Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Research Abstract Details 

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Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Abstract Text:

Joshua M Blose,Michelle L Manni,Kelly A Klapec,Yukiko Stranger-Jones,Allison C Zyra,Vasiliy Sim,Chad A Griffith,Jason D Long,Martin J Serra,Joshua M Blose,Michelle L Manni,Kelly A Klapec,Yukiko Stranger-Jones,Allison C Zyra,Vasiliy Sim,Chad A Griffith,Jason D Long,Martin J Serra,

Fifty-nine RNA duplexes containing single-nucleotide bulge loops were optically melted in 1 M NaCl, and the thermodynamic parameters DeltaH degrees , DeltaS degrees , DeltaG degrees 37, and TM for each sequence were determined. Sequences from this study were combined with sequences from previous studies [Longfellow, C. E., et al. (1990) Biochemistry 29, 278-285; Znosko, B. M., et al. (2002) Biochemistry 41, 10406-10417], thus examining all possible group I single-nucleotide bulge loop and nearest-neighbor sequence combinations. The free energy increments at 37 degrees C for the introduction of a group I single-nucleotide bulge loop range between 1.3 and 5.2 kcal/mol. The combined data were used to develop a model for predicting the free energy of a RNA duplex containing a single-nucleotide bulge. For bulge loops with adjacent Watson-Crick base pairs, neither the identity of the bulge nor the nearest-neighbor base pairs had an effect on the influence of the bulge loop on duplex stability. The proposed model for prediction of the stability of a duplex containing a bulged nucleotide was primarily affected by non-nearest-neighbor interactions. The destabilization of the duplex by the bulge was related to the stability of the stems adjacent to the bulge. Specifically, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. The stability of a duplex containing a bulged nucleotide adjacent to a wobble base pair also was primarily affected by non-nearest-neighbor interactions. Again, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. However, when one or both of the bulge nearest neighbors was a wobble base pair, the free energy increment for insertion of a bulge loop is dependent upon the position and orientation of the wobble base pair relative the bulged nucleotide. Bulge sequences of the type %@mt;sys@%%@fn;(;vis;full;auto@%%@st;c;2.5q@%5'%@ov@%3'%@stx@%%@mh;1q@%%@st;c;2.5q@%U%@ov@%G%@stx@%%@st;c;2.5q@%B%@ov@% %@stx@%%@st;c;2.5q@%X%@ov@%Y%@stx@%%@fnx;);vis;full@%%@mx@% , %@mt;sys@%%@fn;(;vis;full;auto@%%@st;c;2.5q@%5'%@ov@%3'%@stx@%%@mh;1q@%%@st;c;2.5q@%G%@ov@%U%@stx@%%@st;c;2.5q@%B%@ov@% %@stx@%%@st;c;2.5q@%G%@ov@%U%@stx@%%@fnx;);vis;full@%%@mx@% , and %@mt;sys@%%@fn;(;vis;full;auto@%%@st;c;2.5q@%5'%@ov@%3'%@stx@%%@mh;1q@%%@st;c;2.5q@%U%@ov@%G%@stx@%%@st;c;2.5q@%B%@ov@% %@stx@%%@st;c;2.5q@%U%@ov@%G%@stx@%%@fnx;);vis;full@%%@mx@% are less destabilizing by 0.6 kcal/mol, and bulge sequences of the type %@mt;sys@%%@fn;(;vis;full;auto@%%@st;c;2.5q@%5'%@ov@%3'%@stx@%%@mh;1q@%%@st;c;2.5q@%G%@ov@%U%@stx@%%@st;c;2.5q@%B%@ov@% %@stx@%%@st;c;2.5q@%X%@ov@%Y%@stx@%%@fnx;);vis;full@%%@mx@% and %@mt;sys@%%@fn;(;vis;full;auto@%%@st;c;2.5q@%5'%@ov@%3'%@stx@%%@mh;1q@%%@st;c;2.5q@%X%@ov@%Y%@stx@%%@st;c;2.5q@%B%@ov@% %@stx@%%@st;c;2.5q@%U%@ov@%G%@stx@%%@fnx;);vis;full@%%@mx@% are more destabilizing by 0.4 kcal/mol than bulge loops adjacent to Watson-Crick base pairs.

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Publishing Authors By Initials

JM Blose,ML Manni,KA Klapec,Y Stranger-Jones,AC Zyra,V Sim,CA Griffith,JD Long,MJ Serra,JM Blose,ML Manni,KA Klapec,Y Stranger-Jones,AC Zyra,V Sim,CA Griffith,JD Long,MJ Serra,

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Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Biochemistry

VOLUME: 46

Page Numbers: 15123-35

Journal Abbreviation: Biochemistry

ISSN: 0006-2960

DAY: 30

MONTH: 11

YEAR: 2007

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Information

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LANGUAGE: eng

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Grant and Affiliation Information for Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.

AFFILIATION: Department of Chemistry, Allegheny College, 520 North Main Street, Meadville, Pennsylvania 16335.

Country: United States

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MEDLINETA: Biochemistry

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