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TA G C G C T A G C C G G C T A A T A T
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(a) Hairpin structure
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A T C G C G A T C G G C C G A T (b) Stem and loop
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FIgure 10-6 A single-stranded DNA or RNA palindrome (a) in a hairpin structure (b) in a stem-and-loop structure
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FIgure 10-7 A cruciform structure can occur when a double-stranded dNA contains a palindrome
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chapter 10 N u c l e i c A c i d B i o p h y s i c s
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Primary structure in DNA is just sequence of nucleotide residues making up the polymer you just learned about a lot of different secondary structures in dNA To try to simplify matters, let s briefly review them here Both single-stranded and double-stranded nucleic acids form a helical secondary structure due to base stacking interactions When a nucleic acid forms a helix of two strands (double stranded), we call it a double helix Even within the double-helix secondary structure there are various conformations These include A-DNA, B-DNA, C-DNA, D-DNA, Z-DNA, and others These differ from each other in terms of tilt of the base pairs, helical pitch, width of the helix, size of the major and minor grooves, helical direction (left-handed vs right-handed), and so on DNA-RNA hybrids, where the double helix is one strand of DNA and one strand of RNA, occur briefly during transcription Evidence suggests that while B-DNA is the most common conformation in nature, DNA-RNA hybrids are most stable in the A-form conformation In addition to the various helical conformations, local secondary structures also occur, for example, kinks in the helix, bubbles, loops, hairpins, stems and loops, and cruciforms
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DNA Melting
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In Chap 9 you learned that when a protein is unfolded out of its natural conformation, it is said to be denatured Denaturation in DNA also refers to the loss of the molecule s typical secondary and tertiary structure In DNA this most often means unwinding of the helix But it is not necessarily the case that an unwound DNA helix is out of its natural state In fact, formation of unwound, single-stranded regions in DNA is a natural part of DNA function The DNA double helix must unwind for nearly all of its biological activities (transcription, replication, etc) For this reason DNA unwinding is commonly called melting (although the term denaturation is sometimes still applied)
Denaturation and Helix-Coil Transitions in Nucleic Acids and Proteins Compared
Another term used to describe melting and denaturation in nucleic acids and proteins is the helix-coil transition In this context you should always remember
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that the term coil (in the expression, helix-coil) is short for random coil The melting transition, or helix-coil transition, is from a highly ordered helical state, to a less ordered random-coil state That is, in the coil state, the polymer has a no specific secondary structure Instead the polymer chain is randomly configured like a piece of string or rope tossed aside Proteins typically contain both helical and nonhelical (beta-sheet) secondary structures So denaturation in proteins includes helix-coil transitions only to the extent that the protein molecule contains helical structures By contrast, nucleic acid secondary structure is almost exclusively helical, with some exceptions such as kinks and loops Even cruciform and stem-and-loop formations are structures made up mostly of helix Therefore denaturation or melting in nucleic acids always involves a helix-coil transition Also, in double-stranded DNA, the transition from helix to coil involves going from a double-stranded to a single-stranded conformation And formation of single-stranded regions in DNA is a natural part of DNA function Table 10-2 compares denaturation in DNA and proteins
TABLE 10-2
comparison of denaturation in dNA and proteins
Common terms for denaturation Helix-coil transition Melting, helix-coil transition Always Relatively easy Helix-coil transition is an intrinsic part of normal function DNA must unwind, and later wind back up again, during transcription, replication, and other functions
Proteins
Denaturation, unfolding Only to the extent that the protein contains some alpha-helix segments Typically not reversible, but may be under specific conditions
Reversibility Biological function
Protein folding is the final part of protein construction, in order for a protein to become useful Some conformational changes take place during biological function, but denaturation is typically destructive rendering the protein useless
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