Summary of "Week 5 - Lecture 25"

Summary of Week 5 - Lecture 25

This lecture focuses on the detailed structural features of DNA and RNA, emphasizing the sugar ring conformations, backbone torsion angles, and the different DNA helical forms. It covers how these molecular details influence the overall 3D structure and stability of nucleic acids.

Main Ideas and Concepts

1. Sugar Ring Structure and Torsion Angles

DNA and RNA sugar rings are five-membered (ribose or deoxyribose).
The sugar ring conformation is defined by several torsion (dihedral) angles: ν0, ν1, ν2, ν3, ν4.
These torsion angles describe rotations around specific bonds in the sugar ring.
Due to the closed ring structure, not all torsion angles are independent; typically only one degree of freedom remains, called the pseudo-rotation angle (P).
The pseudo-rotation angle determines the sugar puckering geometry.
Sugar puckering conformations are classified into:
- North (N) conformations: 3′-endo sugar pucker (common in RNA).
- South (S) conformations: 2′-endo sugar pucker (common in DNA).
- Twisted conformations involving O4′ puckering.
The sugar puckering affects the overall nucleic acid structure due to steric and electronic differences (e.g., 2′-OH in RNA vs. 2′-H in DNA).

2. DNA Helical Forms

A-DNA
- Shorter, wider helix.
- Bases are tilted relative to the helix axis.
- Sugar pucker is predominantly 3′-endo (North).
- Occurs under dehydrated conditions or in RNA duplexes.
B-DNA
- The most common form in physiological conditions.
- Bases nearly perpendicular to helix axis.
- Sugar pucker is predominantly 2′-endo (South).
- Has distinct major and minor grooves.
Z-DNA
- Left-handed helix with zigzag backbone.
- Dinucleotide repeating unit (not mononucleotide).
- Occurs in CG-rich sequences, often under high salt conditions.
- Has alternating sugar puckers (C and G residues differ).
Other minor DNA forms include C-DNA, D-DNA, T-DNA, A′-RNA, etc., which are variations based on environmental conditions and sequence.

3. Backbone Torsion Angles

DNA backbone is defined by six torsion angles: α, β, γ, δ, ε, ζ.
χ (chi) angle defines the orientation of the base relative to the sugar (torsion around C1′-N bond).
These angles vary between DNA forms and influence the overall helix shape.
The δ angle is closely related to sugar pucker:
- ~79°–91° corresponds to 3′-endo (RNA/A-DNA).
- ~120°–140° corresponds to 2′-endo (B-DNA).
Backbone torsion angles have typical ranges that characterize each DNA form.

4. Base Pair Geometry and Orientation

Base pairs are not always perfectly planar or parallel.
Parameters describing base pair geometry include:
- Tilt, Roll, Twist: describe how one base pair is oriented relative to adjacent pairs.
- Shift, Slide: describe lateral displacements of base pairs.
- Opening, Propeller twist, Buckle: describe distortions within base pairs.
Base pairs open into major and minor grooves, which are critical for protein-DNA interactions.
These parameters are essential for understanding DNA flexibility and recognition by proteins.

5. Experimental Methods and Structural Determination

Early fiber diffraction provided limited resolution.
High-resolution structures come from:
- X-ray crystallography of short DNA segments.
- NMR spectroscopy for solution structures.
Self-complementary DNA sequences are often used to form stable duplexes for structural studies.
Structural data help understand DNA conformation variability and dynamics.

Methodologies / Instructional Points

Determining Sugar Pucker: Measure torsion angles ν0 to ν4, calculate the pseudo-rotation angle (P), and classify sugar conformation as North (3′-endo) or South (2′-endo).
Classifying DNA Helical Forms: Analyze sugar puckering and backbone torsion angles, measure base pair tilt and twist, and identify groove dimensions (major vs. minor).
Analyzing Backbone Conformations: Measure α, β, γ, δ, ε, ζ torsion angles and χ angle for base orientation.
Characterizing Base Pair Geometry: Measure roll, tilt, twist, shift, slide, opening, buckle, and propeller twist using coordinate frames (x, y, z) relative to the base pair plane.
Experimental Approach: Use self-complementary oligonucleotides for crystallography/NMR, compare fiber diffraction data with high-resolution structures, and use hydration and salt conditions to induce different DNA forms.

Speakers / Sources Featured

Primary Speaker: Unnamed lecturer (likely a professor or expert in nucleic acid chemistry/biophysics).
Referenced Source: Paper by R.E. Dickerson (1989) on DNA structure parameters.
Experimental Techniques Discussed: Fiber diffraction, X-ray crystallography, NMR spectroscopy.

This lecture provides a comprehensive overview of nucleic acid structural chemistry, focusing on sugar ring puckering, backbone conformations, and DNA helical forms, supported by experimental structural data.