1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. SEP-SBI074-CP02-02 Introduction Programmes and Courses SEP –SBI074-CP02- U02

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com

4. School of Science and Technology, Online Counseling Resource… How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives After studying this module, you should be able to: Describe different conformations DNA as A,B,Z Compare Geometries of different DNA Forms

6. School of Science and Technology, Online Counseling Resource… Alternative Double-helical Structures  DNA exists in several possible conformations. The conformations so far identified are: A-DNA, B-DNA, C-DNA, D-DNA, E-DNA,H-DNA, L-DNA, P-DNA, and Z-DNA.  However, only A-DNA, B-DNA, and Z-DNA have been observed in naturally occurring biological systems.  Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of metal ions and polyamines.  Of these three conformations, the "B" form described above is most common under the conditions found in cells.  The alternative double-helical forms of DNA differ in their geometry and dimensions.

7. School of Science and Technology, Online Counseling Resource… Watson-Crick B-Form DNA:1  Original X ray studies of DNA done using fiber of bulk DNA (B-DNA) or simple copolymer DNA (A- DNA).  The structure of DNA as originally proposed by Watson and Crick depended on one major assumption, that the structure of DNA was independent of its sequence.  X-ray diffraction suggested a helical structure The cross pattern suggested a helical pitch angle about 45°. Axial reflections gave repeating units of 3.4 and 34 Å Radial reflections gave a fiber width of 20 Å.D.

8. School of Science and Technology, Online Counseling Resource… Watson-Crick B-Form DNA:2  Most common DNA conformation in vivo  Narrower, more elongated helix than A.  Wide major groove easily accessible to proteins  Narrow minor groove  Favored conformation at high water concentrations (hydyration of minor groove seems to favor B-form)  Base pairs nearly perpendicular to helix axis  Sugar pucker C2'-endo

9. School of Science and Technology, Online Counseling Resource… Watson-Crick B-Form DNA:3  Watson and Crick then connected base pairs with phosphodiester bonds that spaced the bases 3.4 Å apart and rotated each subsequent base pair by 36°.  This rotation generates a right-handed double helix with 10 base per turn and repeating elements every 3.4 and 34 Å.  The obtuse angle of the glycosylic linkages leads to major and minor grooves in helix with specific groups in each group.  The bases were perpendicular to the helix axis.

10. School of Science and Technology, Online Counseling Resource… The Z-DNA Structure:1  Z-DNA is one of the many possible double helical structures of DNA.  It is a left-handed double helical structure in which the double helix winds to the left in a zig- zag pattern (instead of to the right, like the more common B- DNA form).  Z-DNA is thought to be one of three biologically active double helical structures along with A- and B-DNA.

11. School of Science and Technology, Online Counseling Resource… The Z-DNA structure:2  Z-DNA was the first crystal structure of a DNA molecule to be solved.  It was solved by Alexander Rich and co-workers in 1979 at MIT.  The crystallization of a B- to Z-DNA junction in 2005 provided a better understanding of the potential role Z-DNA plays in cells.  Whenever a segment of Z-DNA forms, there must be B-Z junctions at its two ends, interfacing it to the B-form of DNA found in the rest of the genome.

12. School of Science and Technology, Online Counseling Resource… The Z-DNA Structure:3  In 2007, the RNA version of Z-DNA was described as a transformed version of an A-RNA double helix into a left-handed helix  Z-DNA is quite different from the right-handed forms.  In fact, Z-DNA is often compared against B- DNA in order to illustrate the major differences.  The Z-DNA helix is left handed and has a structure that repeats every 2 base pairs.  The major and minor grooves, unlike A- and B- DNA, show little difference in width.

13. School of Science and Technology, Online Counseling Resource… The Z-DNA Structure:4  Formation of this structure is generally unfavourable, although certain conditions can promote it; such as alternating purine -pyrimidine sequence, DNA supercoiling or high salt and some cations.  Z-DNA can form a junction with B-DNA in a structure which involves the extrusion of a base pair.  It is possible to predict the likelihood of a DNA sequence forming a Z-DNA structure.  An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form, ZHunt, was written by Dr. P. Shing Ho in 1984 (at MIT).

