Reading Assignments

rev (1/18/2006)

Nucleic Acid Structure and Biochemistry

Reference

Mon

1/9

Hydrogen Bonding of Nucleic Acid Bases
Voet and Voet, Section 5-1 to 5-3A (pages 80-86).

Wed

1/11

Williams et al. "Dimers, trimers and tetramers of cytosine with guanine", J. Am. Chem. Soc.,
111, 7205-9 (1989) (here)

Voet and Voet, Sections 29-2B (pages 1118-1121)  

Fri

1/13

R. A. Newinark, Charles R. Cantor, "Nuclear Magnetic Resonance Study of the Interactions
of Guanosine and Cytidine in Dimethyl Sulfoxide," Journal of the American Chemical Society
90, 5010-5017 (1968) (here).

Qinn and Zimmerman, "Structure-function studies on a synthetic guanosine receptor that
simultaneously binds Watson-Crick and Hoogsteen sites" J. Org. Chem. 70, 7459-7467 (here)

Tirumala and Davis "Self-assembled ionophores. An isoguanosine-K+ octamer"
J. Am. Chem. Soc. 119, 2769-2776 (1997) (here).

Hud and Anet "Intercalation-Mediated Synthesis and Replication: A New Approach to the Origin of Life"
J. Theor. Biol. 205, 543-562 (2000) (here)

Mon

1/16

Official school holiday

Wed

1/18

Nucleotide Conformation

Sundaralingam, M., "Conformations of the furanose ring in nucleic acids and other carbohydrate
derivatives in the solid state", J. Am. Chem. Soc., 87, 599-606. (1965) (here)

Voet and Voet 29-2A (pages 1116-1118)

Fri

1/20

Jardetzky, C.D. "Proton Magnetic Resonance Studies on Puribes, Pyrimidines, Ribose Nucleosides and
Nucleotides. III. Ribose Conformations." J. Am. Chem. Soc. 82, 229-233 (1960) (here).

Sundaralingam, M. "Stereochemistry of Nucleic Acids and Their Constituents. XVIII. Conformational
Analysis of a Nucleosides by X-Ray Crystallography" J. Am. Chem. Soc. 93 6644-6647 (1971) (here)

Sundaralingam, M. "Conformational Analysis of the Sugar Ring in Nucleosides and Nucleotides. A New Description
Using the Concept of Pseudorotation" J. Am. Chem. Soc. 94, 8205 - 8212 (1972) (here).

Haromy & Raleigh "Enzyme-Bound Conformations of Nucleotide Substrates. X-ray Structure
and Absolute Configuration of 8,S-Cycloadenosine Monohydrate", Biochemistry, 19, 1718-1722 (1980) (here).

Gelbin A, et al, "Geometric parameters in nucleic acids: Sugar and phosphate constituents",
J. Am. Chem. Soc., 118 519-529 (1996) (here)

Mon

1/23

G-Quadruplexes

M Gellert, M N Lipsett, D Davis, "Helix Formation by Guanylic Acid" PROC. N. A. S.,
48, 12, 2013-2018 (1962) (here).

Williamson J.R., Raghuraman M.K., Cech T.R., "Monovalent Cation-Induced Structure
of Telomeric DNA: The G-Quartet Model". Cell, 59, 871-880 (1989) (here).

Wed

1/25

Scheller K., Hofstetter F., Mitchell P., Prijs B., Sigel H. "Macrochelate
Formation in Monomeric Metal Ion Complexes of Nucleoside 5'-Triphosphates and
the Promotion of Stacking by Metal Ions. Comparsion of the Self-Association of
Purine and Pyrimidine 5'-Triphosphates Using Proton Nuclear Magnetic Resonance",
J Am Chem Soc. 103, 247-260 (1981) (here)

Mezzina E, et al,"The Self-Assembly of a Lipophilic Guanosine Nucleoside into
Polymeric Columnar Aggregates: The Nucleoside Structure Contains Sufficient Information to
Drive the Process towards a Strikingly Regular Polymer", Chem. Eur. J, 7, 388-395 (2001)
(here)

M Cai, X Shi, .... and J Davis "Cation-directed self-assembly of lipophilic nucleosides: the
cation's central role in the structure and dynamics of a hydrogen-bonded
assembly" Tetrahedron, 58, 661-671 (2002) (here).

