東華大學圖書館 |

Language: English

Help

回圖書館首頁

手機版館藏查詢

Back

Switch To: Labeled | MARC Mode | ISBD

Insights into RNA tertiary folding: ...

Stanford University.

Linked to FindBook

Google Book

Amazon

博客來

Insights into RNA tertiary folding: Examination of structure formation between the P1 helix and the pre-folded Tetrahymena group I ribozyme.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Insights into RNA tertiary folding: Examination of structure formation between the P1 helix and the pre-folded Tetrahymena group I ribozyme./
Author:	Bartley, Laura Elizabeth.
Description:	179 p.
Notes:	Adviser: Daniel Herschlag.
Contained By:	Dissertation Abstracts International63-01B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3038065
ISBN:	0493516794

Insights into RNA tertiary folding: Examination of structure formation between the P1 helix and the pre-folded Tetrahymena group I ribozyme.
Bartley, Laura Elizabeth.

Insights into RNA tertiary folding: Examination of structure formation between the P1 helix and the pre-folded Tetrahymena group I ribozyme. - 179 p.

Adviser: Daniel Herschlag.

Thesis (Ph.D.)--Stanford University, 2002.

To function, many RNAs must fold into complex tertiary structures. To reveal the basic properties of RNA folding, the formation of tertiary structure between an isolated duplex, termed P1, and the pre-folded core of the <italic> Tetrahymena</italic> ribozyme was examined. The P1 duplex is composed of the oligonucleotide substrate (S) and a single-stranded region of the ribozyme. Docking of P1 positions S for cleavage within the active site of the ribozyme, so cleavage can be used to monitor docking. Studies with substrates of various lengths revealed the properties of different steps of the ribozyme reaction. S binding was found to be independent of temperature and pH, consistent with the model that the P1 duplex is similar to a free model duplex. The temperature dependence of the rate constant of docking suggested that the transition state for docking was unrelated to the docked state. In addition, a single-molecule fluorescence resonance energy transfer (smFRET) assay was developed to follow docking. Examination of single molecules allows the properties of states that do not accumulate to be measured. Control experiments indicated that the smFRET assay faithfully reports on the cleavage activity, overall folding, and P1 docking of the ribozyme. SmFRET studies facilitated a thorough characterization of the transition state for docking. Modification of the eight functional groups of P1 known to form tertiary interactions gave no effects on the rate constant for docking, suggesting that the transition state for docking is early in the docking process. The time scale for the docking of seconds is slow compared to other RNA folding events with many more degrees of freedom. This and experimental observations suggest that docking is slow due to escape from a kinetic trap. However, urea does not accelerate the docking rate, suggesting that there is not an increase in accessible surface area between the undocked state and the transition state. Breaking and forming structure in the process of folding may explain the failure of urea to accelerate this and other slow folding events in RNA. Overall, the results suggest that specifying a single native structure may generally be a challenge for RNA.

ISBN: 0493516794Subjects--Topical Terms:

1019105
Biophysics, General.

Insights into RNA tertiary folding: Examination of structure formation between the P1 helix and the pre-folded Tetrahymena group I ribozyme.
LDR:03167nam 2200277 a 45 001 932987
005 20110505
008 110505s2002 eng d
020 $a 0493516794
035 $a (UnM)AAI3038065
035 $a AAI3038065
040 $a UnM $c UnM
100 1 $a Bartley, Laura Elizabeth. $3 1256727
245 1 0 $a Insights into RNA tertiary folding: Examination of structure formation between the P1 helix and the pre-folded Tetrahymena group I ribozyme.
300 $a 179 p.
500 $a Adviser: Daniel Herschlag.
500 $a Source: Dissertation Abstracts International, Volume: 63-01, Section: B, page: 0234.
502 $a Thesis (Ph.D.)--Stanford University, 2002.
520 $a To function, many RNAs must fold into complex tertiary structures. To reveal the basic properties of RNA folding, the formation of tertiary structure between an isolated duplex, termed P1, and the pre-folded core of the <italic> Tetrahymena</italic> ribozyme was examined. The P1 duplex is composed of the oligonucleotide substrate (S) and a single-stranded region of the ribozyme. Docking of P1 positions S for cleavage within the active site of the ribozyme, so cleavage can be used to monitor docking. Studies with substrates of various lengths revealed the properties of different steps of the ribozyme reaction. S binding was found to be independent of temperature and pH, consistent with the model that the P1 duplex is similar to a free model duplex. The temperature dependence of the rate constant of docking suggested that the transition state for docking was unrelated to the docked state. In addition, a single-molecule fluorescence resonance energy transfer (smFRET) assay was developed to follow docking. Examination of single molecules allows the properties of states that do not accumulate to be measured. Control experiments indicated that the smFRET assay faithfully reports on the cleavage activity, overall folding, and P1 docking of the ribozyme. SmFRET studies facilitated a thorough characterization of the transition state for docking. Modification of the eight functional groups of P1 known to form tertiary interactions gave no effects on the rate constant for docking, suggesting that the transition state for docking is early in the docking process. The time scale for the docking of seconds is slow compared to other RNA folding events with many more degrees of freedom. This and experimental observations suggest that docking is slow due to escape from a kinetic trap. However, urea does not accelerate the docking rate, suggesting that there is not an increase in accessible surface area between the undocked state and the transition state. Breaking and forming structure in the process of folding may explain the failure of urea to accelerate this and other slow folding events in RNA. Overall, the results suggest that specifying a single native structure may generally be a challenge for RNA.
590 $a School code: 0212.
650 4 $a Biophysics, General. $3 1019105
650 4 $a Chemistry, Biochemistry. $3 1017722
690 $a 0487
690 $a 0786
710 2 0 $a Stanford University. $3 754827
773 0 $t Dissertation Abstracts International $g 63-01B.
790 $a 0212
790 1 0 $a Herschlag, Daniel, $e advisor
791 $a Ph.D.
792 $a 2002
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3038065