If you like us, please share us on social media.
The latest UCD Hyperlibrary newsletter is now complete, check it out.

GeoWiki.png
ChemWiki: The Dynamic Chemistry E-textbook > Biological Chemistry > Nucleic Acids > DNA > DNA: Double Helix

MindTouch
Copyright (c) 2006-2014 MindTouch Inc.
http://mindtouch.com

This file and accompanying files are licensed under the MindTouch Master Subscription Agreement (MSA).

At any time, you shall not, directly or indirectly: (i) sublicense, resell, rent, lease, distribute, market, commercialize or otherwise transfer rights or usage to: (a) the Software, (b) any modified version or derivative work of the Software created by you or for you, or (c) MindTouch Open Source (which includes all non-supported versions of MindTouch-developed software), for any purpose including timesharing or service bureau purposes; (ii) remove or alter any copyright, trademark or proprietary notice in the Software; (iii) transfer, use or export the Software in violation of any applicable laws or regulations of any government or governmental agency; (iv) use or run on any of your hardware, or have deployed for use, any production version of MindTouch Open Source; (v) use any of the Support Services, Error corrections, Updates or Upgrades, for the MindTouch Open Source software or for any Server for which Support Services are not then purchased as provided hereunder; or (vi) reverse engineer, decompile or modify any encrypted or encoded portion of the Software.

A complete copy of the MSA is available at http://www.mindtouch.com/msa

DNA: Double Helix

The secondary structure of DNA is actually very similar to the secondary structure of proteins. The protein single alpha helix structure held together by hydrogen bonds was discovered with the aid of X-ray diffraction studies. The X-ray diffraction patterns for DNA show somewhat similar patterns.

Introduction

In addition, chemical studies by E. Chargaff indicate several important clues about the structure of DNA. In the DNA of all organisms:

  1. The concentration of adenine equals that of thymine.
  2. The concentration of guanine equals that of cytosine.

Chargaff's findings clearly indicate that some type of heterocyclic amine base pairing exists in the DNA structure. X-ray diffraction data shows that a repeating helical pattern occurs every 34 Angstrom units with 10 subunits per turn. Each subunit occupies 3.4 Angstrom units which is the same amount of space occupied by a single nucleotide unit. Using Chargaff's information and the X-ray data in conjunction with building actual molecular models, Watson and Crick developed the double helix as a model for DNA.

The double helix in DNA consists of two right-handed polynucleotide chains that are coiled about the same axis. The heterocyclic amine bases project inward toward the center so that the base of one strand interacts or pairs with a base of the other strand. According to the chemical and X-ray data and model building exercises, only specific heterocyclic amine bases may be paired.

 

582basepair.gif

Base Pairing Principle

The Base Pairing Principle is that adenine pairs with thymine (A - T) and guanine pairs with cytosine (G - C)

The base pairing is called complementary because there are specific geometry requirements in the formation of hydrogen bonds between the heterocylic amines. Heterocyclic amine base pairing is an application of the hydrogen bonding principle. In the structures for the complementary base pairs given in the graphic on the left, notice that the thymine - adenine pair interacts through two hydrogen bonds represented as (T=A) and that the cytosine-guanine pair interacts through three hydrogen bonds represented as (C=G).

Although other base pairing-hydrogen bonding combinations may be possible, they are not utilized because the bond distances do not correspond to those given by the base pairs already cited. The diameter of the helix is 20 Angstroms.

 

582basepair.gif

DNA Double Helix

The double-stranded helical model for DNA is shown in the graphic on the left. The easiest way to visualize DNA is as an immensely long rope ladder, twisted into a cork-screw shape. The sides of the ladder are alternating sequences of deoxyribose and phosphate (backbone) while the rungs of the ladder (bases) are made in two parts with each part firmly attached to the side of the ladder. The parts in the rung are heterocyclic amines held in position by hydrogen bonding. Although most DNA exists as open ended double helices, some bacterial DNA has been found as a cyclic helix. Occasionally, DNA has also been found as a single strand.

582dnacomplete.gif

Problems

QUES. Describe the structure of the double helix of DNA in your own words including the terms: backbone, heterocyclic amines, complementary base pairings, hydrogen bonding, deoxyribose, phosphate.

Quiz: In RNA, which base hydrogen bonds with uracil? Carefully compare the structure of uracil to the others to find the one that is most similar.

 

Quiz: If DNA is heated, what happens to the double helix? Hint: The result is similar to the denaturing of a protein by the same method. What type of bonding holds the secondary structure of both proteins and DNA?

Outside Links

  • The structure of the 'Dickerson Dodecamer' was originally reported in: Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA 78, 2179-2183. and the coordinates were acquired from the Brookhaven Protein Data Bank. The filename is 1BNA.

Contributors

You must to post a comment.
Last Modified
10:37, 5 Apr 2014

Tags

Classifications

(not set)
(not set)

Creative Commons License Unless otherwise noted, content in the UC Davis ChemWiki is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. Permissions beyond the scope of this license may be available at copyright@ucdavis.edu. Questions and concerns can be directed toward Prof. Delmar Larsen (dlarsen@ucdavis.edu), Founder and Director. Terms of Use