Helical structures Nucleic acid tertiary structure

1 helical structures

1.1 double helix
1.2 major , minor groove triplexes
1.3 quadruplexes

helical structures

the structures of a-, b-, , z-dna double helix structures.


double helix

the double helix dominant tertiary structure biological dna, , possible structure rna. 3 dna conformations believed found in nature, a-dna, b-dna, , z-dna. b form described james d. watson , francis crick believed predominate in cells. james d. watson , francis crick described structure double helix radius of 10 Å , pitch of 34 Å, making 1 complete turn axis every 10 bp of sequence. double helix makes 1 complete turn axis every 10.4-10.5 base pairs in solution. frequency of twist (known helical pitch) depends largely on stacking forces each base exerts on neighbours in chain. double-helical rna adopts conformation similar a-form structure.

other conformations possible; in fact, letters f, q, u, v, , y available describe new dna structure may appear in future. however, of these forms have been created synthetically , have not been observed in naturally occurring biological systems.

major , minor groove triplexes

the minor groove triple ubiquitous rna structural motif. because interactions minor groove mediated 2 -oh of ribose sugar, rna motif looks different dna equivalent. common example of minor loop triple a-minor motif, or insertion of adenosine bases minor groove (see above). however, motif not restricted adenosines, other nucleobases have been observed interact rna minor groove.

the minor groove presents near-perfect complement inserted base. allows optimal van der waals contacts, extensive hydrogen bonding , hydrophobic surface burial, , creates highly energetically favorable interaction. because minor groove triples capable of stably packing free loop , helix, key elements in structure of large ribonucleotides, including group intron, group ii intron, , ribosome.

although major groove of standard a-form rna narrow , therefore less available triplex interaction minor groove, major groove triplex interactions can observed in several rna structures. these structures consist of several combinations of base pair , hoogsteen interactions. example, ggc triplex (ggc amino(n-2)-n-7, imino-carbonyl, carbonyl-amino(n-4); watson-crick) observed in 50s ribosome, composed of watson-crick type g-c pair , incoming g forms pseudo-hoogsteen network of hydrogen bonding interactions between both bases involved in canonical pairing. other notable examples of major groove triplexes include (i) catalytic core of group ii intron shown in figure @ left (ii) catalytically essential triple helix observed in human telomerase rna , (iii) sam-ii riboswitch.

triple-stranded dna possible hoogsteen or reversed hoogsteen hydrogen bonds in major groove of b-form dna.

quadruplexes

besides double helices , above-mentioned triplexes, rna , dna can both form quadruple helices. there diverse structures of rna base quadruplexes. 4 consecutive guanine residues can form quadruplex in rna hoogsteen hydrogen bonds form “hoogsteen ring” (see figure). g-c , a-u pairs can form base quadruplex combination of watson-crick pairing , noncanonical pairing in minor groove.

the core of malachite green aptamer kind of base quadruplex different hydrogen bonding pattern (see figure). quadruplex can repeat several times consecutively, producing immensely stable structure.

the unique structure of quadruplex regions in rna may serve different functions in biological system. 2 important functions binding potential ligands or proteins, , ability stabilize whole tertiary structure of dna or rna. strong structure can inhibit or modulate transcription , replication, such in telomeres of chromosomes , utr of mrna. base identity important towards ligand binding. g-quartet typically binds monovalent cations such potassium, while other bases can bind numerous other ligands such hypoxanthine in u-u-c-u quadruplex.

along these functions, g-quadruplex in mrna around ribosome binding regions serve regulator of gene expression in bacteria. there may more interesting structures , functions yet discovered in vivo.