DNA Structure: Base Orientation and Sugar Puckering
Understanding the structural differences between various DNA forms, like A-form and B-form DNA, is crucial. Key features include the orientation of the nitrogenous base relative to the sugar and the sugar's ring conformation (puckering).
Base Orientation (Glycosidic Bond Conformation)
- Anti Conformation: The nitrogenous base is oriented away from the C5' atom of the sugar. This is the most common orientation found in B-form and A-form DNA.
- Syn Conformation: The nitrogenous base is oriented over the C5' atom of the sugar. This is less common in standard DNA forms but seen in specific contexts like Z-DNA or modified bases.
Sugar Puckering
The deoxyribose sugar ring is not planar and can adopt different conformations, described as puckering. The position of the C2' or C3' atom out of the plane defines the type of puckering:
- 2'-endo: The C2' atom is displaced towards the base/base pair. Characteristic of B-form DNA.
- 3'-endo: The C3' atom is displaced towards the base/base pair. Characteristic of A-form DNA.
A-form vs. B-form DNA Characteristics
Comparing the two major DNA forms:
| DNA Form | Base Orientation | Sugar Puckering |
|---|---|---|
| A-form DNA | Anti | 3'-endo |
| B-form DNA | Anti | 2'-endo |
Evaluating the Options
Based on the established characteristics:
- Option 1 (Anti, 2'-endo in A form DNA): Incorrect. A-form typically has 3'-endo puckering.
- Option 2 (Anti, 2'-endo in B form DNA): Correct. This accurately describes the common base orientation and sugar puckering in B-form DNA.
- Option 3 (Syn, 3'-endo in A form DNA): Incorrect. A-form typically has anti base orientation.
- Option 4 (Syn, 3'-endo in B form DNA): Incorrect. B-form typically has anti base orientation and 2'-endo puckering.
Important Questions from Structure and Function of Biomolecules
- An element that is present in a nucleotide but not in a nucleoside is __________.
- Which one of the following coenzymes is utilised by alanine racemase for the conversion of L-Alanine to D-Alanine?
- Which of the following show(s) optical activity at 100 mM concentration in water?
An octapeptide composed of these L-amino acids – Lys, Thr, Ser, Met, Arg, Trp, Tyr, Glu was subjected to analyses with the following outcomes:
P. The N-terminal sequencing analysis by Sanger's method yielded 'Ser' at the N-terminus
Q. Chymotrypsin treatment gave a pentapeptide, a ‘Tyr' containing dipeptide and a free ‘Glu'
R. Cyanogen bromide treatment gave two tetrapeptides
S. Trypsin treatment gave two tripeptides and a dipeptide
Which one of the following is the correct octapeptide sequence?
- Which of the following amino acids contain(s) two chiral carbons?
