G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy

被引：409

作者：

del Villar-Guerra, Rafael ^{[1
]}

Trent, John O. ^{[1
]}

Chaires, Jonathan B. ^{[1
]}

机构：

[1] Univ Louisville, James Graham Brown Canc Ctr, 505 S Hancock St, Louisville, KY 40202 USA

来源：

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION | 2018年 / 57卷 / 24期

关键词：

circular dichroism; DNA; G-quadruplexes; secondary structure; CD SPECTRA; DNA; CONFORMATION; PROTEINS;

D O I：

10.1002/anie.201709184

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

A curated library of circular dichroism spectra of 23G-quadruplexes of known structure was built and analyzed. The goal of this study was to use this reference library to develop an algorithm to derive quantitative estimates of the secondary structure content of quadruplexes from their experimental CD spectra. Principal component analysis and singular value decomposition were used to characterize the reference spectral library. CD spectra were successfully fit to obtain estimates of the amounts of base steps in anti-anti, syn-anti or anti-syn conformations, in diagonal or lateral loops, or in other conformations. The results show that CD spectra of nucleic acids can be analyzed to obtain quantitative structural information about secondary structure content in an analogous way to methods used to analyze protein CD spectra.

引用

页码：7171 / 7175

页数：5

共 31 条

[1]

[Anonymous], 2011, Angew. Chem., DOI DOI 10.1002/ANGE.201105193

[2] OLIGONUCLEOTIDE INTERACTIONS .3. CIRCULAR DICHROISM STUDIES OF CONFORMATION OF DEOXYOLIGONUCLEOTIDES [J].

CANTOR, CR ;

WARSHAW, MM ;

SHAPIRO, H .

BIOPOLYMERS, 1970, 9 (09) :1059-&

[3]

Chaires J. B., 2015, 13 HYDRODYNAMIC MODE, V562, P287

[4]

COMPTON LA, 1987, J BIOL CHEM, V262, P13039

[5] ANALYSIS OF PROTEIN CIRCULAR-DICHROISM SPECTRA FOR SECONDARY STRUCTURE USING A SIMPLE MATRIX MULTIPLICATION [J].

COMPTON, LA ;

JOHNSON, WC .

ANALYTICAL BIOCHEMISTRY, 1986, 155 (01) :155-167

[6] Geometric formalism for DNA quadruplex folding [J].

da Silva, Mateus Webba .

CHEMISTRY-A EUROPEAN JOURNAL, 2007, 13 (35) :9738-9745

[7]

DelVillar-Guerra R., 2017, CURR PROTOC NUCL ACI, V68, p17.8.1

[8]

Garbett N. C., 2010, J B CHAIRES SEDIMENT, P97

[9] Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities [J].

Gray, Donald M. ;

Wen, Jin-Der ;

Gray, Carla W. ;

Repges, Rudolf ;

Repges, Charlotte ;

Raabe, Gerhard ;

Fleischhauer, Joerg .

CHIRALITY, 2008, 20 (3-4) :431-440

[10] Using circular dichroism spectra to estimate protein secondary structure [J].

Greenfield, Norma J. .

NATURE PROTOCOLS, 2006, 1 (06) :2876-2890

← 1 2 3 4 →