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(a) Single-stranded loop
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(b) Bubble
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FIgure 10-5 Some localized DNA secondary structures (a) A single-stranded loop results if a portion of the complementary nucleotide sequence is missing from the opposite strand (b) A bubble occurs when a portion of the double helix unwinds
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Other localized double-helix secondary structures include single-stranded loops, bubbles, hairpins, stem-and-loop formations, and cruciform structures A single-stranded loop can form within the double helix where a portion of the nucleotide sequence on one strand is not complementary to the other strand, but the nucleotides surrounding that portion are complementary to the other strand This is illustrated in Fig 10-5a As a secondary structure, a bubble is simply a portion of double helix that is unwound (see Fig 10-5b) Bubbles can form in two ways A portion of the double helix can be permanently unwound if that portion of the double helix contains bases that are not complementary between the two strands This is unusual and not often found in nature More often, however, although the two strands of DNA are entirely complementary, a portion of the double helix can unwind temporarily forming a bubble This temporary secondary structure can be recognized by proteins that bind to DNA and thus serve a biological purpose Unwound portions of the double helix are probably the most common biologically significant secondary structures found in DNA Hairpin, stem-and-loop, and cruciform structures can occur when a nucleotide sequence contains a palindrome In molecular biology, a palindrome is defined a bit differently than it is for words or sentences A word or sentence is considered a palindrome if reading it forward or backward gives the same result, for example the word racecar is a palindrome, as is the word rotator However, in molecular biology we take into account the complement of the nucleotide sequence, that is, the sequence of nucleotides that base-pairs with a given nucleotide sequence A nucleic acid palindrome is a nucleotide sequence that is its own complement when read backward For example, consider the sequence AATGCGTGGTACCACGCATT
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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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The complement of this sequence is the sequence of bases that pair with each of the bases listed T pairs with A, and vice versa, and C pairs with G, and vice versa So the complement is TTACGCACCATGGTGCGTAA But notice that this is just the same sequence read backward! Nucleic acid palindromes can be contiguous, as in this example, or can contain intervening sequences that are not part of the palindrome For example, ACGCACCATGCTGTTTGGTGCGT has the palindrome portion of the sequence is shown shaded The intervening sequence, TGCTGTT, is not part of the palindrome Palindrome sequences do occur quite often in nature, at least much more often than one might expect if an organism s nucleotide sequence were entirely random The types of secondary structures that palindromes can form depend on whether the nucleic acid is single stranded or double stranded and on whether the sequence is contiguous or noncontiguous When a palindrome is single stranded and contiguous, a hairpin structure can form One end of the palindrome is complementary to the other, so the nucleotide strand is able to fold back on itself and form base pairs in the region of the palindrome This is illustrated in Fig 10-6a The hairpin region is a double helix even though the nucleic acid is a single strand This is an important point to keep in mind If the palindrome is noncontiguous (ie, it contains an intervening sequence), then when the strand folds back on itself, the conformation is a stem-and-loop structure: a stem where the palindrome bases are self-complementary, and a loop where the intervening sequence is not self-complementary This is shown in Fig 10-6b When a palindrome sequence occurs in a double-stranded DNA, each of the two strands contains its own palindrome One palindrome is the complementary sequence of the other, and both palindromes (by definition) are their own complement when read backward The result is that both strands are able to form either a hairpin or stem-and-loop conformation (a hairpin if the palindrome is contiguous or a stem and loop if not) When both strands form a hairpin or a stem and loop, the resulting structure is called a cruciform See Fig 10-7 Some cruciform structures have been shown experimentally to be binding sites for specific proteins They also can have a significant influence on tertiary structure of DNA
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