Nucleobase orientation and ordering in films of single-stranded DNA on gold.
Identifieur interne : 000391 ( Ncbi/Checkpoint ); précédent : 000390; suivant : 000392Nucleobase orientation and ordering in films of single-stranded DNA on gold.
Auteurs : Dmitri Y. Petrovykh [États-Unis] ; V. Pérez-Dieste ; Aric Opdahl ; Hiromi Kimura-Suda ; J M Sullivan ; Michael J. Tarlov ; F J Himpsel ; Lloyd J. WhitmanSource :
- Journal of the American Chemical Society [ 0002-7863 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Single-Stranded, Gold, Oligodeoxyribonucleotides, Thymine.
- methods : Spectroscopy, Fourier Transform Infrared, Spectrum Analysis.
- Models, Molecular, Nucleic Acid Conformation, X-Rays.
Abstract
We demonstrate how the orientation and ordering of DNA bases in ultrahigh vacuum (UHV) and ambient environments can be determined using complementary spectroscopic methods. Near-edge X-ray absorption fine structure (NEXAFS) with fluorescence detection, X-ray photoelectron (XPS), and Fourier transform infrared (FTIR) spectroscopies are used to quantify the coverage, chemical composition, orientation, and ordering of thymine bases in model self-assembled monolayers of thymine homo-oligonucleotides [oligo(dT)] on gold. We find that, in monolayers of thiol-modified oligo(dT), thymine bases tend to orient parallel to the Au substrate, and this preferential orientation is significantly more pronounced in monolayers of thiolated 5-mers compared to 25-mers. We interpret this preferential orientation as a signature of significant correlations (local ordering) between individual nuleobases, which offers a way to quantify and compare nucleobase interactions in films under both ambient and UHV conditions.
DOI: 10.1021/ja052443e
PubMed: 16390092
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002290
- to stream PubMed, to step Curation: 002290
- to stream PubMed, to step Checkpoint: 002107
- to stream Ncbi, to step Merge: 000391
- to stream Ncbi, to step Curation: 000391
Links to Exploration step
pubmed:16390092Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Nucleobase orientation and ordering in films of single-stranded DNA on gold.</title>
<author><name sortKey="Petrovykh, Dmitri Y" sort="Petrovykh, Dmitri Y" uniqKey="Petrovykh D" first="Dmitri Y" last="Petrovykh">Dmitri Y. Petrovykh</name>
<affiliation wicri:level="4"><nlm:affiliation>Physics Department, University of Maryland, College Park, MD 20742, USA. dmitri.petrovykh@nrl.navy.mil</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Physics Department, University of Maryland, College Park, MD 20742</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Perez Dieste, V" sort="Perez Dieste, V" uniqKey="Perez Dieste V" first="V" last="Pérez-Dieste">V. Pérez-Dieste</name>
</author>
<author><name sortKey="Opdahl, Aric" sort="Opdahl, Aric" uniqKey="Opdahl A" first="Aric" last="Opdahl">Aric Opdahl</name>
</author>
<author><name sortKey="Kimura Suda, Hiromi" sort="Kimura Suda, Hiromi" uniqKey="Kimura Suda H" first="Hiromi" last="Kimura-Suda">Hiromi Kimura-Suda</name>
</author>
<author><name sortKey="Sullivan, J M" sort="Sullivan, J M" uniqKey="Sullivan J" first="J M" last="Sullivan">J M Sullivan</name>
</author>
<author><name sortKey="Tarlov, Michael J" sort="Tarlov, Michael J" uniqKey="Tarlov M" first="Michael J" last="Tarlov">Michael J. Tarlov</name>
</author>
<author><name sortKey="Himpsel, F J" sort="Himpsel, F J" uniqKey="Himpsel F" first="F J" last="Himpsel">F J Himpsel</name>
</author>
<author><name sortKey="Whitman, Lloyd J" sort="Whitman, Lloyd J" uniqKey="Whitman L" first="Lloyd J" last="Whitman">Lloyd J. Whitman</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2006">2006</date>
<idno type="RBID">pubmed:16390092</idno>
<idno type="pmid">16390092</idno>
<idno type="doi">10.1021/ja052443e</idno>
<idno type="wicri:Area/PubMed/Corpus">002290</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002290</idno>
<idno type="wicri:Area/PubMed/Curation">002290</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002290</idno>
<idno type="wicri:Area/PubMed/Checkpoint">002107</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002107</idno>
<idno type="wicri:Area/Ncbi/Merge">000391</idno>
<idno type="wicri:Area/Ncbi/Curation">000391</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000391</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Nucleobase orientation and ordering in films of single-stranded DNA on gold.</title>
<author><name sortKey="Petrovykh, Dmitri Y" sort="Petrovykh, Dmitri Y" uniqKey="Petrovykh D" first="Dmitri Y" last="Petrovykh">Dmitri Y. Petrovykh</name>
<affiliation wicri:level="4"><nlm:affiliation>Physics Department, University of Maryland, College Park, MD 20742, USA. dmitri.petrovykh@nrl.navy.mil</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Physics Department, University of Maryland, College Park, MD 20742</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Perez Dieste, V" sort="Perez Dieste, V" uniqKey="Perez Dieste V" first="V" last="Pérez-Dieste">V. Pérez-Dieste</name>
</author>
<author><name sortKey="Opdahl, Aric" sort="Opdahl, Aric" uniqKey="Opdahl A" first="Aric" last="Opdahl">Aric Opdahl</name>
</author>
