Section

These notes are from the Spring 1995 Structural Biology class given at Berkeley.

Note: These are incomplete and I have no intention of completing them.

Structure of Base Pairs and Base Steps
Sugar Puckers and Base Stacking
part3

Structure of Base Pairs and Base Steps

At an EMBO Workshop on DNA Curvature and Bending in 1988, a group of scientists agreed on Definitions and Nomenclature of Nucleic Acid Structure Parameters, published in the Journal of Molecular Biology (1989)205, p. 787-791. The following definitions from this paper are relevant to this course:

Unambiguous Reference Frame: The axes of DNA

Z: Helical Axis
y: Long Axis of Base Pair
z: Short Axis of Base Pair

The following sections for nomenclature are only a few of the terms used to describe displacement of base pairs and base steps. These are the most common.

Translations of Base Pairs

X-displacement. The base pair is no longer centered on the helix axis. This usually occurs in groups, and can be thought of as deepening or widing the major or minor groove. A-DNA tends towards a negative x-displacement resulting in a shallow minor groove.

Rotations of Base Pairs

Propeller twist. Each base pair is rotated along the Y axis. The propeller twist in DNA is always less than or equal to zero. In this case, the rotation is such that the side of the base on the major groove points towards the 3' end of the DNA strand.

Translations of Base Steps

Rise: The distance between the base pairs. In A-DNA, the rise is 3.1 Angstroms. In B-DNA, the rise is 3.4 Angstroms.
Slide: One base pair is moved along the y-axis

Rotations of Base Steps

Helical Twist refers to the degree of rotation about the Z-axis with regards to the previous base step. In A-DNA, this is 31 degrees, while in B-DNA, it is 36 degrees. This is related to the number of base pairs per turn (11 for A-DNA, 10 for B-DNA -- calculated by dividing 360 degrees by the helical twist)
Roll refers to the degree of rotation about the y-axis with regards to the previous base step.
Tilt or Inclination refers to the degree of rotation about the x-axis with regards to the previous step. In A-DNA, this is positive, while in B-DNA, it is zero.

Back to the DNA Structure Table of Contents

Sugar Puckers and Base Stacking

Sugars in A-DNA are in the C3'endo form, while sugars in B-DNA are in the C2'endo form. Examination of RNA shows that RNA is A-like because the extra hydroxyl present in RNA forces the sugar into the C3'endo form due to sterics. However, this encouragement for the C3'endo sugar pucker is not present in DNA. It has been found that base stacking Back to the DNA Structure Table of Contents

Last revised: 1995 May 12 by sev@byzantium.mckusick.com