electrode attachment of a conducting silver wire, Nature 391, 775-778.

3. Thorp HH (1998) Cutting out the middleman: DNA biosensors based on electrochemical oxidation, Trends in Biotech. 16, 117-121.

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