DNA Structures Dr. Helen Berman September 18, 2002.

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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 DNA CGCGAATTCGCG 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 sequence CGCGCG

Mismatches GT Local changes Global structure same as parent

PNA Triple 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