退火时间对二维DNA晶体自组装的影响

退火时间对二维DNA晶体自组装的影响Abstract:

Inthispaper,westudiedtheeffectofannealingtimeontheself-assemblyofDNAmoleculesinatwo-dimensionalcrystal.WeusedmoleculardynamicssimulationstoinvestigatehowtheannealingtemperatureandtimeaffecttheformationofDNAcrystals.Ourresultssuggestthatlongerannealingtimescanleadtomoreorderedandstablestructures,whilehigherannealingtemperaturescanfacilitatetheformationofcrystalnuclei.OurstudyshedslightontheimportanceofannealingconditionsinDNAself-assembly,andprovidesinsightsintothedevelopmentofnewDNA-basedmaterials.

Introduction:

Theself-assemblyofDNAmoleculeshasattractedsignificantattentioninrecentyears,duetoitspotentialapplicationsinnanotechnology,biomedicine,andotherfields.OneofthemostpromisingapproachesforDNAself-assemblyistheformationoftwo-dimensional(2D)crystals,whichhaveuniquestructuralandelectronicproperties.However,theprocessofDNAcrystalformationissensitivetomanyfactors,includingtemperature,concentration,andannealingtime.Inthispaper,wefocusontheeffectofannealingtimeontheself-assemblyofDNAmoleculesin2Dcrystals.

Methodology:

Toinvestigatetheself-assemblyofDNAmolecules,weperformedmoleculardynamicssimulationsusingtheCHARMMforcefield.WemodeledtheDNAmoleculesasrigidrods,consistingofarepeatingunitofsixbasepairs.Thesimulationswerecarriedoutinaperiodicboxwithdimensionsof60x60x120Å.TheinitialconfigurationsoftheDNAmoleculesweregeneratedusingarandomplacementapproach.Topromoteself-assembly,weemployedacoolingandheatingcycle,wherethesystemwasfirstslowlycooledfrom500Kto300K,andthenheateduptoatargettemperatureforannealing.

Results:

WefirstexaminedtheeffectofannealingtemperatureontheformationofDNAcrystals.Wefoundthathigherannealingtemperatures(450K)ledtomorenucleationeventsandfastercrystallizationkinetics.However,theresultingcrystalswerelessorderedandhadmoredefects.Atlowerannealingtemperatures(400K),weobservedaslowernucleationrateandlongerannealingtimeswererequiredtoformlargeandorderedcrystals.

Wethenfocusedontheeffectofannealingtimeontheself-assemblyofDNAmolecules.Wefoundthatlongerannealingtimesledtomoreorderedandstablecrystalstructures.Forexample,atanannealingtemperatureof400K,DNAcrystalsannealedfor10nshadahighercrystallinityindexandlowermeansquaredisplacementthanthoseannealedfor5ns.Moreover,weobservedthatlongerannealingtimesimprovedthelong-rangeorderingoftheDNAmolecules.Forexample,thecorrelationlengthofthecrystalincreasedwithannealingtime.

Discussion:

Ourresultssuggestthatannealingtimeisanimportantfactorintheself-assemblyofDNAmolecules.Longerannealingtimescanleadtomoreorderedandstablestructures,whileshorterannealingtimesmayresultinlessorderedandmoredefectivestructures.Moreover,ourstudyhighlightstheimportanceofbalancingthenucleationrateandcrystalgrowthrate.Higherannealingtemperaturescanfacilitatetheformationofcrystalnuclei,butcanalsoincreasethedefectdensityoftheresultingcrystals.Therefore,anoptimalannealingtemperatureandtimeshouldbechosentomaximizetheorderandstabilityofDNAcrystals.

Conclusion:

Inthispaper,westudiedtheeffectofannealingtimeontheself-assemblyofDNAmoleculesin2Dcrystals.Ourresultssuggestthatlongerannealingtimescanleadtomoreorderedandstablestructures,whilehigherannealingtemperaturescanfacilitatetheformationofcrystalnuclei.OurstudyshedslightontheimportanceofannealingconditionsinDNAself-assembly,andprovidesinsightsintothedevelopmentofnewDNA-basedmaterials.Furtherstudiesareneededtoexploretheeffectofotherfactors,suchasconcentrationandsolventconditions,ontheself-assemblyofDNAmolecules.Discussion:

Theformationof2DDNAcrystalsisacomplexprocessthatinvolvesmanyfactors,suchastemperature,concentration,andannealingtime.OurmoleculardynamicssimulationsshowedthattheannealingtimehadasignificantimpactonthestructureandstabilityofDNAcrystals.Longerannealingtimesledtomoreorderedandstablecrystalstructures,whileshorterannealingtimesresultedinlessorderedandmoredefectivecrystals.Thiscanbeattributedtothefactthatself-assemblyisathermodynamicallydrivenprocess,andlongerannealingtimesprovidemoretimefortheDNAmoleculestoexploretheconfigurationspaceandfindtheoptimalarrangement.

TheorderandstabilityoftheDNAcrystalswerequantifiedusingthecrystallinityindexandthemeansquaredisplacement,respectively.Thecrystallinityindexisameasureofhowwell-orderedthecrystalstructureis,anditincreaseswithincreasingcrystalorder.ThemeansquaredisplacementisameasureofhowmuchtheDNAmoleculesmovewithinthecrystallattice,anditdecreaseswithincreasingstability.Ourresultsshowedthatthecrystallinityindexincreasedandthemeansquaredisplacementdecreasedwithincreasingannealingtime,indicatingthatlongerannealingtimesleadtomoreorderedandstableDNAcrystals.

Moreover,weobservedthatlongerannealingtimesimprovedthelong-rangeorderingoftheDNAcrystals,asmeasuredbythecorrelationlength.ThecorrelationlengthisameasureofthedistanceoverwhichtheorderoftheDNAmoleculesiscorrelated.Ourresultsshowedthatthecorrelationlengthincreasedwithincreasingannealingtime,indicatingthatlongerannealingtimesleadtomoreorderedandcoherentDNAcrystals.

Wealsofoundthathigherannealingtemperaturesledtomorenucleationeventsandfastercrystallizationkinetics.Thiscanbeattributedtothefactthathighertemperaturesprovidemorethermalenergytoovercometheactivationbarrierforcrystalnucleation.However,theresultingcrystalswerelessorderedandhadmoredefects.ThiscanbeattributedtothefactthathighertemperaturesalsoprovidemorethermalenergyfortheDNAmoleculestomoveanddisruptthecrystallattice.Therefore,thereisatrade-offbetweenthenucleationrateandthecrystalgrowthrate,andanoptimalannealingtemperatureandtimeshouldbechosentobalancethesefactors.

Conclusion:

Inconclusion,wehaveinvestigatedtheeffectofannealingtimeontheself-assemblyofDNAmoleculesin2Dcrystalsusingmoleculardynamicssimulations.OurresultssuggestthatlongerannealingtimesleadtomoreorderedandstableDNAcrystals,whileshorterannealingtimesresultinlessorderedandmoredefectivecrystals.Moreover,wefoundthathigherannealingtemperaturesfacilitatetheformationofcrystalnuclei,butalsoincreasethedefectdensityoftheresultingcrystals.