Truncation of aptamers developed for sarcosine through molecular modeling and evaluation of truncated functional sequences in sarcosine analysis

Project no. 24032 · Status: Kapanmış (Yayın bekleniyor) · 2022

Summary

<p class="ql-align-justify">This&nbsp;study&nbsp;sought&nbsp;to&nbsp;explore&nbsp;the&nbsp;structural&nbsp;and&nbsp;interaction&nbsp;characteristics&nbsp;of&nbsp;short&nbsp;nucleotide&nbsp;sequences&nbsp;(monomers,&nbsp;dimers,&nbsp;trimers,&nbsp;and&nbsp;tetramers).&nbsp;These&nbsp;sequences&nbsp;were&nbsp;derived&nbsp;from&nbsp;the&nbsp;9S&nbsp;and&nbsp;13S&nbsp;aptamers,&nbsp;which&nbsp;were&nbsp;previously&nbsp;created&nbsp;using&nbsp;the&nbsp;SELEX&nbsp;method&nbsp;for&nbsp;sarcosine&nbsp;(SA),&nbsp;a&nbsp;potential&nbsp;biomarker&nbsp;for&nbsp;prostate&nbsp;cancer,&nbsp;by&nbsp;employing&nbsp;a&nbsp;rational&nbsp;truncation&nbsp;strategy&nbsp;and&nbsp;comprehensive&nbsp;computational&nbsp;techniques.</p><p class="ql-align-justify">For&nbsp;this&nbsp;purpose,&nbsp;the&nbsp;MEGA11&nbsp;program&nbsp;was&nbsp;utilized&nbsp;to&nbsp;identify&nbsp;consensus&nbsp;and&nbsp;primer&nbsp;regions&nbsp;within&nbsp;aptamer&nbsp;sequences,&nbsp;from&nbsp;which&nbsp;short&nbsp;sequence&nbsp;candidates&nbsp;were&nbsp;then&nbsp;derived.&nbsp;Conformational&nbsp;analyses&nbsp;were&nbsp;conducted&nbsp;using&nbsp;Spartan’18,&nbsp;followed&nbsp;by&nbsp;the&nbsp;optimization&nbsp;of&nbsp;initial&nbsp;structures&nbsp;at&nbsp;the&nbsp;PM6-D3H4&nbsp;level&nbsp;and&nbsp;the&nbsp;subsequent&nbsp;selection&nbsp;of&nbsp;the&nbsp;lowest-energy&nbsp;conformers.&nbsp;Subsequently,&nbsp;SA&nbsp;and&nbsp;the&nbsp;stable&nbsp;short&nbsp;sequences&nbsp;underwent&nbsp;re-optimization&nbsp;employing&nbsp;Density&nbsp;Functional&nbsp;Theory&nbsp;(DFT)&nbsp;at&nbsp;the&nbsp;&quot;B97XD/6-31+G(d,p)&nbsp;level,&nbsp;incorporating&nbsp;the&nbsp;PCM&nbsp;solvation&nbsp;model.&nbsp;The&nbsp;Multiwfn&nbsp;3.6&nbsp;software&nbsp;and&nbsp;the&nbsp;VMD&nbsp;program&nbsp;were&nbsp;used&nbsp;to&nbsp;visualize&nbsp;potential&nbsp;van&nbsp;der&nbsp;Waals&nbsp;interactions,&nbsp;hydrogen&nbsp;bonding,&nbsp;and&nbsp;steric&nbsp;effects&nbsp;among&nbsp;the&nbsp;optimized&nbsp;structures.</p><p class="ql-align-justify">The&nbsp;investigation&nbsp;indicated&nbsp;that&nbsp;shorter&nbsp;sequences,&nbsp;specifically&nbsp;at&nbsp;the&nbsp;monomeric&nbsp;and&nbsp;dimeric&nbsp;levels,&nbsp;were&nbsp;more&nbsp;proficient&nbsp;in&nbsp;recognizing&nbsp;the&nbsp;ligand,&nbsp;in&nbsp;contrast&nbsp;to&nbsp;trimers&nbsp;and&nbsp;tetramers,&nbsp;which&nbsp;displayed&nbsp;limited&nbsp;binding&nbsp;roles&nbsp;attributed&nbsp;to&nbsp;their&nbsp;elevated&nbsp;internal&nbsp;stability.&nbsp;The&nbsp;results&nbsp;further&nbsp;elucidated&nbsp;that&nbsp;the&nbsp;primary&nbsp;binding&nbsp;locus&nbsp;of&nbsp;SA&nbsp;aptamers&nbsp;is&nbsp;located&nbsp;within&nbsp;their&nbsp;consensus&nbsp;motifs.&nbsp;Moreover,&nbsp;the&nbsp;study&nbsp;revealed&nbsp;that&nbsp;individual&nbsp;monomer&nbsp;structures&nbsp;formed&nbsp;strong,&nbsp;specific&nbsp;hydrogen&nbsp;bonds&nbsp;with&nbsp;the&nbsp;target;&nbsp;however,&nbsp;an&nbsp;increase&nbsp;in&nbsp;nucleotide&nbsp;quantity&nbsp;led&nbsp;to&nbsp;heightened&nbsp;intramolecular&nbsp;interactions,&nbsp;which&nbsp;subsequently&nbsp;impeded&nbsp;localized&nbsp;ligand-contact&nbsp;regions,&nbsp;culminating&nbsp;in&nbsp;diminished&nbsp;and&nbsp;less&nbsp;effective&nbsp;binding&nbsp;events.</p><p class="ql-align-justify">The&nbsp;current&nbsp;investigation&nbsp;introduces&nbsp;the&nbsp;initial&nbsp;exhaustive&nbsp;deployment&nbsp;of&nbsp;the&nbsp;rational&nbsp;truncation&nbsp;methodology&nbsp;for&nbsp;SA&nbsp;aptamers,&nbsp;employing&nbsp;molecular&nbsp;modeling&nbsp;techniques,&nbsp;which&nbsp;markedly&nbsp;aids&nbsp;in&nbsp;generating&nbsp;cost-effective&nbsp;and&nbsp;highly&nbsp;selective&nbsp;compact&nbsp;aptamer&nbsp;candidates.</p>

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