Fri

1/27

Qi JY, Shafer RH, "Covalent ligation studies on the human telomere quadruplex"
Nucleic Acid Research 33 (10): 3185-3192 2005 (here).

Alexender Rich et. al.,Crystal Structure of four-stranded oxytricha Telomeric DNA.;
Nature, 1992, 356, 126-131 (here).

Smith FW, Feigon J, "Strand orientation in the dna quadruplex formed from the
oxytricha telomere repeat oligonucleotide d(G4T4G4) in solution" Biochemistry 32
8682-8692 1993

Parkinson GN, Lee MP, Neidle S. Nature. "Crystal structure of parallel quadruplexes from
human telomeric DNA" 2002 417, 807-8.

Lauglan G, Murchie AIH, et al. "The High-Resolution Crystal-Structure of a
Parallel-Stranded Guanine Tetraplex" Science 265, 520-524 (1994) (here).

Li, J., Correia, J. J., Wang, L., Trent, J. O. and Chaires, J. B. (2005) "Not so crystal clear:
The structure of the human telomere G-quadruplex in solution differs from that present in a crystal.
Nucleic Acids Res., 33, 4649-4659. Print 2005. (here)

Mon

1/30

Base Stacking

[*] C. E. Bugg, J. M. Thomas 1, M. Sundaralingam, S. T. Rao, "Stereochemistry of nucleic
acids and their constituents. X. solid-slate base-slacking patterns in nucleic acid constituents
and polynucleotides" Biopolymers, 10, 175 - 219. (here)

Wed

2/1

T S'O, P.O.P; Melvin, I.S.; Olson, A. C.; "Interaction and Association of Bases and
Nucleosides in Aqueous Solutions' J.Amer.Chem.soc, 85, 1289 (1963) (here)

Schweizer MP, Broom AD, Ts'o POP, Hollis DP. Studies of inter- and intramolecular
interaction in mononucleotides by proton magnetic resonance. J Am Chem Soc. 90,
1042-1055 (1968). (here)

Arthur D.B., Schweizer M.P., Ts'o O.P., "Interaction and Association of Bases and
Nucleosides in Aqueous Solutions. V. Studies of the Association of Purine Nucleosides by
Vapor Pressure Osmometry and by Proton Magnetic Resonance" J.Amer.Chem.soc, 89, 3612-3622
(1967) (here).

Ishida, t, Shibata, m, Fujii, k, Inoue, m "Structural Studies of the Interaction between
Indole-derivatives and Biologically Important Aromatic- Compounds: Intermolecular and
Intramolecular Stacking Interaction between Indole and Adeninium rings" Biochemistry 22
(15): 3571-3581 1983 (here).

Petersheim and Turner D. "Base-Stacking and Base-Pairing Contributions To Helix Stability
- Thermodynamics of Double-Helix Formation With CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and
ACCGGUp" Biochemistry. (1983) 22: 256-263 (here)

Freier, S.M., Alkema, D., Sinclair, A., Neilson, T. and Turner, D.H. (1985) Contributions
of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp,
XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry, 24, 4533-4539 (here).

Sugimoto, N., Kierzek, R. and Turner, D.H. (1987) Sequence dependence for the energetics of
dangling ends and terminal base pairs in ribonucleic acid. Biochemistry, 26, 4554-4558 (here).

Sponer, J; Leszczynski, J; Hobza, P, "Nature of nucleic acid-base stacking: Nonempirical
ab initio and empirical potential characterization of 10 stacked base dimers. Comparison
of stacked and H-bonded base pairs" J Phys Chem, 100, 5590-5596 28 1996 (here)

Floria, J.; Sponer, J.; Warshel, A.; "Thermodynamic Parameters for Stacking and Hydrogen
Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study", J.
Phys. Chem. B 1999, 103, 884-892 (here).

Kevin M. Guckian, Barbara A. Schweitzer, Rex X.-F. Ren, Charles J.
Sheils,Deborah C. Tahmassebi, and Eric T. Kool, "Factors Contributing to Aromatic
Stacking in Water: Evaluation in the Context of DNA" J. Am. Chem. Soc. 2000, 122,
2213-2222 (here).

Sponer, J; et al,"Electronic properties, hydrogen bonding, stacking, and cation binding of
DNA and RNA bases," Biopolymers, 61, 1, 3-31 (2001) (here)

Fri

2/3

Sunney I. Chan, S. I., Bangerter, B. W.; Peter, H. H.; "Purine Binding to Dinucleotides:
Evidence For Base Stacking and Insertion" Proc. Natl. Acad. Sci. USA, 55(4), 720-727 (1966) (here).

Janiak C., "A Critical Account on pi-pi Stacking in Metal Complexes with Aromatic
Nitrogen-Containing Ligands", J. Chem. Soc., Dalton Trans., 21, 3885-3896 (2000) (here).

Sivanesan, D., et al, "Does a Stacked DNA Base Pair Hydrate Better than a Hydrogen-Bonded
One?: An ab Initio Study," J. Phys. Chem. A, 104, 10887-10894 (2000) (here).

Kool, E. "Hydrogen Bonding, Base Stacking, and Steric Effects in DNA Replication," Annual
Review of Biophysical and Biomolecular Structure, 30, 1-22, 2001 (here).

Kim, T. W. and Kool, E. "A Series of Nonpolar Thymidine Analogues of Increasing Size: DNA
Base Pairing and Stacking Properties" J Organic Chemistry 70, 2048-2053 (2005) (here).

Mon

2/6

Helical Forms

Wed

2/8

Watson, J. D. and Crick, F. H. (1974) "Molecular structure of nucleic acids: A structure
for deoxyribose nucleic acid", J.D. Watson and f.H.C. Crick.
1953. Nature, 248, 765 (here).

Vargason, J. M., Henderson, K. and Ho, P. S. (2001) "A crystallographic map of the
transition from B-DNA to A-DNA", Proc. Natl. Acad. Sci., U.S.A., 98, 7265-7270
(here).

Dickerson, R. E. and Ng, H. L. (2001) DNA structure from A to B. Proc. Natl. Acad. Sci.,
U.S.A., 98, 6986-6988 (here).

Ha, S. C., Lowenhaupt, K., Rich, A., Kim, Y. G. and Kim, K. K. (2005) "Crystal structure
of a junction between B-DNA and Z-DNA reveals two extruded bases", Nature, 437, 1183-1186
(here).

Fri

2/17

RNA Tetraloops

Leontis. N. B.; Westhofy. E., "Analysis of RNA motifs", Current Opinion in Structural
Biology, 13:300-308 (2003) (here).

Wu, H.; Yang, P ... and Feigon "A novel family of RNA tetraloop structure forms the recognition
site for Saccharomyces cerevisiae RNAse III"EMBO Journal; 20, 7240 (2001) (here).

Comolli, L. ... and Gmeiner "NMR structure of the 3' stem-loop from human U4 snRNA". Nucliec Acids
Research, 20: 4371-4379 (2002) (here).

Correll C.C., Swinger K., "Common and distinctive features of GNRA tetraloops based on a
GUAA tetraloop structure at 1.4 A resolution", RNA, 9, 355-363 (2003) (here).

Ellen M. Moody, Jessica C. Feerrar, and Philip C. Bevilacqua, "Evidence that Folding of
an RNA Tetraloop Hairpin Is Less Cooperative than Its DNA Counterpart" Biochemistry, 43,
7992-7998 (2004) (here).

Santini, G.P.H, "DNA tri- and tetra-loops and RNA tetra-loops hairpins folds as elastic
biopolymer chains in agreement with PDB coordinates," Nucleic Acids Research, 31,
1086-1096 (2003) (here).

Wed

2/22

Kink Turns

Klein, D. J., Schmeing, T. M., Moore, P. B. and Steitz, T. A., "The kink-turn: A new RNA
secondary structure motif", EMBO J., 20, 4214-21 (2001) (here)

Nolivos, S., Carpousis, A. J. and Clouet-d'Orval, B., "The k-loop, a general feature of
the pyrococcus c/d guide RNAs, is an RNA structural motif related to the k-turn", Nucleic
Acids Res., 33, 6507-14 (2005) (here).

Goody, T. A., Melcher, S. E., Norman, D. G. and Lilley, D. M., "The kink-turn motif in
RNA is dimorphic, and metal ion-dependent", RNA, 10, 254-64 (2004) (here).

Matsumura, S., Ikawa, Y. and Inoue, T., "Biochemical characterization of the kink-turn
RNA motif", Nucleic Acids Res., 31, 5544-51. (2003) (here).

Strobel, S. A., Adams, P. L., Stahley, M. R. and Wang, J., "RNA kink turns to the left
and to the right", RNA., 10, 1852-4. (2004) (here).

Fri

3/3

DNA Ligand Interactions

Dervan, P., "Design of sequence-specific DNA binding molecules", Science, 232, 464-71 (1986) (here)

Van Dyke, M. W., Hertzberg, R. P. and Dervan, P. B., "Map of distamycin, netropsin, and
actinomycin binding sites on heterogenous DNA: DNA cleavage-inhibition patterns with
methidium-propyl-edtafe(II)", Proc. Natl. Acad. Sci., U.S.A., 79, 5470-4 (1982)
(here)

Fechter, E. J., Olenyuk, B. and Dervan, P. B., "Design of a sequence-specific DNA
bisintercalator", Angew Chem Int Ed Engl., 43, 3591-4. (2004) (here)

Chao 2004 (here)

Reynisson, J., Schuster, G. B., Howerton, S. B., Williams, L. D., Barnett, R. N.,
Cleveland, C. L., Landman, U., Harrit, N. and Chaires, J. B., "The intercalation of
trioxatriangulenium ion (TOTA+) in DNA: Binding, electron transfer, x-ray
crystallography, and electronic structure", J. Am. Chem. Soc., 125, 2072-83 (2003) (here)

Wed

3/8

RNA Ligand Interactions

HM LSU navigator (here)

HM LSU coordinate file (here)

Pymol Script File (here)

Belova, L., Tenson, T., Xiong, L., McNicholas, P. M. and Mankin, A. S., "A novel site of
antibiotic action in the ribosome: Interaction of evernimicin with the large ribosomal
subunit", Proc Natl Acad Sci U S A., 98, 3726-31 (2001) (here)

Schmeing, T. M., Moore, P. B. and Steitz, T. A., "Structures of deacylated tRNA mimics
bound to the e site of the large ribosomal subunit", RNA., 9, 1345-52 (2003) (here)

Hansen, J. L., Moore, P. B. and Steitz, T. A., "Structures of five antibiotics bound at
the peptidyl transferase center of the large ribosomal subunit", J Mol Biol., 330, 1061-75 (2003) (here)

Tu, D., Blaha, G., Moore, P. B. and Steitz, T. A., "Structures of mlsbk antibiotics bound
to mutated large ribosomal subunits provide a structural explanation for resistance",
Cell., 121, 257-70 (2005) (here).

Wed

3/29

Sequence-Specific DNA Protein Interactions

Seeman, N. C.; Rosenberg, J. M.; Rich, A., Sequence-Specific Recognition of Double
Helical Nucleic Acids by Proteins. Proc. Natl. Acad. Sci. U.S.A. 1976, 73, 804-808
(here).

Motif: Helix-Turn-Helix (Horace)

First Crystal Structure:

seminal structure, protein only: McKay, D. B.; Steitz, T. A., Structure of catabolite gene
activator protein at 2.9 a resolution suggests binding to left-handed B-DNA.
Nature 1981, 290, (5809), 744-9 (here).

seminal structure, protein only Anderson, W. F.; Ohlendorf, D. H.; Takeda, Y.;
Matthews, B. W., Structure of the cro repressor from bacteriophage lambda and
its interaction with DNA. Nature 1981, 290, (5809), 754-8 (here).

highest resolution structure: Jain, D.; Kim, Y.; Maxwell, K. L.; Beasley, S.; Zhang, R.; Gussin, G. N.;
Edwards, A. M.; Darst, S. A., Crystal structure of bacteriophage lambda cii
and its DNA complex. Mol Cell 2005, 19, (2), 259-69 (here).


Kodandapani, R.; Pio, F.; Ni, C. Z.; Piccialli, G.; Klemsz, M.; McKercher, S.; Maki, R.
A.; Ely, K. R., A new pattern for helix-turn-helix recognition revealed by the PU.1
ETS-domain-DNA complex. Nature 1996, 380, (6573), 456-60
(here)

Motif: bZip (Emma)

seminal structure: Keller, W.; Konig, P.; Richmond, T. J., Crystal
structure of a bzip/DNA complex at 2.2 a: Determinants of DNA specific
recognition. J Mol Biol 1995, 254, (4), 657-67 (here).

highest resolution structure: Fujii, Y.; Shimizu, T.; Toda, T.;
Yanagida, M.; Hakoshima, T., Structural basis for the diversity of DNA
recognition by bzip transcription factors. Nat Struct Biol 2000, 7, (10),
889-93 (here).

Nair, S. K.; Burley, S. K., X-ray structures of Myc-Max and Mad-Max recognizing DNA.
Molecular bases of regulation by proto-oncogenic transcription factors. Cell 2003, 112,
193-205 (here).

Motif: Zinc Finger (Ali)

seminal structure: Pavletich, N. P.; Pabo, C. O., Zinc finger-DNA recognition: Crystal structure
of a zif268-DNA complex at 2.1 a. Science 1991, 252, (5007), 809-17 (here).

highest resolution structure: Elrod-Erickson, M.; Rould, M. A.; Nekludova, L.; Pabo, C. O., Zif268
protein-DNA complex refined at 1.6 a: A model system for understanding zinc
finger-DNA interactions. Structure 1996, 4, (10), 1171-80 (here).

high resolution, RNA complex: Lu, D.; Searles, M. A.; Klug, A., Crystal
structure of a zinc-finger-RNA complex reveals two modes of molecular
recognition. Nature 2003, 426, (6962), 96-100 (here).

Nolte, R. T.; Conlin, R. M.; Harrison, S. C.; Brown, R. S., Differing roles for zinc
fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
Proc Natl Acad Sci U S A 1998, 95, (6), 2938-43 (here).

Winkler, F. K.; Banner, D. W.; Oefner, C.; Tsernoglou, D.; Brown, R. S.; Heathman, S. P.;
Bryan, R. K.; Martin, P. D.; Petratos, K.; Wilson, K. S., The crystal structure of EcoRV
endonuclease and of its complexes with cognate and non-cognate DNA fragments. Embo J
1993, 12, (5), 1781-95 (here).

Motif: Homeodomain (Bree)

seminal structure: Kissinger, C. R.; Liu, B. S.; Martin-Blanco, E.; Kornberg, T. B.; Pabo, C. O.,
Crystal structure of an engrailed homeodomain-DNA complex at 2.8 a resolution:
A framework for understanding homeodomain-DNA interactions. Cell 1990, 63,
(3), 579-90 (here).

highest resolution structure: LaRonde-LeBlanc, N. A.; Wolberger,
C., Structure of hoxa9 and pbx1 bound to DNA: Hox hexapeptide and DNA
recognition anterior to posterior. Genes Dev 2003, 17, (16), 2060-72 (here).


Wilson, D. S.; Guenther, B.; Desplan, C.; Kuriyan, J., High resolution crystal structure
of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell 1995, 82, (5), 709-19
(here).

Beta Saddle (Richard)

seminal structure: Nikolov, D. B.; Chen, H.; Halay, E. D.; Hoffman, A.; Roeder, R. G.; Burley, S.
K., Crystal structure of a human tata box-binding protein/tata element complex. Proc.
Natl. Acad. Sci. U.S.A. 1996, 93, (10), 4862-7 (here).

highest resolution structure: Patikoglou, G. A.; Kim, J. L.; Sun,
L.; Yang, S. H.; Kodadek, T.; Burley, S. K., Tata element recognition by the
tata box-binding protein has been conserved throughout evolution. Genes Dev
1999, 13, (24), 3217-30 (here).