14. School of Science and Technology, Online Counseling Resource… Biological Significance of Z-DNA  While no definitive biological significance of Z-DNA has been found, it is commonly believed to provide torsional strain relief (supercoiling) while DNA transcription occurs.  The potential to form a Z-DNA structure also correlates with regions of active transcription.  A comparison of regions with a high sequence- dependent, predicted propensity to form Z-DNA in human chromosome 22 with a selected set of known gene transcription sites suggests there is a correlation.  Z-DNA formed after transcription initiation, in some cases may be bound by RNA modifying enzymes which then alter the sequence of the newly-formed RNA

15. School of Science and Technology, Online Counseling Resource… The A-DNA structure:1  A-DNA is one of the many possible double helical structures of DNA. It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more compact helical structure.  A-DNA is thought to be one of three biologically active double helical structures along with B- and Z-DNA.  It appears likely in dehydrated samples of DNA.

16. School of Science and Technology, Online Counseling Resource… The A-DNA Structure:2  A-DNA is fairly similar to B-DNA given that it is a right-handed double helix with major and minor grooves.  However, as shown in the comparison table, there is a slight increase in the number of base pairs per rotation (resulting in a tighter rotation angle), and smaller rise/turn.  This results in a deepening of the major groove and a shallowing of the minor.

17. School of Science and Technology, Online Counseling Resource… Comparison Geometries of Most Common DNA Forms  DNA molecule assume different configurations on the basis of its nucleotide sequence and/or state of hybridization.  These configuration are all double helices, but they differ in their direction of coiling of the sugar-phosphate backbone, and in few other details, which are summarized as follows.

18. School of Science and Technology, Online Counseling Resource… Comparison Geometries of Most Common DNA Forms

19. School of Science and Technology, Online Counseling Resource… Comparison Geometries of Most Common DNA Forms  The currently accepted fibre model structures for A-, B- and Z-DNA are shown here using the ball-and- stick representation (Chandrasekaran et al., 1989; Chandrasekaran & Arnott, 1996; Arnott et al., 1980).  The nucleotides are colour-coded (cytosine in yellow, guanine in cyan, thymine in green and adenine in red) and a ribbon is superposed on the backbones connecting the P atoms.  A-DNA and B-DNA are both righthanded uniform double-helical structures, while Z-DNA is a left- handed double helix with a dinucleotide repeat and the backbone follows a zigzag path.

20. School of Science and Technology, Online Counseling Resource… Comparison Geometries of Most Common DNA Forms

21. School of Science and Technology, Online Counseling Resource… ABZ Helix senseRight handedRight-handedLeft handed Repeating unit 1 bp 2 bp Rotation/bp33.6°35.9°60°/2 Mean bp/turn10.710.012 Inclination of bp to axis+19 ° -1.2°-9° Rise/bp along axis2.3Å3.32Å3.8Å Pitch/turn of helix24.6Å33.2Å 45.6Å Mean propeller twist +18°+16°0° Glycosyl angleanti C: anti, G: syn Sugar puckerC3'-endoC2'-endoC: C2'-endo, G: C2'-exo Diameter26Å20Å 18Å Structures of A, B and Z DNA

22. School of Science and Technology, Online Counseling Resource… What You Learn…  You have learnt : Different types of DNA conformation A,B,Z A and B are the right handed double helix where as Z is left-handed double helix. B-DNA Most common DNA conformation in vivo A-DNA is fairly similar to B-DNA Z-DNA double helix winds to the left in a zig-zag pattern

23. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe the different possible conformation of DNA? 2.Compare the different possible conformation of DNA. © 2007, YCMOU. All Rights Reserved.23

24. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.The conformations so far identified are: A-DNA, B- DNA and Z-DNA 2.Comparison Geometries of the Most Common DNA Forms © 2007, YCMOU. All Rights Reserved.24

25. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Biophysical Chemistry (principles and techniques ) Author: Upadhay. Upadhay.Nath Publisher: Himalaya publishing House  Book2 Title: Physical Biochemistry (application to Biochemistry and molecular biology) Author: Freifelder Publisher: W. H. Freeman and Company

26. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Essentials of Biophysics Author: Narayanan Publisher: New Age Int. Pub. New Delhi.  Book4 Title: A Text Book of Biophysics Author: Roy R.N. Publisher: New Central Book Agency

27. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia

28. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You !