RNA, double-helical

The atomic structure of this subunit and its complexes with substrate analogs revealed the enzymatic activity of the rRNA backbone. Thus, the ribosome is in fact a ribozyme P Nissen, J Hansen, N Ban, PB Moore, TA Steitz. Science 289 920-930, 2000. Atomic structure of the ribosome s small 30S subunit, resolved at 5 A WM Clemons Jr, JL May, BT Wimberly, JP McCutcheon, MS Capel, V Ramakrishnan. Nature 400 833-840, 1999. The 8-A crystal structure of the 70S ribosome reveals a double-helical RNA bridge between the 50S and the 30S subunit GM Culver, JH Cate, GZ Yusupova, MM Yusupov, HF Noller. Science 285 2133-2136, 1999. 

Cp6 together with the Intercalator acridine orange solved at atoaiic resolution (36). It can be seen tha the 3 end of the double helical RNA fragment has adopted the C2 endo conformation while the S end maintains the normal C3 endo conformation. A large number of intercalator structures of this type have been solved and they have been summaried elsewhere. Sobell and his colleages pointed out that the Intercalation is associated with a modification of the pucker of the ribonucleotide chain on the 3 end of the intercalator (37-38). Although intercalation is generally associated with the conformations similar to those seen in Fig. 10. a number of alternative conformations have been found with more complex Intercalators. 

Answer The RNA helix assumes the A conformation the DNA helix generally assumes the B conformation. (The presence of the 2 -OH group on ribose makes it sterically impossible for double-helical RNA to assume the B-form helix.)... 

De Clercq, E., Stollar, B. D., Hobbs, J., et al. (1980) Interferon induction by two 2 -modi(icd double-helical RNAs, poly(2 -nuoro-2 -deoxymosimc acid) poly(cytidylic acid) and poly(2 -chloro-2 -deoxyinosinic acid) poly(cytidylic acid). Ear. J. Biochem., 107, 279-288. 

The Raman spectrum of an ordered, single-stranded or double-helical RNA shows an intense sharp band at 810-815 cm which shifts to near 795 cm upon disordering. This trmsition is clearly seen in the spectrum of poly(rA)poly(rU) in Fig. 15 while the same spectrum demonstrates the insensitivity of the 1100 cm feature to disruption of secondary structure. The intensity of the PO Raman mode remains constant at constant ionic strength. For RNA, at low ionic strength, the ratios of intensities of the bands at 851 and 1100 cm can be used to monitor the amount of secondary structure. 7(815)/( 7(1100) = 1.66 in completely ordered ribopolymers (double-helical or single-stranded) and 0.0 in completely disordered ribopolymers [50]. 

RNA differs from DNA in that every T is replaced t>y U, which has one less methyl group, and the backtxme sugar is ribose Instead of deoxyrtbose. Double helical RNA adopts the Aform geometry. The repeat unit of Z-ONA is a dinucleotide, necessitating two values of each angular parameter. adopts a range of values in Z-DNA. 

Han, H. and Dervan, P.B. (1993) Sequence-specific recognition of double-helical RNA and RNA-DNA by triple helix formation, Proc. Natl. Acad. Sci., USA, 90, 3806-3810. 

Chou, S -H, Flynn, P., and Reid, B. (1989) Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers r(CGCGAAUUGCG) and r(CGCGUAUACGCG). Biochemistry 28,2422-2435. 

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