PDBsum entry 2kp4

DNA/RNA

PDB id: 2kp4

Contents

DNA/RNA

Ligands

GFL-CFL-TAF-A5L-TAF-A5L-A5L-TAF-GFL-GFL

PDB id:

2kp4

Name:

DNA/RNA

Title:

Structure of 2'f-ana/RNA hybrid duplex

Structure:

DNA (5'-d( (Gfl)p (Cfl)p (Taf)p (A5l)p (Taf)p (A5l)p (A5l) p (Taf)p (Gfl)p (Gfl))-3'). Chain: a. Engineered: yes. RNA (5'-r( Cp Cp Ap Up Up Ap Up Ap Gp C)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

10 models

Authors:

C.Gonzalez,N.Martin-Pintado,J.Watts,I.Gomez-Pinto,M.Dhama,M.Orozco, J.Schwartzentruber,G.Portella

Key ref:

J.K.Watts et al. (2010). Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res, 38, 2498-2511. PubMed id: 20071751

Date:

06-Oct-09 Release date: 09-Feb-10

DNA/RNA chain

C-C-A-U-U-A-U-A-G-C 10 bases

Nucleic Acids Res 38:2498-2511 (2010)

PubMed id: 20071751

Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.

J.K.Watts, N.Martín-Pintado, I.Gómez-Pinto, J.Schwartzentruber, G.Portella, M.Orozco, C.González, M.J.Damha.

ABSTRACT

Hybrids of RNA with arabinonucleic acids 2'F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2'F-ANA*RNA and ANA*RNA hybrids indicates that the increased binding affinity of 2'F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2'F-purine H8) which contrasts with unfavorable 2'-OH-nucleobase steric interactions in the case of ANA. While both 2'F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2'F-ANA strand's structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA*RNA duplex showed lower uptake of counterions than its 2'F-ANA*RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2'F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2'F-ANA*RNA and ANA*RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important.