<author><name sortKey="Kimura Suda, Hiromi" sort="Kimura Suda, Hiromi" uniqKey="Kimura Suda H" first="Hiromi" last="Kimura-Suda">Hiromi Kimura-Suda</name>
</author>
<author><name sortKey="Sullivan, J M" sort="Sullivan, J M" uniqKey="Sullivan J" first="J M" last="Sullivan">J M Sullivan</name>
</author>
<author><name sortKey="Tarlov, Michael J" sort="Tarlov, Michael J" uniqKey="Tarlov M" first="Michael J" last="Tarlov">Michael J. Tarlov</name>
</author>
<author><name sortKey="Himpsel, F J" sort="Himpsel, F J" uniqKey="Himpsel F" first="F J" last="Himpsel">F J Himpsel</name>
</author>
<author><name sortKey="Whitman, Lloyd J" sort="Whitman, Lloyd J" uniqKey="Whitman L" first="Lloyd J" last="Whitman">Lloyd J. Whitman</name>
</author>
</analytic>
<series><title level="j">Journal of the American Chemical Society</title>
<idno type="ISSN">0002-7863</idno>
<imprint><date when="2006" type="published">2006</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA, Single-Stranded (chemistry)</term>
<term>Gold (chemistry)</term>
<term>Models, Molecular</term>
<term>Nucleic Acid Conformation</term>
<term>Oligodeoxyribonucleotides (chemistry)</term>
<term>Spectroscopy, Fourier Transform Infrared (methods)</term>
<term>Spectrum Analysis (methods)</term>
<term>Thymine (chemistry)</term>
<term>X-Rays</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN simple brin ()</term>
<term>Analyse spectrale ()</term>
<term>Conformation d'acide nucléique</term>
<term>Modèles moléculaires</term>
<term>Oligodésoxyribonucléotides ()</term>
<term>Or ()</term>
<term>Rayons X</term>
<term>Spectroscopie infrarouge à transformée de Fourier ()</term>
<term>Thymine ()</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Single-Stranded</term>
<term>Gold</term>
<term>Oligodeoxyribonucleotides</term>
<term>Thymine</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Spectroscopy, Fourier Transform Infrared</term>
<term>Spectrum Analysis</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Models, Molecular</term>
<term>Nucleic Acid Conformation</term>
<term>X-Rays</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ADN simple brin</term>
<term>Analyse spectrale</term>
<term>Conformation d'acide nucléique</term>
<term>Modèles moléculaires</term>
<term>Oligodésoxyribonucléotides</term>
<term>Or</term>
<term>Rayons X</term>
<term>Spectroscopie infrarouge à transformée de Fourier</term>
<term>Thymine</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">We demonstrate how the orientation and ordering of DNA bases in ultrahigh vacuum (UHV) and ambient environments can be determined using complementary spectroscopic methods. Near-edge X-ray absorption fine structure (NEXAFS) with fluorescence detection, X-ray photoelectron (XPS), and Fourier transform infrared (FTIR) spectroscopies are used to quantify the coverage, chemical composition, orientation, and ordering of thymine bases in model self-assembled monolayers of thymine homo-oligonucleotides [oligo(dT)] on gold. We find that, in monolayers of thiol-modified oligo(dT), thymine bases tend to orient parallel to the Au substrate, and this preferential orientation is significantly more pronounced in monolayers of thiolated 5-mers compared to 25-mers. We interpret this preferential orientation as a signature of significant correlations (local ordering) between individual nuleobases, which offers a way to quantify and compare nucleobase interactions in films under both ambient and UHV conditions.</div>
</front>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Maryland</li>
</region>
<settlement><li>College Park (Maryland)</li>
</settlement>
<orgName><li>Université du Maryland</li>
</orgName>
</list>
<tree><noCountry><name sortKey="Himpsel, F J" sort="Himpsel, F J" uniqKey="Himpsel F" first="F J" last="Himpsel">F J Himpsel</name>
<name sortKey="Kimura Suda, Hiromi" sort="Kimura Suda, Hiromi" uniqKey="Kimura Suda H" first="Hiromi" last="Kimura-Suda">Hiromi Kimura-Suda</name>
<name sortKey="Opdahl, Aric" sort="Opdahl, Aric" uniqKey="Opdahl A" first="Aric" last="Opdahl">Aric Opdahl</name>
<name sortKey="Perez Dieste, V" sort="Perez Dieste, V" uniqKey="Perez Dieste V" first="V" last="Pérez-Dieste">V. Pérez-Dieste</name>
<name sortKey="Sullivan, J M" sort="Sullivan, J M" uniqKey="Sullivan J" first="J M" last="Sullivan">J M Sullivan</name>
<name sortKey="Tarlov, Michael J" sort="Tarlov, Michael J" uniqKey="Tarlov M" first="Michael J" last="Tarlov">Michael J. Tarlov</name>
<name sortKey="Whitman, Lloyd J" sort="Whitman, Lloyd J" uniqKey="Whitman L" first="Lloyd J" last="Whitman">Lloyd J. Whitman</name>
</noCountry>
<country name="États-Unis"><region name="Maryland"><name sortKey="Petrovykh, Dmitri Y" sort="Petrovykh, Dmitri Y" uniqKey="Petrovykh D" first="Dmitri Y" last="Petrovykh">Dmitri Y. Petrovykh</name>
</region>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000391 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 000391 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Ncbi |étape= Checkpoint |type= RBID |clé= pubmed:16390092 |texte= Nucleobase orientation and ordering in films of single-stranded DNA on gold. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/RBID.i -Sk "pubmed:16390092" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |