PHAR201 Lecture Principles of DNA and RNA Structure PHAR 201/Bioinformatics I Philip E. Bourne Department of Pharmacology, UCSD Prerequisite Reading: Structural Bioinformatics Chapters 3 Thanks to Helen Berman for many slides

PHAR201 Lecture We start with DNA

PHAR201 Lecture History 1946 – DNA is the main constituent of genes (Avery) 1950 – First X-ray pictures of DNA (Franklin) 1953 – DNA structure revealed (Watson and Crick) 1970 onwards - Multiple conformations and structures, initially from fibers X-ray structure confirms double helix (Rich) t-RNA structure (Kim) 1980 – Structure of first complete turn of B (“normal”) DNA (Dickerson)

PHAR201 Lecture What Have we Learnt from These Structures? Hydration, ionic strength and sequence all impact the type of structure We see single stranded helices, double, triple and quadruple Alone DNA and RNA does not crystallize easily, hence strands are short – eg 10-mer (unless complexed) Contrast this to the ribosome (1FFK)

PHAR201 Lecture NOTE: Components Sugar Base Phosphate 5’ to 3’ direction T->U in RNA RNA - extra –OH at 2’ of pentose sugar DNA - deoxyribose Numbering Single vs double strands DNA more stable Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p DNA and RNA Structure

PHAR201 Lecture NOTE: Pyrimadines and Purines T->U in RNA Names Numbering Bonding character Position of hydrogen Tautomers Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 18. The 5 Bases of DNA and RNA Purines Pyrimadines

PHAR201 Lecture Keto vs enol (OH) Different hydrogen bonding patterns Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, p Tautomeric Structures

A:T and G:C pairs are spatially similar 3 H-bonds vs 2 (GC rich?) Sugar groups are attached asymmetrically on the same side of the pair Leads to a major and minor grove Bases are flat but the hydrogen bonding leads to considerable flexibility Base stacking is flexible Geometry of Watson Crick Base Pairs Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p PHAR201 Lecture

9 Hydrogen bonding of WC base pair Mechanisms of recognition The canonical Watson-Crick base pair, shown as the G-C pair. Positions of the minor and major grooves are indicated. The glycosidic sugar-base bond is shown by the bold line; hydrogen bonding between the two bases is shown in dashed lines. Definition of Major and Minor Groove

PHAR201 Lecture Base Stacking is a Major Defining Feature of DNA Morphology Dependant on: –Nature of the bases and base pairs –Stacking interactions Explains sequence dependant features Important for understanding molecular recognition

PHAR201 Lecture Base Morphology The base-pair reference frame is constructed such that the x-axis points away from the (shaded) minor groove edge. Images illustrate positive values of the designated parameters. Reprinted with permission from Adenine Press from (Lu, et al., 1999).

PHAR201 Lecture Backbone Conformation Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 807.

PHAR201 Lecture A Beta-nucleoside Ring is never flat – has 5 internal torsional angles The pucker is determined by what is bound A variety of puckers have been observed Pucker has a strong influence on the overall conformation

PHAR201 Lecture Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p The Ribose Ring is Never Flat

PHAR201 Lecture Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 27. The Glycosidic Bond Connects ribose sugar to the base Anti Syn

PHAR201 Lecture Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p Change in sugar conformation affects the backbone C2’-Endo C3’-Endo C3’ C2’

PHAR201 Lecture A DNA B DNA..and the position of the bases relative to the helix axis

PHAR201 Lecture Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 34. Canonical B DNA

PHAR201 Lecture Canonical B DNA First determined experimentally by fiber diffraction (Arnott) C2’-endo sugar puckers High anti glycosidic angles Right handed – 10 base pairs per turn Bases perpendicular to the helix axis and stacked over the axis Overall bending as much as 15 degrees (result of base morphologies – twist and roll) – {machine learning – sequence vs overall conformation?} Over 230 structures 25 with base mis-pairing – only cause local perturbations Strong influence of hydration along spine

PHAR201 Lecture Major vs Minor Groove – distinctly different environments – important for recognition and binding Major –Richer in base substituents Minor –Hydrophobic H atoms of ribose groups forming its walls

PHAR201 Lecture Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 97. Spine of Hydration

PHAR201 Lecture Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 36. A DNA

PHAR201 Lecture Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p Canonical A DNA

PHAR201 Lecture Canonical A DNA C3’-endo sugar puckers – brings consecutive phosphates closer together 5.9A rather than 7.0 Glycosidic angle from high anti to anti Base pairs twisted and nearly 5A from helix axis Helix rise 2.56A rather than 3.4A Helix wider and 11 base pairs per repeat Major groove now deep and narrow Minor grove wide and very shallow

PHAR201 Lecture Z-DNA Helix has left-handed sense Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure. Narrower, more elongated helix than A or B. Major "groove" not really groove Narrow minor groove Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence. N2-amino of G H-bonds to 5' PO: explains slow exchange of proton, need for G purine. Base pairs nearly perpendicular to helix axis GpC repeat, not single base-pair –P-P distances: vary for GpC and CpG –GpC stack: good base overlap –CpG: less overlap. Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformation Conformations: –G; syn, C2'-endo –C; anti, C3'-endo

PHAR201 Lecture Z-DNA

PHAR201 Lecture Z-DNA Convex major groove Deep minor groove Alternate C then G Spine of hydration

PHAR201 Lecture Drug complexes to DNA Bound to the base pair – double helix can accommodate this Bound in the minor grove – show base specificity Cis-platinum drugs

PHAR201 Lecture Quadruplex DNA 1NP9 Jmol

PHAR201 Lecture Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, p tRNA 1EVV jmol Invariant L-shape

PHAR201 Lecture Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p tRNA H bonds between distant regions

PHAR201 Lecture The Ribosome Complex of protein and RNA Small 30S subunit – controls interactions between mRNA and tRNA Large 50S subunit – peptide transfer and formation of the peptide bond

PHAR201 Lecture Putting it all Together – Major Categories of DNA Binding Proteins Jones et al JMB 287(5) 877 Protein residues that make no contacts with the DNA are colored blue, those contacting the sugar- phosphate backbone are colored red, and those making base contacts are colored yellow. (a) Proteins with a single binding head: T4 endonuclease V (1vas), PU.1 ETS domain (1pue). (b) Proteins with a double binding head: lambda repressor (1lmb), papillomavirus-1 E2 DNA-binding domain (2bop). (c) Proteins with an enveloping mode of binding: NF-kB (1nfk),EcoRI restriction endonuclease (1eri).