Chasman, D. I.; Flaherty, K. M.; Sharp, P. A.; Kornberg, R. D., Crystal structure of
yeast TATA-binding protein and model for interaction with DNA. Proc Natl Acad Sci U S A
1993, 90, (17), 8174-8 (here).

Restriction Endonucleases

seminal structure: Kim, Y. C.; Grable, J. C.; Love, R.; Greene, P.
J.; Rosenberg, J. M., Refinement of eco ri endonuclease crystal structure: A
revised protein chain tracing. Science 1990, 249, (4974), 1307-9 (here).


Deibert, M.; Grazulis, S.; Janulaitis, A.; Siksnys, V.; Huber, R., Crystal structure of
MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. Embo J
1999, 18, (21), 5805-16 (here).

Deibert, M.; Grazulis, S.; Sasnauskas, G.; Siksnys, V.; Huber, R., Structure of the
tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat Struct Biol
2000, 7, (9), 792-9 (here).

(Chiaolong) Grazulis, S.; Manakova, E.; Roessle, M.; Bochtler, M.; Tamulaitiene, G.; Huber, R.;
Siksnys, V., Structure of the metal-independent restriction enzyme BfiI reveals fusion of
a specific DNA-binding domain with a nonspecific nuclease. Proc Natl Acad Sci U S A 2005,
102, (44), 15797-802 (here).

Mucke, M.; Kruger, D. H.; Reuter, M., Diversity of type II restriction endonucleases that
require two DNA recognition sites. Nucleic Acids Res 2003, 31, (21), 6079-84
(here).

Wed

4/19

Chemical Reactions of Nucleic Acids

(Endonucleases: Magnesium-Dependent Cleavage of DNA by Proteins) Galburt, E. A.; Stoddard, B. L., Catalytic
mechanisms of restriction and homing endonucleases. Biochemistry 2002, 41, (47),
13851-60 (here).

(DNA catalysis) Feldman, A. R.; Leung, E. K.; Bennet, A. J.; Sen, D., The RNA-Cleaving
Bipartite Dnazyme Is a Distinctive Metalloenzyme. Chembiochem 2006, 7, (1),
98-105 (here).

(RNA Catalysis) Conn, Prudent and Schultz, "Porphyrin Metalation
Catalyzed by a Small RNA Molecule," J. Am. Chem Soc, 118, 7012-7013 (1996) (here)

(Group I Splicing Mech) Stahley, M. R.; Strobel, S. A., Structural Evidence for a Two-Metal-Ion
Mechanism of group I Intron Splicing. Science 2005, 309, (5740), 1587-90 (here).

(DNA Photodimerization) Ramaiah, D.; Koch, T.; Orum, H.; Schuster, G. B., Detection of
Thymine [2+2] Photodimer Repair in DNA: Selective Reaction of Kmno4. Nucleic
Acids Res 1998, 26, (17), 3940-3 (here).

(benz-pyrene addition) Mao, B.; Gu, Z.; Gorin, A.; Chen, J.; Hingerty, B. E.; Amin, S.; Broyde, S.;
Geacintov, N. E.; Patel, D. J., Solution Structure of the
(+)-Cis-Anti-Benzo[a]Pyrene-Da ([Bp]Da) Adduct Opposite Dt in a DNA Duplex.
Biochemistry 1999, 38, (33), 10831-42 (here).

(Pt crosslinking) Coste, F.; Malinge, J. M.; Serre, L.; Shepard, W.; Roth, M.; Leng, M.; Zelwer,
C., Crystal Structure of a Double-Stranded DNA Containing a Cisplatin
Interstrand Cross-Link at 1.63 a Resolution: Hydration at the Platinated Site.
Nucleic Acids Res 1999, 27, (8), 1837-46 (here).

Oxidation of Guanine

Methylation

Metallation

Hydroxyl Radical/Fenton Chemistry

Cleavage by Bleomycin, Neocarzinstatin, etc

Fri

4/21

TBD 

Mon

4/24

TBD 

Wed

4/26

TBD 

Fri

4/28

TBD