2.RNA - Patterns and principles of RNA structure RNA...

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RNA structure can be specific, stable and complex. (As a result, RNA mediates specific recognition and catalytic reactions.) Principles/ideas--RNAs contain characteristic 2° and 3° motifs Secondary structure--stems, bulges & loops Coaxial stacking Metal ion binding Tertiary motifs (Pseudoknots, A-A platform, tetraloop/tetraloop receptor, A-minor motif, ribose zipper) Patterns and principles of RNA structure
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RNA vs. DNA nucleoside nucleotide glycosidic bond
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RNA vs. DNA: who cares? Base-catalyzed RNA cleavage! - OH Stable backbone Unstable
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RNA transesterification mechanism Base-catalyzed RNA cleavage! transition state + + - OH
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Different bases in RNA and DNA RNA only DNA DNA and RNA
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RNA chain is made single stranded! Chain is directional. Chemical schematic One-letter code ssDNA can signal DNA damage and promote cell death dsRNA can block protein synthesis and signal viral infections
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Six backbone dihedral angles (α-ζ29 per nucleotide in RNA and DNA I s ssDNA floppy or rigid? I s RNA more or less flexible than ssDNA?
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Two orientations of the bases: Anti and syn DNA and RNA Absent from undamaged dsDNA
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-OH, what a difference an O makes! Different functions of DNA and RNA Stores genetic info ssDNA signals cell death ssRNA OK E.g. mRNA = gene copy dsDNA OK dsRNA (“A” form) signals infection, mediates editing, RNA interference, . . . Double helical (B form) Forms complex structures Supercoiled Enzymes (e.g. ribosome), Binding sites & scaffolds Signals Templates (e.g. telomeres) gene1gene2 gene3 . . .
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2.RNA - Patterns and principles of RNA structure RNA...

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