DNA Structures

Dr. Helen Berman

September 18, 2002

Canonical DNA

Helical parameters

Conformation angles

Groove dimensions

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, pp. 33, 35.

B DNA

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 34.

B DNA View down helix axis

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. 799.

Space filling B DNA

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. 796.

Defined sequence DNACGCGAATTCGCG

High propeller in center

Narrow minor groove

Spine of hydration

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. ###

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. ###

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 97.

A DNA•Right handed•Bases tilted•Deep major groove

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 36.

A DNA

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. 800.

Defined sequence

CG rich

Conformation of Z DNA

2 nucleotide repeat

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 33.

Z DNA

•Left handed•Very deep minor groove•Major groove on outside

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. 802.

Defined sequenceCGCGCG

Mismatches

GT

•Local changes•Global structure same as parent

PNATriple strand

DNA strand+

Peptide nucleic acid sequence

Quadruplex DNA

G pairing in quadruplex

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 76.

Diversity of folds

Two different dimer folds

Also possible•single strand•four strands

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 77.

Holliday junction

formed by 4 decamer strands

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. ###

Voet, Donald and Judith G. Biochemistry.John Wiley & Sons, 1990, p. ###

Neidle, Stephen. Nucleic Acid Structure and Recognition.Oxford University Press, 2002, p. 83.

4 way junction

RNA-DNA complex with

a junction structure