04_DNASpartan2011

04_DNASpartan2011 - I N V EST I G A T I O N O F T H E T H R...

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1 INV ESTIG A TI ON O F T H E T HRE E-DIM ENSIONA L STRUC TURE O F DNA OBJE C TIV E : Students will use the Spartan ES molecular modeling program to examine the structure of the DNA double helix, discover the structural properties of DNA bases, and identify the hydrogen bonds between them. The difference between the structures of one full turn of two different DNA conformations will be explored. Ba c kground : Nucleic acids (DNA and RNA) are the macromolecules that carry genetic information. The classical DNA ³GRXEOH KHOL[´ is a pair of complementary strands of ³EDVHV±´ RU IODW ULQJ V\VWHPV± OLQNHG E\ sugar-phosphate ³EDFNERQHV²´ 7KH WZR VWUDQGV DUH held together by specific inter-strand hydrogen bonding between the bases (adenine is paired with thymine, and guanine is paired with cytosine) and YDQ GHU :DDOV IRUFHV µ³EDVH VWDFNLQJ´ IRUFHV¶ between the planes of base pairs. Figur e 1 . Base pairs (top) attached to the phosphate-sugar backbone (bottom). The bottom Figure was created by Madeleine Price Ball. It was obtained from the WikiMedia commons through which P e rmi ss ion i s gran t d o c opy , di st ribu and / or modi f y hi do um n und r h rm o GNU Fr ee Do a ion Li ce ( s ee http: // e n . wikip e dia . org / wiki / Fil e :DNA _ c h e mi c al _ s tru c tur e . s vg Last accessed January 2009.) [1]
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2 As shown below, the two strands are wound around each other to create the well-known double helix structure. This structure exhibits two structurally significant grooves: the so- called minor and major groov e s . Figur e 2 . Double helix structure of DNA is shown with the major and minor grooves indicated. This figure of the overview of the structure of DNA was created by Michael Ströck February 8, 2006. Released under the GFDL (GNU Free Document License, http://en.wikipedia.org/wiki/GNU_Free_Documentation_License , last accessed January 2009). [1] DNA c onformation s Right-handed DNA (found in cells) can exist in two distinct double helix conformations. At high humidity (and low salt concentration) the favored form is called B-DNA and at low humidity (and high salt concentration) the dominant structure is called A-DNA. The bases in the B-form duplex (right side of the Figure 3) are virtually planar, and perpendicular to the helix axis. Each base pair rotates 36° relative to its neighbors. There are 10 base pairs per turn of a B-DNA helix. The B-DNA arrangement results in similar major and minor groove depths with the major groove width approximately twice the size of the minor groove width. Minor Groov e Major Groov e
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3 The base pairs of A-DNA (left side of Figure 3) are not perpendicular to the helical axis, but rather are tilted by about 20°. A-DNA helices have 11 base pairs per turn. The diameter (width) of the A-DNA helix is approximately 6 ångströms greater than that of B-DNA. The shape of the A-DNA duplex is characterized by the presence of a deep narrow major
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04_DNASpartan2011 - I N V EST I G A T I O N O F T H E T H R...

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